1.
Lethin, Johanna, et al.
(author)
Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines
2020
In: Bmc Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 20:1
Journal article (peer-reviewed) abstract
Background Triticum aestivum (wheat) is one of the world's oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance. Results After titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0-30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested. Conclusion The mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming.
2.
Ortiz Rios, Rodomiro Octavio
(author)
Genetics and cytogenetics of the potato
2020
In: The potato crop : its agricultural, nutritional and social contribution to humankind. - Cham : Springer International Publishing. - 9783030286828 ; , s. 219-247
Book chapter (peer-reviewed) abstract
Tetraploid potato (Solanum tuberosum L.) is a genetically complex, polysomic tetraploid (2n = 4x = 48), highly heterozygous crop, which makes genetic research and utilization of potato wild relatives in breeding difficult. Notwithstanding, the potato reference genome, transcriptome, resequencing, and single nucleotide polymorphism (SNP) genotyping analysis provide new means for increasing the understanding of potato genetics and cytogenetics. An alternative approach based on the use of haploids (2n = 2x = 24) produced from tetraploid S. tuberosum along with available genomic tools have also provided means to get insights into natural mechanisms that take place within the genetic load and chromosomal architecture of tetraploid potatoes. This chapter gives an overview of potato genetic and cytogenetic research relevant to germplasm enhancement and breeding. The reader will encounter findings that open new doors to explore inbred line breeding in potato and strategic roads to access the diversity across the polyploid series of this crop's genetic resources. The text includes classical concepts and explains the foundations of potato genetics and mechanisms underlying natural cytogenetics phenomena as well as their breeding applications. Hopefully, this chapter will encourage further research that will lead to successfully develop broad-based potato breeding populations and derive highly heterozygous cultivars that meet the demands of having a resilient crop addressing the threats brought by climate change.
3.
Hu, Jia
(author)
Climate-friendly rice - characterisation of rice varieties associated with low-methane emissions and improved bioenergy properties
2023
Doctoral thesis (other academic/artistic) abstract
Paddy rice cultivation contributes to global warming by emitting methane into the atmosphere. The aims of the work presented in this thesis were to breed climatefriendly rice varieties, to increase rice straw utilisation to reduce the impact of rice cultivation on the environment. The results showed that fumarate and ethanol were the two major exudate compounds from SUSIBA2-rice roots regulating methane emissions from SUSIBA2-rice paddies. A naturally occurring low-methane rice variety was identified and field testing demonstrated that it could be successfully grown in Uppsala, Sweden, opening up possibilities for expanding rice cultivation into high-latitude countries. Key candidate genes important in adaptation of rice to Scandinavian light and climate conditions were identified. By crossing a naturally occurring low-methane rice variety with four high-yielding elite varieties, four independent lines of low-methane rice with high yield potential were developed. Field trials demonstrated that methane emissions from the selected lines were reduced by 70%. Analysis of carbon allocation and molecular analyses of gene activities revealed that sugar transporters such as SUT and SWEET participated in allocation of carbon to aboveground tissues, contributing to the high yield and lowmethane properties. The results also indicated that increasing the lipid content in rice straw could increase its value in bioenergy production. Overall, this thesis shows that plant breeding can successfully address several pressing issues affecting sustainability in rice production by reducing greenhouse gas emissions, increasing crop productivity and diversity, and improving bioenergy production from straw.
4.
Abebe, Admas Alemu, et al.
(author)
Genomic selection in plant breeding: key factors shaping two decades of progress
2024
In: Molecular Plant. - 1674-2052 .- 1752-9867. ; 17, s. 552-578
Research review (peer-reviewed) abstract
Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP—theoretically reaching one when using the Pearson’s correlation as a metric—is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.
5.
Abreha, Kibrom Berhe, et al.
(author)
Understanding the Sorghum–Colletotrichum sublineola interactions for enhanced host resistance
2021
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
Research review (peer-reviewed) abstract
Improving sorghum resistance is a sustainable method to reduce yield losses due to anthracnose, a devastating disease caused by Colletotrichum sublineola. Elucidating the molecular mechanisms of sorghum–C. sublineola interactions would help identify biomarkers for rapid and efficient identification of novel sources for host-plant resistance improvement, understanding the pathogen virulence, and facilitating resistance breeding. Despite concerted efforts to identify resistance sources, the knowledge about sorghum–anthracnose interactions remains scanty. Hence, in this review, we presented an overview of the current knowledge on the mechanisms of sorghum-C. sublineola molecular interactions, sources of resistance for sorghum breeding, quantitative trait loci (QTL), and major (R-) resistance gene sequences as well as defense-related genes associated with anthracnose resistance. We summarized current knowledge about C. sublineola populations and its virulence. Illustration of the sorghum-C. sublineola interaction model based on the current understanding is also provided. We highlighted the importance of genomic resources of both organisms for integrated omics research to unravel the key molecular components underpinning compatible and incompatible sorghum–anthracnose interactions. Furthermore, sorghum-breeding strategy employing rapid sorghum germplasm screening, systems biology, and molecular tools is presented.
6.
Andreasson, Erik, et al.
(author)
Insights on cisgenic plants with durable disease resistance under the European Green Deal
2023
In: Trends in Biotechnology. - 0167-7799 .- 1879-3096. ; 41, s. 1027-1040
Research review (peer-reviewed) abstract
Significant shares of harvests are lost to pests and diseases, therefore, minimizing these losses could solve part of the supply constraints to feed the world. Cisgenesis is defined as the insertion of genetic material into a recipient organism from a donor that is sexually compatible. Here, we review (i) conventional plant breeding, (ii) cisgenesis, (iii) current pesticide-based disease management, (iv) potential economic implications of cultivating cisgenic crops with durable disease resistances, and (v) potential environmental implications of cultivating such crops; focusing mostly on potatoes, but also apples, with resistances to Phytophthora infestans and Venturia inaequalis, respectively. Adopting cisgenic varieties could provide benefits to farmers and to the environment through lower pesticide use, thus contributing to the European Green Deal target.
7.
Brhanie Mesfin, Haftom, et al.
(author)
Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses
2022
In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13
Journal article (peer-reviewed) abstract
Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09-0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.
8.
Chaudhary, Rajiv, et al.
(author)
Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce
2020
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10
Journal article (peer-reviewed) abstract
The Heterobasidion annosum s.l species complex comprises the most damaging forest pathogens to Norway spruce. We revisited previously identified Quantitative Trait Loci (QTLs) related to Heterobasidion-resistance in Norway spruce to identify candidate genes associated with these QTLs. We identified 329 candidate genes associated with the resistance QTLs using a gene-based composite map for Pinaceae. To evaluate the transcriptional responses of these candidate genes to H. parviporum, we inoculated Norway spruce plants and sequenced the transcriptome of the interaction at 3 and 7 days post inoculation. Out of 298 expressed candidate genes 124 were differentially expressed between inoculation and wounding control treatment. Interestingly, PaNAC04 and two of its paralogs in the subgroup III-3 of the NAC family transcription factors were found to be associated with one of the QTLs and was also highly induced in response to H. parviporum. These genes are possibly involved in the regulation of biosynthesis of flavonoid compounds. Furthermore, several of the differentially expressed candidate genes were associated with the phenylpropanoid pathway including a phenylalanine ammonia-lyase, a cinnamoyl-CoA reductase, a caffeoyl-CoA O-methyltransferase and a PgMYB11-like transcription factor gene. Combining transcriptome and genetic linkage analyses can help identifying candidate genes for functional studies and molecular breeding in non-model species.
9.
Desta, Zeratsion Abera, et al.
(author)
Molecular mapping and identification of quantitative trait loci for domestication traits in the field cress (Lepidium campestre L.) genome
2020
In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540.
