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Numrering	Referens	Omslagsbild	Hitta
1.	Munthe, Christian, 1962 (författare) Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies 2017 Bok (övrigt vetenskapligt/konstnärligt)abstract This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
2.	Sandin, Per, et al. (författare) Technology neutrality and regulation of agricultural biotechnology 2018 Ingår i: Professionals in food chains: ethics, rules and responsibility. EurSafe 2018, Vienna, Austria 13 – 16 June 2018 / edited by: Svenja Springer, Herwig Grimm. - Wageningen, Netherlands : Wageningen Academic Publishers. - 9789086863211 Konferensbidrag (refereegranskat)abstract Agricultural biotechnology, in particular genetically modified organisms (GMOs), is subject to regulation in many areas of the world, not least in the European Union (EU). A number of authors have argued that those regulatory processes are unfair, costly, and slow and that regulation therefore should move in the direction of increased ‘technology neutrality’. The issue is becoming more pressing, especially since new biotechnologies such as CRISPR increasingly blur the regulatory distinction between GMOs and non-GMOs. This paper offers a definition of technology neutrality, uses the EU GMO regulation as a starting point for exploring technology neutrality, and presents distinctions between variants of the call for technology neutral GMO regulation in the EU.
3.	The Routledge Handbook of Food and Nutrition Security 2016 Samlingsverk (redaktörskap) (refereegranskat)
4.	Lillie, Mette, et al. (författare) Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens 2018 Ingår i: Poultry Science. - : Elsevier BV. - 0032-5791 .- 1525-3171. ; 97:3, s. 781-790 Tidskriftsartikel (refereegranskat)abstract Sixty years, constituting 60 generations, have passed since the founding of the Virginia body weight lines, an experimental population of White Plymouth Rock chickens. Using a stringent breeding scheme for divergent 8-week body weight, the lines, which originated from a common founder population, have responded to bidirectional selection with an approximate 15-fold difference in the selected trait. They provide a model system to study the genetics of complex traits in general and the influences of artificial selection on quantitative genetic architectures in particular. As we reflect on the 60th anniversary of the initiation of the Virginia body weight lines, there is opportunity to discuss the findings obtained using different analytical and experimental genetic and genomic strategies and integrate them with a recent pooled genome resequencing dataset. Hundreds of regions across the genome show differentiation between the 2 lines, reinforcing previous findings that response to selection relied on standing variation across many genes and giving insights into the haplotype complexity underlying regions associated with body weight.
5.	Zubair, Muhammad (författare) Genetic variation, biochemical contents and wound healing activity of Plantago major 2012 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Plantago major L. (greater plantain, common plantain) has been used as a wound healing remedy in different parts of the world for centuries. Different bioactive compounds have been proposed to contribute to the wound healing properties of this plant. The present study was undertaken to investigate the impact of some genetic and environmental factors on the wound healing activity of common plantain. Seeds of P. major were collected from five populations in different parts of Sweden, and were germinated and grown in a greenhouse. As expected for an inbreeding species, RAPD analyses demonstrated considerable between-population variation but very sparse within-population and within-subpopulation variation. Six major phenolic compounds were encountered in samples of P. major, four of which were identified for the first time in this thesis; PLMA 1–PLMA 4. Between-population and sub-population differences in the contents of these chemical compounds showed no correlation with RAPD-based estimates of genetic relatedness. The contents of these compounds differed greatly between different plant organs of P. major. The highest concentration of plantamajoside and PLMA 2 was found in leaves whereas the highest concentration of verbascoside was found in flower stalks and seeds. Contents were significantly higher in freeze-dried leaf samples compared to samples dried at higher temperatures. Both water and ethanol-based extracts of P. major leaves stimulated the cell proliferation and migration in an in vitro scratch assay, and also showed anti-inflammatory activity in an in vitro NF-kB assay with oral epithelial cell cultures. Similarly, these extracts stimulated wound healing activities in ex vivo tests using detached pig ears. Further breeding efforts aimed at developing P. major as a crop plant, and medicinal research aimed at elucidating and optimizing extracts with wound healing properties, are thus warranted.
6.	Roos, Jonas (författare) Verticillium longisporum and plant immunity responses in Arabidopsis 2014 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Verticillium spp. are soil-borne ascomycete fungi belonging to a subgroup of Sordariomycetes, and the three major plant pathogens Verticillium longisporum, V. dahliae and V. albo-atrum cause disease on numerous plant species worldwide. In Sweden, V. longisporum poses a threat to Brassica oilseed crops, and is thus emphasized in this thesis. Here the early immune responses to V. longisporum in the model plant Arabidopsis and recent data on the V. longisporum genome are presented. Three genes of importance in the Arabidopsis–V. longisporum interaction were studied. The genes were identified via transcriptome and single nucleotide polymorphism (SNP) analysis. RabGAP22, a RabGTPase-regulating protein, was found to contribute to V. longisporum resistance. Pull-down assays revealed SERINE:GLYOXYLATE AMINOTRANSFERASE (AGT1) as an interacting partner during V. longisporum infection and the two proteins were shown to co-localize in the peroxisomes. Unexpectedly, a role for RabGAP22 was also found in stomatal immunity. The monoterpene synthase TPS23/27 was on the other hand found to contribute to fungal invasion, by triggering germination of V. longisporum conidia. The third gene codes for a nitrate/peptide transporter, NPF5.12. Pull-down experiments and fluorescent imaging revealed interaction between NPF5.12 and a major latex protein family member, NPFBP1. Implications in plant immunity processes of these three genes are further discussed. The genomes of two Swedish V. longisporum isolates were sequenced and found to have a size of approximately 70 Mb and harbor ~21,000 protein-coding genes. Initial analyses revealed that 86% of the V. longisporum genomes are shared with V. dahliae and V. albo-atrum, with a high extent of gene duplications. Large numbers of proteins were predicted to contain secretion motifs, and this group of proteins is presumed to play major roles in the interactions with V. longisporum host plants. In conclusion, this thesis work has revealed new fungal and plant host genes and thereby laid the basis for new plant breeding and disease protection strategies.
7.	Tengvall, Katarina, 1980-, et al. (författare) Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis 2022 Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 5:1 Tidskriftsartikel (refereegranskat)abstract Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.
8.	Abreha, Kibrom Berhe, et al. (författare) Understanding the Sorghum–Colletotrichum sublineola interactions for enhanced host resistance 2021 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12 Forskningsöversikt (refereegranskat)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.
9.	Brhanie Mesfin, Haftom, et al. (författare) Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses 2022 Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13 Tidskriftsartikel (refereegranskat)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.
10.	Calleja-Rodriguez, Ainhoa, et al. (författare) Functional QTL Analysis for Adaptive Traits in a Three-Generation Scots Pine Pedigree 2018 Konferensbidrag (övrigt vetenskapligt/konstnärligt)
11.	Calleja-Rodriguez, Ainhoa (författare) Quantitative Genetics and Genomic Selection of Scots pine 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract The final objective of tree improvement programs is to increase the frequency of favourable alleles in a population, for the traits of interest within the breeding programs. To achieve this, it is crucial to decompose the phenotypic variance accurately into its genetic and environmental components in order to obtain a precise estimation of genetic parameters and to increase genetic gains. The overall aim of this thesis was to increase the accuracy of genetic parameter estimation by incorporating new quantitative genetics models to the analysis of multiple traits in multiple trials of Scots pine, and to develop a genomic selection protocol to accelerate genetic gain. Factor analysis was incorporated to multivariate multi-environment analyses and it allowed to evaluate up to 19 traits simultaneously. As a result, precise patterns of genotype-by-environment interactions (G  E) were observed for tree vitality and height; moreover, it was possible to detect the main driver of the G  E: differences in temperature sum among sites. Traditional quantitative trait loci (QTL) analysis of phenotypic data was compared with the detection of QTL with estimated breeding values (EBV) for the first time in a three generation pedigree and, as outcome, it was noticed that if a QTL was associated to a EBV and to a phenotypic trait, the proportion of variance explained by the QTLEBV was higher than the QTL-phenotype. Additionally, several QTL were detected across several ages, which may make them suitable as candidates for early selection. Genomic selection (GS) could aid to reduce the breeding cycle by shortening the periods of progeny field testing, and consequently increasing genetic gains per year. Genomic predictions, including additive and non-additive effects through different prediction models were compared with traditional pedigree-based models; it was seen an overestimation of genetic parameters for pedigree-based models, even larger when nonadditive effects could not be discerned from additive and residual effects. Prediction accuracies and abilities of the genomic models were sufficient to achieve higher selection efficiencies and responses per year varying between 50-90% by shortening 50% the breeding cycle. For the selection of the top 50 individuals, higher gains were estimated if non-additive effects are incorporated to the models (7 – 117%).