Journal article (peer-reviewed) abstract
Lepidium campestre (L.) or field cress is a multifaceted oilseed plant, which is not yet domesticated. Moreover, the molecular and genetic mechanisms underlying the domestication traits of field cress remain largely elusive. The overarching goal of this study is to identify quantitative trait loci (QTL) that are fundamental for domestication of field cress. Mapping and dissecting quantitative trait variation may provide important insights into genomic trajectories underlying field cress domestication. We used 7624 single nucleotide polymorphism (SNP) markers for QTL mapping in 428 F-2 interspecific hybrid individuals, while field phenotyping was conducted in F-2:3 segregating families. We applied multiple QTL mapping algorithms to detect and estimate the QTL effects for seven important domestication traits of field cress. Verification of pod shattering across sites revealed that the non-shattering lines declined drastically whereas the shattering lines increased sharply, possibly due to inbreeding followed by selection events. In total, 1461 of the 7624 SNP loci were mapped to eight linkage groups (LGs), spanning 571.9 cM map length. We identified 27 QTL across all LGs of field cress genome, which captured medium to high heritability, implying that genomics-assisted selection could deliver domesticated lines in field cress breeding. The use of high throughput genotyping can accelerate the process of domestication in novel crop species. This is the first QTL mapping analysis in the field cress genome that may lay a foundational framework for positional or functional QTL cloning, introgression as well as genomics-assisted breeding in field cress domestication.
10.
11.
Eriksson, Dennis, et al.
(author)
Editorial: Leeway to operate with plant genetic resources
2020
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11
Journal article (peer-reviewed) abstract
Editorial on the Research Topic Leeway to Operate With Plant Genetic Resources Different legal frameworks are applicable to the use of genetic resources (GR). These can broadly be categorized into (1) access and benefit-sharing (ABS), (2) biosafety aspects related to the technologies for improving the genetic material, and (3) intellectual property (IP) systems including plant variety rights (PVR) and patents specific to the plant innovation sector. With scientific and technical progress in research and breeding, as well as expanding internationalization, legal frameworks have become increasingly complex in the past few decades. In this context, the Research Topic “Leeway to operate with plant genetic resources” addresses the latest and most pertinent legalissues related to the use of GR in plant research and breeding.The contributions are summarized here and put into the larger societal and legal context that modern-day plant geneticists are facing.
12.
Gebeyehu Demissie, Adane, et al.
(author)
RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome
2022
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
Journal article (peer-reviewed) abstract
Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
13.
Gustavsson, Larisa, et al.
(author)
Resistance to Neonectria ditissima in apple : insights from metabolomics and lipidomics analyses
2023
In: Xxxi international horticultural congress (ihc2022). - : International Society for Horticultural Science. - 9789462613614 ; , s. 329-335, s. 329-336
Conference paper (peer-reviewed) abstract
European canker, caused by the necrotrophic fungus Neonectria ditissima, is the most serious disease in apple production in Sweden. The disease is favored by a relatively cool and rainy climate. The canker damages have a significant economic impact due to reduced bearing surface and increased orchard management costs. The possibilities for chemical and biological control are very limited. Therefore, directed breeding for new resistant cultivars is urgently needed. Knowledge of inheritance of canker resistance and understanding of molecular mechanisms involved in resistant and susceptible responses to fungal attacks would facilitate breeding. In this study, we evaluated the tempo-spatial differences in plant-pathogen interactions in a set of partially resistant and susceptible cultivars by conducting metabolomic and lipidomic analyses. The major trends in metabolomics and lipidomic profiles were common among cultivars, irrespective of the degree of susceptibility. Several metabolites and lipids varied with time point and cultivar under N. ditissima infection. Putative key metabolites such as suberic acid and jasmonic acid were upregulated in all cultivars upon infection. Additionally, several lipids exhibited changes 30 to 45 days post-inoculation. Thus, the approach used seems to have resulted in a rich data set to be further analyzed in light of ongoing QTL-mapping efforts.
14.
Hammenhag, Cecilia, et al.
(author)
Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars
2021
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
Journal article (peer-reviewed) abstract
Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.
15.
Hammenhag, Cecilia, et al.
(author)
QTL mapping for domestication-related characteristics in field cress (Lepidium campestre)—a novel oil crop for the Subarctic region
2020
In: Genes. - : MDPI AG. - 2073-4425. ; 11
Journal article (peer-reviewed) abstract
Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F-2 mapping population and its F-3 progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p < 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress.
16.
Karlsson, Milla, et al.
(author)
Möjliga tillämpningar av nya genomiska tekniker inom integrerat växtskydd
2023
Reports (other academic/artistic) abstract
Det pågår en omställning av jord- och trädgårdsbruket, både med hänsyn till hållbar produktion och pågående klimatförändringar. Som en del av EUs arbete att utveckla lantbruket mot en mer hållbar produktion har kommissionen lagt fram ett förslag på minskning av växtskyddsmedel om minst 50 %, totalt sett inom EU, senast 2030. För Sveriges del innebär förslaget, enligt preliminära beräkningar, att vi behöver minska mängden växtskyddsmedel med 35-36 %. För att ersätta funktionen av denna mängd växtskyddsmedel behövs ett integrerat tillvägagångssätt som kräver tillgång till andra effektiva metoder för bekämpning av skadegörare på odlade växter.Under det senaste decenniet har nya genomiska tekniker inom växtförädlingen utvecklats, vilka möjliggör riktade förändringar i många grödors genom. Teknikerna innebär antingen att man introducerar enstaka förändringar i DNA-sekvensen (s.k. genomredigering), eller att man sätter in en längre DNA-sekvens från samma art eller en korsningsbar art i en gröda (s.k. cisgenes). Dessutom har kunskapen om växters försvarssystem framskridit avsevärt. Med den ökade kunskapen och de nya teknikerna ökar möjligheten att kombinera gener och öka variationen av de gener som gör grödorna resistenta mot olika växtsjukdomar. På så sätt kan förädlingen av sjukdomsresistenta sorter ske med betydligt bättre precision och på kortare tid än vad traditionella förädlingstekniker tillåter. Tidsaspekten kan ses som extra viktig i resistenssammanhang eftersom skadegörarpopulationerna ändras kontinuerligt. Potentialen att kombinera flera olika resistensmekanismer för att uppnå mer uthållig resistens samt möjligheten att lösa ett eller flera växtskyddsproblem i samma sort bör också noteras.Enligt nuvarande EU-lagstiftning regleras dock genomredigerade och cisgena grödor på samma sätt som traditionellt genetiskt modifierade organismer (GMO), en lagstiftning som i praktiken omöjliggör kommersiell odling inom EU. Detta trots att resultatet av de moderna teknikerna kan efterlikna vad som kan ske spontant i naturen (mutationer) eller via traditionella oreglerade förädlingsmetoder (t.ex. mutations-, eller korsningsförädling). I lagstiftningen tas det ej i beaktande att sjukdomsresistenta grödor kan bidra till en minskad användning av växtskyddsmedel.Idag är potatisodling ofta förknippad med en användning av stora mängder växtskyddsmedel mot potatisbladmögel. Samtidigt är det möjligt att göra potatissorterna helt resistenta mot potatisbladmögel med hjälp av cisgenes och ge dem en ökad motståndskraft med hjälp av genomredigering. Om det vore möjligt att odla potatis som förädlats med nya genomiska tekniker inom EU idag, visar denna rapport att det skulle vara möjligt att kraftigt minska användningen av växtskyddsmedel i potatisodlingen. Det skulle innebära en reducering av mängden växtskyddsmedel som används inom det svenska lantbruket och skulle även innebära besparingar runt 91 miljoner SEK per år för odlarna.Vete och annan spannmål är de grödor där flest totala hektardoser av fungicider appliceras, till en årlig kostnad av två miljarder SEK. För dessa grödor finns inget lika tydligt exempel på enskilda sjukdomar som så kraftigt kan minska fungicidanvändningen. Vi ser dock en tydlig framtida potential att minska antalet bekämpningar och därmed kostnaden för lantbruket med hjälp av nya genomiska tekniker inom sädesslagen.Möjligheten att öka växters egen resistens för att minska användningen av växtskyddsmedel finns redan idag även i flera andra grödor, och möjligheterna förväntas fortsatt växa i takt med att teknikutveckling och forskning fortgår. En förändrad lagstiftning runt nya genomiska tekniker skulle även öppna för applikationer inom områden där det idag inte finns någon effektiv metod att bekämpa växtskadegörare. Exempel på sådana skadegörare är många virussjukdomar och skador som orsakas av nematoder. Därför kan skördestabiliteten och konkurrenskraften förväntas öka i grödor där det idag finns skadegörare där effektiva bekämpningsmetoder saknas.Sammanfattningsvis ser vi nya genomiska tekniker för att förädla resistenta grödor som en viktig del i arbetet mot ett hållbart jordbruk och för att uppnå EU-kommissionens mål om att reducera användningen av växtskyddsmedel inom jord- och trädgårdsbruket.