12.	Dida, Mulatu Geleta, et al. (författare) Genetic Diversity within a Global Panel of Durum Wheat (Triticum durum) Landraces and Modern Germplasm Reveals the History of Alleles Exchange 2017 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 8 Tidskriftsartikel (refereegranskat)abstract Durum wheat is the 10th most important crop in the world, and its use traces back to the origin of agriculture. Unfortunately, in the last century only part of the genetic diversity available for this species has been captured in modern varieties through breeding. Here, the population structure and genetic diversity shared among elites and landraces collected from 32 countries was investigated. A total of 370 entries were genotyped with Axiom 35K array to identify 8,173 segregating single nucleotide polymorphisms (SNPs). Of these, 500 were selected as highly informative with a PIC value above 0.32 and used to test population structure via DAPC, STRUCTURE, and neighbor joining tree. A total of 10 sub-populations could be identified, six constituted by modern germplasm and four by landraces of different geographical origin. Interestingly, genomic comparison among groups indicated that Middle East and Ethiopia had the lowest level of allelic diversity, while breeding programs and landraces collected outside these regions were the richest in rare alleles. Further, phylogenetic analysis among landraces indicated that Ethiopia might represent a second center of origin of durum wheat, rather than a second domestication site as previously believed. Together, the analyses carried here provide a global picture of the available genetic diversity for this crop and shall guide its targeted use by breeders.
13.	Eriksson, Dennis, et al. (författare) Editorial: Leeway to operate with plant genetic resources 2020 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 11 Tidskriftsartikel (refereegranskat)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.
14.	Eriksson, Dennis, et al. (författare) Overview and Breeding Strategies of Table Potato Production in Sweden and the Fennoscandian Region 2016 Ingår i: Potato Research. - : Springer Science and Business Media LLC. - 0014-3065 .- 1871-4528. ; 59, s. 279-294 Tidskriftsartikel (refereegranskat)abstract Recent reductions in the public commitment to potato breeding in Sweden, Norway and Finland call for an evaluation of the current situation regarding the commercial basis for, and structure of, potato breeding in these countries. We here review the extent of cultivation, processing and consumption of table potato in Sweden, as well as provide an overview of the potato breeding tools and programmes in the three countries. We then discuss various strategies to provide long-term stability and increase the impact of public potato breeding, based on the similar overall conditions for potato cultivation across the Fennoscandian region. The conclusions are twofold; first, an increased long-term funding of the public potato breeding programmes is necessary to maintain a minimum level of material, and second, a coordination of the breeding activities in the Fennoscandian region would be of great benefit to all involved stakeholders and allow an enhancement of the current national breeding programmes. In addition, we propose a minimum first field year population size for potato breeding.
15.	Ghasemkhani, Marjan (författare) Genetic basis for resistance against fruit tree canker in apple 2012 Rapport (övrigt vetenskapligt/konstnärligt)abstract Neonectria ditissima (formerly Neonectria galligena, anamorph Cylindrocarpon heteronema) is the causal agent of fruit tree canker which is regarded as a serious economic problem in horticulture. This fungus causes notable damage to apple trees and it is very important in some regions, especially North western Europe, where it can result in death of spur shoots and branches. Although it occurs in a wide range of temperatures, it is associated with wet weather and climate has an important effect on the geographic distribution. The fungus produces conidia and ascospores, both of which are dispersed and cause infection during prolonged periods of rainy weather. Also, spores produced on the infected wood can act as an infection source in the orchards. The fungus can therefore be introduced into new orchards with infected planting material from other orchards or tree nurseries. Chemical and mechanical control like spraying of fungicides, covering wounds with paint, and cutting out infected branches, do not prevent the occurrence of epidemics. Breeding cultivars with a high level of resistance towards canker would be of great help towards the avoidance of this disease. Apple cultivars show variable levels of partial resistance to the fungus, whereas complete resistance has not yet been reported and no major genes have been identified. Therefore, apple genotypes with comparatively high levels of genetically determined partial resistance should be identified for use in apple breeding.
16.	Hammenhag, Cecilia, et al. (författare) Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars 2021 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12 Tidskriftsartikel (refereegranskat)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.
17.	Hammenhag, Cecilia, et al. (författare) QTL mapping for domestication-related characteristics in field cress (Lepidium campestre)—a novel oil crop for the Subarctic region 2020 Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 11 Tidskriftsartikel (refereegranskat)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.
18.	Jin, Yunkai, et al. (författare) New Energy Crops for Biofuel Production 2015 Ingår i: Handbook of clean energy systems. - Chichester, UK : John Wiley & Sons, Ltd. - 9781118388587 ; , s. 49-62 Bokkapitel (refereegranskat)
19.	Karlsson, Milla, et al. (författare) Möjliga tillämpningar av nya genomiska tekniker inom integrerat växtskydd 2023 Rapport (övrigt vetenskapligt/konstnärligt)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.
20.	Lehrman, Anna, et al. (författare) Framtidens mat - om husdjursavel och växtförädling 2014 Bok (övrigt vetenskapligt/konstnärligt)abstract Du har kanske inte funderat över varför tomater ser ut som de gör, varför våra husdjur är så lugna och vänliga, eller hur det är möjligt att köpa en vattenmelon utan kärnor. Trots att växtförädling och djuravel har format det mesta vi äter, är det få människor som är medvetna om vilka vetenskapliga upptäckter och vilket omfattande arbete som ligger bakom maten vi lägger på våra tallrikar. Med den här boken vill vi ge en översikt över domesticeringens och förädlingens bakgrund, från jordbrukets början för mer än 10 000 år sedan till dagens molekylära arbete. Vi beskriver grunderna för genernas strukturer och funktioner, varför och hur olika avels- och förädlingsmetoder används och ger en inblick i lagstiftningen kring användning av genteknik i Sverige och EU. Vi ger också en överblick över olika produkter som tagits fram genom genetisk modifiering (GM) och en sammanfattning av de ekonomiska konsekvenserna av GM-grödor. Vidare diskuterar vi etiska frågor som rör avel och förädling i allmänhet och genetisk modifiering i synnerhet.