17.
Kianersi, Farzad, et al.
(author)
Biosynthesis of rutin changes in Capparis spinosa due to altered expression of its pathway genes under elicitors' supplementation
2020
In: Plant Cell Tissue and Organ Culture. - : Springer Nature. - 0167-6857 .- 1573-5044. ; 141:3, s. 619-631
Journal article (peer-reviewed) abstract
Caper plant is (Capparis spinosa L.) a good source of rutin which plays a key role in the human diet. In this study, the effect of different concentrations of salicylic acid (SA) and methyl jasmonate (MeJA) on the weight of anther-derived calli and their rutin contents were assessed in caper plants. Also, we investigated the rutin content and expression pattern of some rutin related genes in leaves of caper plants at vegetative and fresh fruiting growth stages under SA and MeJA treatments. In the first experiment, the highest rutin contents were observed in anther-derived calli treated with 10 mu M MeJA and 100 mg L-1 SA after 2 weeks from initial treatments, which were 2.44 and 2.22-fold higher than control. Also, the treatment of caper plants with150 mu M MeJA and 100 mg L-1 SA resulted in a higher increase in the rutin content of leaves at the fresh fruiting stage (61.46 and 9.99 mg g(-1) DW, respectively), in the second experiment. Among the studied genes, the FLS gene showed the highest expression in the leaves of the MeJA- and SA-treated plants at vegetative growth stage, while in the fresh fruiting stage the highest expression was related to the RT gene. Use of 150 mu M MeJA and 100 mg L-1 SA enhanced the expression levels of the RT gene up to 7.36 and 2.89 times of the control, respectively. These results suggest that rutin content and the expression patterns of rutin biosynthesis genes in caper can be significantly enhanced by the SA and MeJA treatments in a growth stage-dependent manner. Key message Methyl jasmonate and salicylic acid treatments enhance the rutin contents of Capparis spinosa in vitro and in vivo and up-regulate the rutin biosynthetic related genes at two different growth stages.
18.
Mulugeta, Behailu, et al.
(author)
Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat
2023
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
Journal article (peer-reviewed) abstract
The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
19.
Ortiz Rios, Rodomiro Octavio
(author)
Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs
2023
In: International Journal of Molecular Sciences. - 1661-6596 .- 1422-0067. ; 24
Research review (peer-reviewed) abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
20.
Ortiz Rios, Rodomiro Octavio
(author)
Challenges for crop improvement
2023
In: Emerging topics in life sciences. - 2397-8554 .- 2397-8562. ; 7, s. 197-205
Research review (peer-reviewed) abstract
The genetic improvement of crops faces the significant challenge of feeding an everincreasing population amidst a changing climate, and when governments are adopting a ‘more with less’ approach to reduce input use. Plant breeding has the potential to contribute to the United Nations Agenda 2030 by addressing various sustainable development goals (SDGs), with its most profound impact expected on SDG2 Zero Hunger. To expedite the time-consuming crossbreeding process, a genomic-led approach for predicting breeding values, targeted mutagenesis through gene editing, high-throughput phenomics for trait evaluation, enviromics for including characterization of the testing environments, machine learning for effective management of large datasets, and speed breeding techniques promoting early flowering and seed production are being incorporated into the plant breeding toolbox. These advancements are poised to enhance genetic gains through selection in the cultigen pools of various crops. Consequently, these knowledge-based breeding methods are pursued for trait introgression, population improvement, and cultivar development. This article uses the potato crop as an example to showcase the progress being made in both genomic-led approaches and gene editing for accelerating the delivery of genetic gains through the utilization of genetically enhanced elite germplasm. It also further underscores that access to technological advances in plant breeding may be influenced by regulations and intellectual property rights.
21.
Ortiz Rios, Rodomiro Octavio
(author)
Genome and Environment Based Prediction Models and Methods of Complex Traits Incorporating Genotype × Environment Interaction
2022
In: Complex Trait Prediction : Methods and Protocols. - New York, NY : Springer US. - 9781071622049 ; :2467, s. 245-283
Book chapter (peer-reviewed) abstract
Genomic-enabled prediction models are of paramount importance for the successful implementation of genomic selection (GS) based on breeding values. As opposed to animal breeding, plant breeding includes extensive multienvironment and multiyear field trial data. Hence, genomic-enabled prediction models should include genotype × environment (G × E) interaction, which most of the time increases the prediction performance when the response of lines are different from environment to environment. In this chapter, we describe a historical timeline since 2012 related to advances of the GS models that take into account G × E interaction. We describe theoretical and practical aspects of those GS models, including the gains in prediction performance when including G × E structures for both complex continuous and categorical scale traits. Then, we detailed and explained the main G × E genomic prediction models for complex traits measured in continuous and noncontinuous (categorical) scale. Related to G × E interaction models this review also examine the analyses of the information generated with high-throughput phenotype data (phenomic) and the joint analyses of multitrait and multienvironment field trial data that is also employed in the general assessment of multitrait G × E interaction. The inclusion of nongenomic data in increasing the accuracy and biological reliability of the G × E approach is also outlined. We show the recent advances in large-scale envirotyping (enviromics), and how the use of mechanistic computational modeling can derive the crop growth and development aspects useful for predicting phenotypes and explaining G × E.
22.
Ortiz Rios, Rodomiro Octavio
(author)
Göte Turesson’s research legacy to Hereditas: from the ecotype concept in plants to the analysis of landraces’ diversity in crops
2020
In: Hereditas. - : Springer Science and Business Media LLC. - 0018-0661 .- 1601-5223. ; 157
Research review (peer-reviewed) abstract
Hereditas began with articles on plants since its first issue in May 1920 (six out of eight) and continued with more original articles (43% of the total of this journal) on plants (of which 72% of those in plants were on crops) until today. In December 1922, the 140-page article The Genotypical Response of the Plant Species to the Habitat by evolutionary botanist Göte Turesson (Institute of Genetics, Lund University, Åkarp, Sweden) became available. This publication shows that plant phenology has a genetic basis and may ensue from local adaptation. As a result of this research involving various plant species, Turesson elaborated further in this article his term ecotype “as an ecological sub-unit to cover the product arising as a result of the genotypical response of an ecospecies to a particular habitat.” Although plant articles included in Hereditas involved from its beginning, trait inheritance, mutants, linkage analysis, cytology or cytogenetics, and more recently gene mapping and analysis of quantitative trait loci with the aid of DNA markers, among others, since the mid-1980s several publications refer to the population biology of plant landraces, which are locally grown cultivars that evolved over time by adapting to their natural and cultural environment (i.e., agriculture), and that may become isolated from other populations of the same crop. This article provides a briefing about research on plant science in the journal with emphasis on crops, summarizes the legacy to genetics of Göte Turesson, and highlights some landrace diversity research results and their potential for plant breeding.