21.	Leonova, Svetlana (författare) Lipids in seeds of oat (Avena spp.), a potential oil crop : content, quality, metabolism, and possibilities for improvement 2013 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract New oil crops with high yield and oil content are urgently needed. Oat is the only cereal that accumulates substantial amount of lipids in the endosperm. This gives it potential as an oil crop, which could address both nutritional and environmental concerns of modern society. To develop oat with increased oil content, thorough investigations on its lipid metabolism and tools for genetic manipulations are needed. Analyses of lipids in seeds of wild and cultivated oat species revealed variation in wild oat accessions in both oil content and quality. This variation should allow for development of new oat varieties for diverse applications. However, to develop oat as an oil crop, a level of 20% of the seed dry weight as oil is required and the range of oil content in the studied accessions was 4-10%. Another feature which showed almost no deviation was the amount of omega 3 fatty acid, -linolenic acid (0.6-2.1%). To develop oat varieties with ultra-high seed oil and increased content of omega 3 fatty acids, a biotechnological approach is preferred to conventional breeding methods. Lipids in oat endosperm have been reported to exist, not enclosed in oil bodies, but as non-structured oil smear. In my study, I also observed oil smears, a phenomenon probably correlated with the reduced amount of oil body associated proteins in the endosperm, as revealed by microscopic and staining methods. This was supported experimentally by SDS-PAGE separation of oil-body proteins and immunoblotting and immunolocalization with antibodies against a 16 kD oil body protein. Biochemical studies on lipid mobilization during oat seed germination demonstrated efficient utilization of oil reserves from the starchy endosperm; these results were corroborated by microscopy. An oat cultivar which is capable of accumulating high amounts of oil in the endosperm was shown to be also efficient in utilizing these reserves upon germination. Agrobacterium-mediated transformation is one of the methods for modification of oat oil content and/or its quality. The results of the analyses aimed at development of an Agrobacterium-mediated oat transformation protocol are presented in this thesis.
22.	Mulugeta, Behailu, et al. (författare) Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat 2023 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13 Tidskriftsartikel (refereegranskat)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.
23.	Nemesio Gorriz, Miguel (författare) Molecular responses against Heterobasidion annosum s.l. in Picea abies 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Norway spruce [Picea abies (L.) Karst.] is a main tree species in European forests and is important both ecologically and economically. The root rot fungus Heterobasidion annosum sensu lato (s.l.) is the main P. abies pathogen. Including resistance in breeding programs would help mitigating the impact of the pathogen but knowledge regarding defense mechanisms in P. abies needs a better understanding. The work within this thesis intended to expand the existing knowledge on P. abies resistance mechanisms focusing on hormone signaling, flavonoid biosynthesis and its transcriptional regulation. I found that jasmonic acid is the major hormone controlling defense signaling pathways in P. abies. Furthermore, we validated a candidate gene, PaLAR3, as a resistance marker for H. annosum s.l. in P. abies. PaLAR3 encodes an enzyme responsible for the synthesis of (+) catechin, which showed a fungistatic effect on H. parviporum. Analysis of genetic diversity revealed two allelic lineages of PaLAR3 that showed significant differences in fungal resistance and (+) catechin content that were explained by dissimilarities in inducibility. We studied the role of PaNAC03, a transcription factor that is associated with H. annosum s.l. infection. PaNAC03 not only showed repression of multiple genes including PaLAR3, but bound only to the promoter of one of the PaLAR3 allelic lineages explaining at least partly the differences in allelic expression that were observed. Finally, we identified a full repertoire of members of a MYB/bHLH/WDR transcription factor complex in Norway spruce, which showed differences in protein interactions and expression patterns, and also in ability to control the expression of genes in the flavonoid biosynthetic pathway including PaLAR3.