23.
Ortiz Rios, Rodomiro Octavio
(author)
Mitigating tradeoffs in plant breeding
2021
In: iScience. - : Elsevier BV. - 2589-0042. ; 24
Research review (peer-reviewed) abstract
Tradeoffs among plant traits help maintain relative fitness under unpredictable conditions and maximize reproductive success. However, modifying tradeoffs is a breeding challenge since many genes of minor effect are involved. The intensive crosstalk and fine-tuning between growth and defense responsive phytohormones via transcription factors optimizes growth, reproduction, and stress tolerance. There are regulating genes in grain crops that deploy diverse functions to overcome tradeoffs, e.g., miR-156-IPA1 regulates crosstalk between growth and defense to achieve high disease resistance and yield, while OsALDH2B1 loss of function causes imbalance among defense, growth, and reproduction in rice. GNI-A1 regulates seed number and weight in wheat by suppressing distal florets and altering assimilate distribution of proximal seeds in spikelets. Knocking out ABA-induced transcription repressors (AITRs) enhances abiotic stress adaptation without fitness cost in Arabidopsis. Deploying AITRs homologs in grain crops may facilitate breeding. This knowledge suggests overcoming tradeoffs through breeding may expose new ones.
24.
25.
Ortiz Rios, Rodomiro Octavio
(author)
Raising productivity of cereal crops in dry and heat stress environments remains a breeding challenge
2021
In: Cab Reviews: Perspectives In Agriculture, Veterinary Science, Nutrition And Natural Resources. - 1749-8848. ; 16
Research review (peer-reviewed) abstract
'Green Revolution' genes have led to the release of input-responsive cultivars, resulting in multifold productivity increases in rice and wheat. Declining precipitation, increased intensity of drought and rising temperature are casting uncertainty over agricultural production. As noted in this mini review, plant genes when over-expressed allow cereals to produce grains in drought- and heat-prone sites.
26.
Ortiz Rios, Rodomiro Octavio
(author)
Transgenic Vegetable Breeding for Nutritional Quality and Health Benefits: A Review
2022
In: Emerging Trends in Disease and Health Research Volume 4. - 9789355473608 ; , s. 36-52
Book chapter (other academic/artistic) abstract
This article discusses recent attempts to characterize and modify nutrients and bioactive compounds in vegetable crops by using transgenic approaches. Malnutrition and unhealthy diets have become major risk factors for non-communicable diseases. Vegetables are an important part of a well-balanced diet. Due to unbalanced diets, around 3 billion people worldwide are malnourished. Vegetables can aid in the prevention of malnutrition-related illnesses. Vegetable breeders can use genetic engineering to add desired transgenes into elite cultivars, greatly increasing their value. It also provides one-of-a-kind chances to improve nutritional quality and provide other health benefits. Many vegetable crops have been genetically modified to improve features like nutritional value or flavor, as well as to minimize bitterness and anti-nutritional elements. Transgenic veggies can also be utilized to deliver vaccines. Consumers may profit even more from eating more nutritious transgenic veggies; for example, increasing crop carotenoids through metabolic sink manipulation via genetic engineering appears to be possible in some crops. Ca uptake may be boosted by genetically engineering carrots with higher Ca levels, reducing the occurrence of calcium shortages such osteoporosis. The lack of this micronutrient, which severely inhibits organ function, will be remedied by fortified transgenic lettuce with zinc. Transgenic tomatoes with folate levels that give a complete adult daily requirement can also help to overcome folate insufficiency, which is considered a global health problem. Genetic engineering has also become an ideal tool to develop anthocyanin-rich tomatoes. Transgenic lettuce with higher levels of tocopherol and resveratrol may help to prevent coronary artery disease and arteriosclerosis, as well as cancer chemoprevention. Transgenic techniques can help improve food safety and health advantages; for example, rural African resource poor consumers will gain from consuming cyanide-free cassava varieties. Growers and consumers will accept biotechnology-derived vegetable crops if clear benefits and safety are demonstrated.
27.
Ortiz Rios, Rodomiro Octavio
(author)
What plant breeding may (and may not) look like in 2050?
2024
In: The Plant Genome. - 1940-3372. ; 17
Research review (peer-reviewed) abstract
At the turn of 2000 many authors envisioned future plant breeding. Twenty years after, which of those authors' visions became reality or not, and which ones may become so in the years to come. After two decades of debates, climate change is a "certainty," food systems shifted from maximizing farm production to reducing environmental impact, and hopes placed into GMOs are mitigated by their low appreciation by consumers. We revise herein how plant breeding may raise or reduce genetic gains based on the breeder's equation. "Accuracy of Selection" has significantly improved by many experimental-scale field and laboratory implements, but also by vulgarizing statistical models, and integrating DNA markers into selection. Pre-breeding has really promoted the increase of useful "Genetic Variance." Shortening "Recycling Time" has seen great progression, to the point that achieving a denominator equal to "1" is becoming a possibility. Maintaining high "Selection Intensity" remains the biggest challenge, since adding any technology results in a higher cost per progeny, despite the steady reduction in cost per datapoint. Furthermore, the concepts of variety and seed enterprise might change with the advent of cheaper genomic tools to monitor their use and the promotion of participatory or citizen science. The technological and societal changes influence the new generation of plant breeders, moving them further away from field work, emphasizing instead the use of genomic-based selection methods relying on big data. We envisage what skills plant breeders of tomorrow might need to address challenges, and whether their time in the field may dwindle.
28.
Osterman, Johanna, et al.
(author)
Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers
2021
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
Journal article (peer-reviewed) abstract
Red clover (Trifolium pratense) is one of the most important fodder crops worldwide. The knowledge of genetic diversity among red clover populations, however, is under development. This study provides insights into its genetic diversity, using single nucleotide polymorphism (SNP) markers to define population structure in wild and cultivated red clover. Twenty-nine accessions representing the genetic resources available at NordGen (the Nordic gene bank) and Lantmännen (a Swedish agricultural company with a red clover breeding program) were used for this study. Genotyping was performed via SeqSNP, a targeted genotype by sequencing method that offers the capability to target specific SNP loci and enables de novo discovery of new SNPs. The SNPs were identified through a SNP mining approach based on coding sequences of red clover genes known for their involvement in development and stress responses. After filtering the genotypic data using various criteria, 623 bi-allelic SNPs, including 327 originally targeted and 296 de novo discovered SNPs were used for population genetics analyses. Seventy-one of the SNP loci were under selection considering both Hardy-Weinberg equilibrium and pairwise FST distributions. The average observed heterozygosity (HO), within population diversity (HS) and overall diversity (HT) were 0.22, 0.21 and 0.22, respectively. The tetraploids had higher average HO (0.35) than diploids (0.21). The analysis of molecular variance (AMOVA) showed low but significant variation among accessions (5.4%; P < 0.001), and among diploids and tetraploids (1.08%; P = 0.02). This study revealed a low mean inbreeding coefficient (FIS = −0.04) exhibiting the strict outcrossing nature of red clover. As per cluster, principal coordinate and discriminant analyses, most wild populations were grouped together and were clearly differentiated from the cultivated types. The cultivated types of red clover had a similar level of genetic diversity, suggesting that modern red clover breeding programs did not negatively affect genetic diversity or population structure. Hence, the breeding material used by Lantmännen represents the major genetic resources in Scandinavia. This knowledge of how different types of red clover accessions relate to each other and the level of outcrossing and heterozygosity will be useful for future red clover breeding.
29.
30.
Selga, Catja, et al.
(author)
A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding
2021
In: Plants. - : MDPI AG. - 2223-7747. ; 10
Journal article (peer-reviewed) abstract
Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.
31.
Selga, Catja, et al.
(author)
The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato
2022
In: G3. - : Oxford University Press (OUP). - 2160-1836. ; 12
Journal article (peer-reviewed) abstract
Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.
32.
33.
Wang, Eu Sheng, et al.
(author)
Tissue Culture and Refreshment Techniques for Improvement of Transformation in Local Tetraploid and Diploid Potato with Late Blight Resistance as an Example
2020
In: Plants. - : MDPI AG. - 2223-7747. ; 9
Journal article (peer-reviewed) abstract
Potato (Solanum tuberosum) is among the best producers of edible biomass in terms of yield per hectare and a variety of different regional cultivars are used as a staple commodity in many countries. However, this crop is attacked by several diseases, with the worst being the late blight disease caused byPhytophthora infestans. Stacking of resistance (R) genes from wildSolanumrelatives are interesting prospects for the sustainable control of late blight. Therefore, we optimized methods for the efficient generation and screening of R-gene-containing transformants in tetraploid and diploid hybrid potato genotypes. Using these methods, a high transformation efficiency was achieved for the transformation of tetraploid and diploid potato lines with a triple resistance (3R) gene construct. Transformation efficiencies were improved by optimizing several factors affecting regeneration, including the quality of the starting plant material, and the composition of the plant growth regulators used during selective regeneration. A refreshment protocol was designed to alleviate in vitro related stress in stock plants, which significantly improved the growth vigor and resulted in a 4- to 10-fold increase in transformation efficiency. Furthermore, long-term exposure to exogenous Indole-3-butyric acid that is usually used for the initiation of roots in vitro, was found to cause aberrant morphological phenotypes in potato.
34.
Willforss, J, et al.
(author)
Interactive proteogenomic exploration of response to Fusarium head blight in oat varieties with different resistance
2020
In: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 218, s. 103688-103688
Journal article (peer-reviewed) abstract
Fusarium species are cereal pathogens that cause the Fusarium Head Blight (FHB) disease. FHB can reduce yield, cause mycotoxin accumulation in the grain and reduce germination efficiency of the harvested seeds. Understanding the biochemical interactions between the host plants and the pathogen is crucial for controlling the disease and for the development of cultivars with improved tolerance to FHB. Here, we studied morphological and proteomic differences between the susceptible oat variety Belinda and the more resistant variety Argamak using variety-specific transcriptome assemblies as references. Measurements of deoxynivalenol toxin levels confirmed the partial resistance in Argamak and the susceptibility in Belinda. To jointly investigate the proteomics- and sequence data, we developed an RShiny-based interface for interactive exploration of the dataset using univariate and multivariate statistics. When applying this interface to the dataset, quantitative protein differences between Belinda and Argamak were detected, and eighteen peptides were found uniquely in Argamak during infection, among them several lipoxygenases. Such proteins can be developed as markers for Fusarium resistance breeding. In conclusion, this study provides the first proteogenomic insight on molecular Fusarium-oat interactions at both morphological and molecular levels and the data are openly available through an interactive interface for further inspection. SIGNIFICANCE: Fusarium head blight causes widespread damage to crops, and chronic and acute toxicity to human and livestock due to the accumulation of toxins during infection. In the present study, two oat varieties with differing resistance were challenged with Fusarium to understand the disease better, and studied both at morphological and molecular levels, identifying proteins which could play a role in the defense mechanism. Furthermore, a proteogenomics approach allows joint profiling of expression and sequence level differences to identify potentially functionally differing mutations. Here such analysis is made openly available through an interactive interface which allows other scientists to draw further findings from the data. This study may both serve as a basis for understanding oat disease response and developing breeding markers for Fusarium resistant oat and future proteogenomic studies using the interactive approach described.
35.
Bottani, Gabriela
(author)
Bolivian creole cattle: population structure, genetic diversity and management practices
2020
Doctoral thesis (other academic/artistic) abstract
Characterization studies of local livestock breeds are important to identify their potential and value for the Global Animal Genetic Resources. Important traits have been attributed to local breeds including adaptability and resilience to harsh environments and other traits with potential use in breeding schemes oriented towards the challenges of climate change. The aim of this thesis was to generate baseline information for the development of future conservation and breeding programs for the Creole cattle in Bolivia. For this purpose, three Creole cattle populations were included in this study: the Chaqueño (CHA), the Saavedreño (CEASIP) and a population from Pasorapa (PASO).In the first part of this thesis, the main characteristics of the production and management system in Pasorapa were described. Further, the identification and evaluation of elements affecting the sustainability of the production system and the development of breeding and conservation programs was done. Open-ended and closedended questionnaires and interviews with 81 smallholders from 11 communities from Pasorapa were performed. Poor infrastructure and deficient health management practices were found. The rearing system based on two stages with animals released in the mountains for about 7 months of the year and feeding mainly of native plant species, showed a strong interaction between the cattle and the environment. Farmer perceptions about diseases, mortality causes and selection criteria were described, showing that additionally to body conformation, farmers considered coat color for selection of breeding and replacement animals. Productivity, income and ecosystem services were identified as the main factors affecting the sustainability of the system.In the second part of this study, the population structure, genetic diversity, linkage disequilibrium (LD) and ROH based inbreeding levels of the three cattle populations were assessed using a 50K SNP array. Pairwise FST values indicated low to moderate differentiation between populations. Admixture analysis showed clear signs of admixture among and within populations. CEASIP had the highest proportion of ROHs for the length classes 4-8 Mb, 8-16 Mb and >16 Mb. FROH coefficient values were higher for CHA and CEASIP populations for the >4 Mb and >16 Mb length classes indicating past and recent inbreeding. PASO had the lowest inbreeding coefficients for all ROH length classes. LD and effective population size of PASO might have been influenced by recurrent bottleneck episodes. LD pattern in CEASIP indicated that a 50K SNP array could be applied for association studies in this population.
36.
Abebe, Admas Alemu, et al.
(author)
Genome-Wide Association Analysis and Genomic Prediction for Adult-Plant Resistance to Septoria Tritici Blotch and Powdery Mildew in Winter Wheat
2021
In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 12
Journal article (peer-reviewed) abstract
Septoria tritici blotch (STB) caused by the fungal pathogen Zymoseptoria tritici and powdery mildew (PM) caused by Blumeria graminis f.sp tritici (Bgt) are among the forefront foliar diseases of wheat that lead to a significant loss of grain yield and quality. Resistance breeding aimed at developing varieties with inherent resistance to STB and PM diseases has been the most sustainable and environment-friendly approach. In this study, 175 winter wheat landraces and historical cultivars originated from the Nordic region were evaluated for adult-plant resistance (APR) to STB and PM in Denmark, Estonia, Lithuania, and Sweden. Genome-wide association study (GWAS) and genomic prediction (GP) were performed based on the adult-plant response to STB and PM in field conditions using 7,401 single-nucleotide polymorphism (SNP) markers generated by 20K SNP chip. Genotype-by-environment interaction was significant for both disease scores. GWAS detected stable and environment-specific quantitative trait locis (QTLs) on chromosomes 1A, 1B, 1D, 2B, 3B, 4A, 5A, 6A, and 6B for STB and 2A, 2D, 3A, 4B, 5A, 6B, 7A, and 7B for PM adult-plant disease resistance. GP accuracy was improved when assisted with QTL from GWAS as a fixed effect. The GWAS-assisted GP accuracy ranged within 0.53-0.75 and 0.36-0.83 for STB and PM, respectively, across the tested environments. This study highlights that landraces and historical cultivars are a valuable source of APR to STB and PM. Such germplasm could be used to identify and introgress novel resistance genes to modern breeding lines.