24.	Ortiz Rios, Rodomiro Octavio (författare) Advances in Host Plant and Rhizobium Genomics to Enhance Symbiotic Nitrogen Fixation in Grain Legumes 2015 Ingår i: Advances in Agronomy. - : Elsevier. - 0065-2113 .- 2213-6789. ; 129, s. 1-116 Forskningsöversikt (refereegranskat)abstract Legumes form symbiotic relationship with root-nodule, rhizobia. The nitrogen (N2) fixed by legumes is a renewable source and of great importance to agriculture. Symbiotic nitrogen fixation (SNF) is constrained by multiple stresses and alleviating them would improve SNF contribution to agroecosystems. Genetic differences in adaptation tolerance to various stresses are known in both host plant and rhizobium. The discovery and use of promiscuous germplasm in soybean led to the release of high-yielding cultivars in Africa. High N2-fixing soybean cultivars are commercially grown in Australia and some countries in Africa and South America and those of pea in Russia. SNF is a complex trait, governed by multigenes with varying effects. Few major quantitative trait loci (QTL) and candidate genes underlying QTL are reported in grain and model legumes. Nodulating genes in model legumes are cloned and orthologs determined in grain legumes. Single nucleotide polymorphism (SNP) markers from nodulation genes are available in common bean and soybean. Genomes of chickpea, pigeonpea, and soybean; and genomes of several rhizobium species are decoded. Expression studies revealed few genes associated with SNF in model and grain legumes. Advances in host plant and rhizobium genomics are helping identify DNA markers to aid breeding of legume cultivars with high symbiotic efficiency. A paradigm shift is needed by breeding programs to simultaneously improve host plant and rhizobium to harness the strength of positive symbiotic interactions in cultivar development. Computation models based on metabolic reconstruction pathways are providing greater insights to explore genotype–phenotype relationships in SNF. Models to simulate the response of N2 fixation to a range of environmental variables and crop growth are assisting researchers to quantify SNF for efficient and sustainable agricultural production systems. Such knowledge helps identifying bottlenecks in specific legume–rhizobia systems that could be overcome by legume breeding to enhance SNF. This review discusses the recent developments to improve SNF and productivity of grain legumes.
25.	Ortiz Rios, Rodomiro Octavio (författare) Application of genomics assisted breeding for generation of climate resilient crops: progress and prospects 2015 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 6 Tidskriftsartikel (refereegranskat)abstract Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops,which can withstand broad-spectrums tresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecula rbreeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
26.	Ortiz Rios, Rodomiro Octavio (författare) Breeding schemes for the implementation of genomic selection in wheat (Triticum spp.) 2016 Ingår i: Plant Science. - : Elsevier BV. - 0168-9452 .- 1873-2259. ; 242, s. 23-36 Tidskriftsartikel (refereegranskat)abstract In the last decade the breeding technology referred to as ‘genomic selection’ (GS) has been implemented in a variety of species, with particular success in animal breeding. Recent research shows the potential of GS to reshape wheat breeding. Many authors have concluded that the estimated genetic gain per year applying GS is several times that of conventional breeding. GS is, however, a new technology for wheat breeding and many programs worldwide are still struggling to identify the best strategy for its implementation. This article provides practical guidelines on the key considerations when implementing GS. A review of the existing GS literature for a range of species is provided and used to prime breeder-oriented considerations on the practical applications of GS. Furthermore, this article discusses potential breeding schemes for GS, genotyping considerations, and methods for effective training population design. The components of selection intensity, progress toward inbreeding in half- or full-sibs recurrent schemes, and the generation of selection are also presented.
27.	Ortiz Rios, Rodomiro Octavio (författare) Challenges for crop improvement 2023 Ingår i: Emerging topics in life sciences. - 2397-8554 .- 2397-8562. ; 7, s. 197-205 Forskningsöversikt (refereegranskat)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.
28.	Ortiz Rios, Rodomiro Octavio (författare) Genome and Environment Based Prediction Models and Methods of Complex Traits Incorporating Genotype × Environment Interaction 2022 Ingår i: Complex Trait Prediction : Methods and Protocols. - New York, NY : Springer US. - 9781071622049 ; :2467, s. 245-283 Bokkapitel (refereegranskat)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.
29.	Ortiz Rios, Rodomiro Octavio (författare) Göte Turesson’s research legacy to Hereditas: from the ecotype concept in plants to the analysis of landraces’ diversity in crops 2020 Ingår i: Hereditas. - : Springer Science and Business Media LLC. - 0018-0661 .- 1601-5223. ; 157 Forskningsöversikt (refereegranskat)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.