37.
Abebe, Admas Alemu, et al.
(author)
Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat
2023
In: TAG Theoretical and Applied Genetics. - 0040-5752 .- 1432-2242. ; 136
Journal article (peer-reviewed) abstract
Genomic prediction is a powerful tool to enhance genetic gain in plant breeding. However, the method is accompanied by various complications leading to low prediction accuracy. One of the major challenges arises from the complex dimensionality of marker data. To overcome this issue, we applied two pre-selection methods for SNP markers viz. LD-based haplotype-tagging and GWAS-based trait-linked marker identification. Six different models were tested with preselected SNPs to predict the genomic estimated breeding values (GEBVs) of four traits measured in 419 winter wheat genotypes. Ten different sets of haplotype-tagged SNPs were selected by adjusting the level of LD thresholds. In addition, various sets of trait-linked SNPs were identified with different scenarios from the training-test combined and only from the training populations. The BRR and RR-BLUP models developed from haplotype-tagged SNPs had a higher prediction accuracy for FHB and SPW by 0.07 and 0.092, respectively, compared to the corresponding models developed without marker pre-selection. The highest prediction accuracy for SPW and FHB was achieved with tagged SNPs pruned at weak LD thresholds (r2 < 0.5), while stringent LD was required for spike length (SPL) and flag leaf area (FLA). Trait-linked SNPs identified only from training populations failed to improve the prediction accuracy of the four studied traits. Pre-selection of SNPs via LD-based haplotype-tagging could play a vital role in optimizing genomic selection and reducing genotyping costs. Furthermore, the method could pave the way for developing low-cost genotyping methods through customized genotyping platforms targeting key SNP markers tagged to essential haplotype blocks.
38.
Abebe, Admas Alemu
(author)
Multi-model genome-wide association and genomic prediction analysis of 16 agronomic, physiological and quality related traits in ICARDA spring wheat
2021
In: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 217
Journal article (peer-reviewed) abstract
Identification and exploration of the genetic architecture of traits related to yield, quality, and drought and heat tolerance is important for yield and quality improvement of wheat through marker-assisted selection. One hundred and ninety-two spring wheat genotypes were tested at two heat-stress locations in Sudan (Wad Medani and Dongula), a drought stress site in Morocco (Marchouch) and a site with high yield potential in Egypt (Sids) in replicated trials during the 2015-2016 and 2016-2017 cropping seasons. A total of 10,577 single nucleotide polymorphism markers identified from the 15 K wheat SNP assay were used in a genome-wide association (GWA) study and genomic prediction for 16 phenotypic traits related to yield, quality and drought and heat tolerance. Significant marker-trait associations were detected across GWAS models for all traits. Most detected marker-trait associations (MTAs) were environment-specific, signifying the presence of high quantitative trait loci-by-environment (QTL x E) interaction. Chromosome arm 5AL had significant multi-model MTAs for grain yield and yield-related traits at the heat-stress locations. Highly significant QTLs were detected on chromosome 2D for waxiness. Homoeologous group 2 and 6 chromosomes were with significant MTAs for grain protein content, gluten content, alveograph strength and Zeleny sedimentation test while chromosome arm 3BL was significant for both Z and W traits. Genomic prediction analysis with ridge regression-best linear unbiased prediction model estimated the breeding values of the studied traits with prediction accuracies ranging from 0.16 for leaf rolling to 0.72 for peduncle length. The identified QTLs could be targeted for marker-assisted selection or further studies aimed at fine mapping and cloning the causative genes and detecting favorable haplotypes with positive effects for agronomic, physiological or quality-related traits.
39.
Abebe, Admas Alemu
(author)
Single- and multi-trait genomic prediction and genome-wide association analysis of grain yield and micronutrient-related traits in ICARDA wheat under drought environment
2023
In: Molecular Genetics and Genomics. - 1617-4615 .- 1617-4623. ; 298, s. 12-
Journal article (peer-reviewed) abstract
Globally, over 2 billion people suffer from malnutrition due to inadequate intake of micronutrients. Genomic-assisted breeding is identified as a valuable method to facilitate developing new improved plant varieties targeting grain yield and micronutrient-related traits. In this study, a genome-wide association study (GWAS) and single- and multi-trait-based genomic prediction (GP) analysis was conducted using a set of 252 elite wheat genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The objective was to identify linked SNP markers, putative candidate genes and to evaluate the genomic estimated breeding values (GEBVs) of grain yield and micronutrient-related traits.. For this purpose, a field trial was conducted at a drought-prone station, Merchouch, Morocco for 2 consecutive years (2018 and 2019) followed by GWAS and genomic prediction analysis with 10,173 quality SNP markers. The studied genotypes exhibited a significant genotypic variation in grain yield and micronutrient-related traits. The GWAS analysis identified highly significantly associated markers and linked putative genes on chromosomes 1B and 2B for zinc (Zn) and iron (Fe) contents, respectively. The genomic predictive ability of selenium (Se) and Fe traits with the multi-trait-based GP GBLUP model was 0.161 and 0.259 improving by 6.62 and 4.44%, respectively, compared to the corresponding single-trait-based models. The identified significantly linked SNP markers, associated putative genes, and developed GP models could potentially facilitate breeding programs targeting to improve the overall genetic gain of wheat breeding for grain yield and biofortification of micronutrients via marker-assisted (MAS) and genomic selection (GS) methods.
40.
Abebe, Admas Alemu, et al.
(author)
Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production
2022
In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
Journal article (peer-reviewed) abstract
Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999-2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.
41.
Aboshady, Hadeer Moursy
(author)
Genomic variation and molecular mechanisms of the host response to gastrointestinal nematodes in small ruminants
2020
Doctoral thesis (other academic/artistic) abstract
Gastrointestinal nematode (GIN) infections are one of the major constrains for sheep and goat production worldwide. One of the promising control strategies is the genetic selection for resistant animals as there are no issues due to anthelmintic resistance and it aligns to demands for chemical-free food. Exploring possible phenotypic and genomic markers that could be used in breeding scheme besides understanding the mechanisms responsible for resistance were the main goals of this thesis. Thesis consists of General introduction, a brief description of GIN biology and methods to control GIN with focus on phenotypic and genomic markers, four papers and General discussion. In paper Ⅰ, a systematic review and meta-analysis were conducted to re-analyse and summarize the findings on immunoglobulins response to GIN in the literature and discuss the potential to use immunoglobulins as biomarkers of the host resistance. A conceptual model summarizing the role of immunoglobulins in resistance to GIN is proposed. In paper Ⅱ, transcriptome profiling of the abomasal mucosa and lymph node tissues were compared between non-infected, resistant and susceptible Creole goats experimentally infected with Haemonchus contortus. Results indicated that the maintenance of the integrity of the mucosa has probably the priority for the host at late infection stage. In paper Ⅲ, the dynamics of the response of the abomasal mucosa of resistant and susceptible Creole goats experimentally infected with H. contortus were compared. The immune response was activated through many relevant pathways including the Th1 immune response at different time post-infection. Interestingly, the results showed a simultaneous time series activation of Th2 related genes in resistant compared to susceptible kids. In paper Ⅳ, the genomic variants of Creole goats resistant and susceptible to H. contortus were discovered from RNAsequencing data at four different times post-infection. Single nucleotide polymorphisms, insertions and deletions that distinguish the resistant and the susceptible groups were identified and characterized through functional analysis. The T cell receptor signalling pathway was one of the top significant pathways that distinguish the resistant from the susceptible group with genomic variants in 78% of genes in this pathway.
42.
Adler, Anneli, et al.
(author)
Variation of growth and phenology traits in poplars planted in clonal trials in Northern Europe-implications for breeding
2021
In: BioEnergy Research. - : Springer Science and Business Media LLC. - 1939-1234 .- 1939-1242. ; 14, s. 426-444
Journal article (peer-reviewed) abstract
The increased demand for wood to replace oil-based products with renewable products has lifted focus to the Baltic Sea region where the environment is favorable for woody biomass growth. The aim of this study was to estimate broad-sense heritabilities and genotype-by-environment (GxE) interactions in growth and phenology traits in six climatically different regions in Sweden and the Baltics. We tested the hypothesis that both bud burst and bud set have a significant effect on the early growth of selected poplar clones in Northern Europe. Provenance hybrids of Populus trichocarpa adapted to the Northern European climate were compared to reference clones with adaptation to the Central European climate. The volume index of stemwood was under low to medium genetic control with heritabilities from 0.22 to 0.75. Heritabilities for phenology traits varied between 0.31 and 0.91. Locally chosen elite clones were identified. GxE interactions were analyzed using pairwise comparisons of the trials. Three different breeding zones for poplars between the latitudes of 55 degrees N and 60 degrees N in the Baltic Sea Region were outlined. The studied provenance hybrids with origin from North America offer a great possibility to broaden the area with commercial poplar plantations in Northern Europe and further improve the collection of commercial clones to match local climates. We conclude that phenology is an important selection criterion after growth.
43.
Affholder, Marie-Cecile, et al.
(author)
Cadmium Reduction in Spring Wheat: Root Exudate Composition Affects Cd Partitioning Between Roots and Shoots
2023
In: Journal of Soil Science and Plant Nutrition. - 0718-9508 .- 0718-9516. ; 23, s. 3537-3547
Journal article (peer-reviewed) abstract
Cadmium (Cd) in cereals is one of the major sources of Cd intake by human diets, and solutions to reduce Cd concentrations in wheat still need to be developed. Plant breeding, by selecting low-Cd varieties, can be an important tool to reduce Cd in crops. Knowing the genotypic variation in Cd accumulation and furthering our understanding of the impact of root exudates composition on Cd accumulation in crops may provide valuable information for plant breeding. In this study, we selected nine spring wheat varieties and analysed the accumulation and distribution of Cd in shoots, roots, root surfaces and kernels in relation to their qualitative and quantitative composition of root exudates, determined by H-1-NMR (Proton Nuclear Magnetic Resonance). Results showed that the Cd concentration in shoots at an early stage could be used as a predictor for Cd concentration in kernels. Total Cd uptake was not correlated to the mobility of Cd in the rhizosphere, but total Cd was negatively correlated to Cd adsorbed at the root surface. Furthermore, (i) exudation of organic acids (primarily succinate and acetate) increased Cd concentration in shoots, and (ii) exudation of nucleosides, DNA (deoxyribonucleic acid) degradation products, increased Cd adsorption at the root surface. Therefore, root exudates composition should be taken into account when selecting for low-Cd wheat traits.
44.
Ahmed, Mukhtar
(author)
Crop Phenotyping
2020
In: Systems Modeling. - Singapore : Springer Singapore. - 9789811547270 ; , s. 45-60
Book chapter (peer-reviewed) abstract
The visible form of an organism is the result of its genotype, environment and complex interaction and is referred to as phenotype. Quick, precise and non-destructive measurement of phenotypic traits has been of key importance in the field of plant breeding and crop production. The image-based non-destructive phenotyping started in early twenty-first century, and these techniques are based on spectra, canopy temperature and visible light. Initially, such approaches were used for phenotyping the plants in a controlled environment, where the influence of the environment could not be considered for phenotypic expression. Hence, the need for the development of high-throughput phenotyping (HTPPs) was realized to get the required information. This chapter provides an overview of advanced phenotyping techniques with special focus on field phenotyping. These techniques have the ability to evaluate multiple traits of interest from mixed populations, monitoring of crop growth and development, and health, and also provide key information on various physiological processes. The range of plant phenotyping techniques starts from phenotyping the whole plant canopy to organ and tissue.
45.
Akech, Violet
(author)
Standard Operating Procedures (SOPs) for Banana Breeding and Data Management
2023
Reports (other academic/artistic) abstract
Banana is an important food and cash crop with a worldwide production of about 114 million metric tons. Banana is among the ten most important crops in the world and a staple food and cash crop in the Great Lakes region of East Africa, where it contributes to the livelihood of millions of people who are mainly small-scale farmers. Despite its importance, the edible yield is still low at just 9% of its yield potential. Bananas’ low yield is attributed to both abiotic and biotic constraints. Breeding for host plant resistance and tolerance is the most ideal method for managing pathogens and pests and abiotic factors, respectively. Significant progress has been made in banana breeding to address these constraints through cross-hybridization and selection of recombinants at the diploid level to generate new improved hybrids by various breeding programmes like the International Institute of Tropical Agriculture (IITA), where sources of host plant resistance to various pathogens and pests are available in wild diploid species. However, the bananas grown for consumption are primarily seedless triploids and vegetatively propagated, which limits gene flow and recombination, thus hampering genetic improvement.Seed set is generally extremely limited and seed viability and germination rates are low, which complicates breeding efforts and intensifies the resources and time required to develop superior cultivars. Crossbreeding of bananas involves a series of activities and data workflows starting with the selection of parents, the crossing of the parents (hand pollination/hybridization), tissue culture activities for embryo rescue and clonal multiplication of hybrids, and evaluation of the progeny in Early Evaluation Trials (EET) for advanced yield trials in which improved hybrids are selected for cultivar release. These processes are costly in terms of resources and time required and thus should be organised efficiently.This manual aims to document standard operating procedures (SOPs) for banana breeding as efforts towards modernization of the breeding process pipeline. Four SOPs have been written and these are: SOP 01: Crossing to obtain hybrids for matooke breeding; SOP 02: Ploidy analysis in banana; SOP 03: Establishment of Early Evaluation Trials; and SOP 04: Phenotyping and data management of Early Evaluation Trials (EET) in matooke (AAA) breeding. These SOPs will be beneficial to the banana breeding programme by their availability as ‘how-to’ manuals, ensuring consistency and accuracy to reduce costly mistakes.
46.
Al Azzawi, Tiba Nazar Ibrahim, et al.
(author)
Evaluation of Iraqi Rice Cultivars for Their Tolerance to Drought Stress
2020
In: Agronomy. - : MDPI. - 2073-4395. ; 10:11
Journal article (peer-reviewed) abstract
Drought stress is a serious problem around the globe and particularly in the Republic of Iraq. Rice is the third most consumed crop for the Iraqi people; however, its cultivation and production is very low due to several challenges including drought. The current study was performed to evaluate five Iraqi rice cultivars along with relevant (drought-tolerant and drought-susceptible) controls under drought stress, either by treatment with 10% PEG (polyethylene glycol) or through water withholding to induce natural drought stress. The phenotypes of all the cultivars were evaluated and the transcriptional responses of key drought-responsive candidate genes, identified through the EST-SSR marker-based approach, were studied. We also studied transcript accumulation of drought-related transcriptional factors, such as OsGRASS23, OsbZIP12, and OsDREB2A. Moreover, the reference cultivars also included a drought-tolerant inter-specific cultivar Nerica 7 (a cross between Oryza sativa ssp. indica X O. glaberrima). Among the cultivars, the more drought-tolerant phenotypic characteristics and higher transcript accumulation of drought-related marker genes OsE647 and OsE1899 and transcriptional factors OsGRASS23, OsbZIP12, and OsDREB2A were observed in four (out of five) significantly drought-tolerant Iraqi cultivars; Mashkab, followed by Furat, Yasmen, and Amber 33. On another note, Amber Barka was found to be significantly drought susceptible. Mashkab and Amber Barka were found to be the most drought-tolerant and-susceptible cultivars, respectively. The identified tolerant cultivars may potentially serve as a genetic source for the incorporation of drought-tolerant phenotypes in rice.