30.	Ortiz Rios, Rodomiro Octavio (författare) New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage 2014 Ingår i: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 200, s. 45-60 Tidskriftsartikel (refereegranskat)abstract Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems. Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace 'Hasawi' as a donor parent to generate three F-2 offspring (consisting each of 500 individuals) with three African cultivars ('NERICA-L-19', 'Sahel 108' and 'BG902') used as recipient parents (RP). The F(2)s and F(2:3)s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F-2-derived offspring, e. g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP's grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. 'Hasawi' contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.
31.	Ortiz Rios, Rodomiro Octavio (författare) Peanut improvement for human health 2014 Ingår i: Plant Breeding Reviews: Volume 38. - Hoboken, New Jersey : John Wiley & Sons, Inc.. - 9781118916834 ; 38, s. 143-185 Bokkapitel (refereegranskat)abstract Peanut (Arachis hypogaea L., Fabaceae) is an energy-dense and nutritious food. Regular consumption of peanuts improves human health. Oil content and oil quality, which is determined by variation in oleic (O) and linoleic (L) fatty acids, are important seed quality traits in peanut. Aflatoxin (produced by fungus Aspergillus flavus and Aspergillus parasiticus) is a serious health problem, whereas peanut allergy is a potentially life-threatening and often lifelong food allergy. High O/L ratio increases shelf life of peanut products and, therefore, their marketability. Germplasm and advanced breeding lines with oil content as high as 55–60% and O/L ratio ranging from 7:1 to 40:1 are available for use in peanut breeding. Global warming has a significant impact on the nutritional quality of food crops. Identification of germplasm with stable seed quality traits will be a prerequisite to initiate quality breeding in peanut. Peanut cultivars with high oleate content, developed by conventional breeding and selection, are widely grown in the United States. Marker-aided backcross breeding has led to the development of ‘Tifguard High O/L’ peanut cultivar in the United States. Enough genetic variation in seed iron and zinc content has been noted, but targeted breeding for these micronutrients in peanut is yet to begin. Peanut is devoid of β-carotene—a precursor of vitamin A. Using a cotyledon-based Agrobacterium-mediated genetic transformation system and the maize psyI gene driven by the At oleosin promoter, β-carotene-rich transgenic peanuts have been achieved. Transgenic peanuts with the antifungal gene cpo-p inhibited A. flavus hyphal growth or those containing the Rchit gene have shown a broader spectrum of resistance against fungal infection including A. flavus. Knocking out genes for the allergenic proteins, using targeting-induced local lesions in genomes (TILLING) or RNAi approaches, has shown promise to derive mutants or transgenic events lacking allergenic seed proteins, with no adverse effect on seed quality or viability. These genetic stocks when available to researchers may lead to breeding agronomically superior nutritionally enhanced peanut cultivars, which will be free from allergens and toxins.
32.	Ortiz Rios, Rodomiro Octavio (författare) Plant Breeding in the Omics Era 2015 Bok (refereegranskat)abstract The field of plant breeding has grown rapidly in the last decade with breakthrough research in genetics and genomics, inbred development, population improvement, hybrids, clones, self-pollinated crops, polyploidy, transgenic breeding and more. This book discusses the latest developments in all these areas but explores the next generation of needs and discoveries including omics beyond genomics, cultivar seeds and intellectual and property rights. This book is a leading-edge publication of the latest results and forecasts important areas of future needs and applications.