47.
Al-Essawe, Essraa M, et al.
(author)
Extenders for alpaca epididymal spermatozoa: Comparison of INRA96 and andromed
2020
In: Animal Reproduction Science. - : Elsevier BV. - 0378-4320 .- 1873-2232. ; 223
Journal article (peer-reviewed) abstract
Artificial insemination would be a useful technique for alpaca breeders to use as an aid to breeding to increase fleece quality. The technique, however, is not well developed in alpacas, partly because of the viscous nature of their seminal plasma. Castration conducted for husbandry purposes can provide a source of epididymal spermatozoa to test semen extenders or handling regimens, thus circumventing the problem of the viscous ejaculate. In this experiment, two semen extenders (Andromed and INRA96) developed for other species (bovine and equine, respectively) were tested with alpaca spermatozoa derived from the cauda epididymis. Sperm total motility (mean ± SEM A: 29.1 ± 4.8 % compared with I: 35.4 ± 4.8 %; NS), membrane integrity (A: 58 ± 9% compared with I: 56 ± 9%; NS) and acrosome integrity (A: 65 ± 7% compared with I: 54 ± 7%; NS) were not different between the two extenders. Progressive motility with use of INRA96 was greater after incubating for 30 min than after incubating for 10 min (35 ± 4% vs. 12 ± 4%, respectively; P = 0.03). In conclusion, viable epididymal spermatozoa could be extracted from the castrated organs after overnight transport. There were no differences in sperm quality between the two extenders; therefore, it appears that either extender could be used for alpaca spermatozoa. These results could help in the development of a technique for artificial insemination in alpacas.
48.
Almeida, Pedro, et al.
(author)
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion
2020
In: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 18:1
Journal article (peer-reviewed) abstract
BackgroundSex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.ResultsHere, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.ConclusionsOur data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
49.
Amuzu, Esinam
(author)
Genomics of heterosis and egg production in White Leghorns
2020
Doctoral thesis (other academic/artistic) abstract
Crossbreeding is practiced extensively in commercial breeding programs of many plant and animal species, in order to exploit heterosis, breed complementarity, and to protect pure line genetic material. The success of commercial crossbreeding schemes depends on identifying and using the right combination of breeds, lines or varieties that produce the desired crossbred offspring. Currently, the selection of pure lines is based on the results of “field tests”, during which the performance of their crossbreds is assessed under typical commercial settings. Field tests are time‐ consuming, and also constitute a large percent of the costs of commercial crossbreeding programs. The research in this thesis therefore set out mainly to develop models for the accurate prediction of heterosis in White Leghorn crossbreds, using genomic information from their parental pure lines. Predicted heterosis could be used as pre‐selection criteria, thus substantially reducing the number of crosses that need to be field‐tested. In Chapter 1, I give an overview of the history of selective breeding in laying hens, and introduce heterosis and its genetic basis. In Chapter 2, based on a dominance model, we showed that a genome‐ wide squared difference in allele frequency between parental pure lines (SDAF) predicts heterosis in egg number (EN) and egg weight (EW) at the line level with an accuracy of ~0.5. With this accuracy, one can reduce the number of field tests by 50%, with only ~4 loss in realised heterosis. In laying hens, selection pressure is highest on the sires. We therefore went further to develop a model to predict heterosis at the individual sire level, in order to exploit the variation between sires from the same line. We found that the within‐line variation between sires in our data was very small (0.7% of the variation in predicted heterosis), and most of the variation was explained by across‐line differences (90%) (Chapter 3). Quantitative genetic theory shows that heterosis is proportional to SDAF and the dominance effect at a locus. In Chapter 4, we estimated variance components and dominance effects of single nucleotide polymorphisms (SNPs) on EN and EW in White Leghorn pure lines. We found that dominance variance accounted for up to 37% of the genetic variance in EN, and up to 4% of that in EW. We then used the estimated dominance effects to calculate dominance‐weighted SDAFs for EN and EW between parental pure lines, and showed that prediction of heterosis based on a weighted SDAF would yield considerably different ranking of crosses for each trait, compared with a prediction based on the raw SDAF. This implies that different crosses would be selected depending on the criterion used to predict heterosis. To gain an insight into the genetic architecture of EN and EW, in Chapter 5 we performed genome‐ wide association studies using data on 16 commercial crossbred populations. We did not identify any significant SNPs for EN, indicating that EN is a highly polygenic trait with no large quantitative trait loci segregating in the populations studied. For EW, however, we identified several significant SNPs. One explanation for these results is that EN has been under intense directional selection for several decades, whereas EW has been under less‐intense, stabilising selection. Finally, in the general discussion of this thesis (Chapter 6), I discuss the genomic prediction of heterosis, focusing on possible reasons for the lack of a consensus on the approach to predict heterosis, even after decades of research. I also discuss new opportunities for the genomic prediction of heterosis, considering the advancements in genotyping and computation methods. Lastly, I give an example of the application of results from this thesis in crossbreeding programs.
50.
Andersson, Göran
(author)
Association of heat-shock protein 70.1 gene with physiological and physical performance of Bali cattle
2024
In: Veterinary World. - 0972-8988 .- 2231-0916. ; 17, s. 17-25
Journal article (peer-reviewed) abstract
Background and Aim: Global warming challenges cattle productivity and welfare since it affects heat stress and scarce feed. The heat-shock protein 70 (HSP70) gene is essential in cytoprotection against stressors, protecting cells from dysregulated gene expression and apoptosis. This study aimed to identify significant genetic markers of the HSP70.1 gene that can be leveraged genetically to enhance thermotolerance and production in Bali cattle further.Materials and Methods: Animals were sampled from three different rearing systems. In this study, 83 healthy adult male Bali cattle without abnormalities were utilized. Single-nucleotide polymorphism (SNP) diversity associated with the physiological and physical traits of Bali cattle was assessed using SNPStat online software. Gene expression for putative SNPs and their genotypic groups was further evaluated.Results: There were 15 polymorphic SNPs (c.-185G>A, c.-69T>G, c.10G>C, c.19A>G, c.45C>T, c.101INS, c.115T>C, c.130T>C, c.136G>T, c.159G>C, c.164G>T, c.234G>A, c.303G>A, c.333C>A, and c.456C>T) identified, of which 12 were associated with the assessed trait. Nine SNPs were associated with physiological traits, while eight were with physical traits. The c.136G>T as a novel, high minor allele frequency, and associative SNP was selected for HSP70 gene expression. Individuals with the TT genotype have a trim physique, susceptible physiology, and high HSP70 mRNA expression. On the other hand, the GG genotype was significantly associated with larger physique, lower physiology, and low HSP70 mRNA expression. The higher expression may indicate that HSP70.1 is involved in mitigating the deleterious effects of stress. As a result, the animal experienced negative energy balance, decreasing body size.Conclusion: Single-nucleotide polymorphism c.136G>T is a candidate biomarker for heat resistance traits in Bali cattle.