33.	Ortiz Rios, Rodomiro Octavio (författare) Preparing Wheat to Face Rising Temperatures Through Improved Heat Tolerance 2024 Ingår i: CSANews. - 1529-9163 .- 2325-3584. ; 69, s. 15-15 Tidskriftsartikel (refereegranskat)
34.	Ortiz Rios, Rodomiro Octavio (författare) Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments 2018 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 9 Forskningsöversikt (refereegranskat)abstract Drought and heat in dryland agriculture challenge the enhancement of crop productivity and threaten global food security. This review is centered on harnessing genetic variation through biotechnology-led approaches to select for increased productivity and stress tolerance that will enhance crop adaptation in dryland environments. Peer-reviewed literature, mostly from the last decade and involving experiments with at least two seasons' data, form the basis of this review. It begins by highlighting the adverse impact of the increasing intensity and duration of drought and heat stress due to global warming on crop productivity and its impact on food and nutritional security in dryland environments. This is followed by (1) an overview of the physiological and molecular basis of plant adaptation to elevated CO2 (eCO(2)), drought, and heat stress; (2) the critical role of high-throughput phenotyping platforms to study phenomes and genomes to increase breeding efficiency; (3) opportunities to enhance stress tolerance and productivity in food crops (cereals and grain legumes) by deploying biotechnology-led approaches [pyramiding quantitative trait loci (QTL), genomic selection, marker-assisted recurrent selection, epigenetic variation, genome editing, and transgene) and inducing flowering independent of environmental clues to match the length of growing season; (4) opportunities to increase productivity in C-3 crops by harnessing novel variations (genes and network) in crops' (C-3, C-4) germplasm pools associated with increased photosynthesis; and (5) the adoption, impact, risk assessment, and enabling policy environments to scale up the adoption of seed-technology to enhance food and nutritional security. This synthesis of technological innovations and insights in seed-based technology offers crop genetic enhancers further opportunities to increase crop productivity in dryland environments.
35.	Ortiz Rios, Rodomiro Octavio (författare) What plant breeding may (and may not) look like in 2050? 2024 Ingår i: The Plant Genome. - 1940-3372. ; 17 Forskningsöversikt (refereegranskat)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.
36.	Osterman, Johanna, et al. (författare) Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers 2021 Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12 Tidskriftsartikel (refereegranskat)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.
37.	Stenberg, Johan A (författare) Den genmodifierade maten: Syndig frestelse eller moralisk skyldighet? 2014 Ingår i: Signum : katolsk orientering om kyrka, kultur och samhälle. - 0347-0423. ; , s. 31-34 Tidskriftsartikel (populärvet., debatt m.m.)
38.	Turesson, Helle, et al. (författare) Starch biosynthetic genes and enzymes are expressed and active in the absence of starch accumulation in sugar beet tap-root 2014 Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 14 Tidskriftsartikel (refereegranskat)abstract Abstract Background: Starch is the predominant storage compound in underground plant tissues like roots and tubers. An exception is sugar beet tap-root (Beta vulgaris ssp altissima) which exclusively stores sucrose. The underlying mechanism behind this divergent storage accumulation in sugar beet is currently not fully known. From the general presence of starch in roots and tubers it could be speculated that the lack in sugar beet tap-roots would originate from deficiency in pathways leading to starch. Therefore with emphasis on starch accumulation, we studied tap-roots of sugar beet using parsnip (Pastinaca sativa) as a comparator. Results: Metabolic and structural analyses of sugar beet tap-root confirmed sucrose as the exclusive storage component. No starch granules could be detected in tap-roots of sugar beet or the wild ancestor sea beet (Beta vulgaris ssp. maritima). Analyses of parsnip showed that the main storage component was starch but tap-root tissue was also found to contain significant levels of sugars. Surprisingly, activities of four main starch biosynthetic enzymes, phosphoglucomutase, ADP-glucose pyrophosphorylase, starch synthase and starch branching enzyme, were similar in sugar beet and parsnip tap-roots. Transcriptional analysis confirmed expression of corresponding genes. Additionally, expression of genes involved in starch accumulation such as for plastidial hexose transportation and starch tuning functions could be determined in tap-roots of both plant species. Conclusion: Considering underground storage organs, sugar beet tap-root upholds a unique property in exclusively storing sucrose. Lack of starch also in the ancestor sea beet indicates an evolved trait of biological importance. Our findings in this study show that gene expression and enzymatic activity of main starch biosynthetic functions are present in sugar beet tap-root during storage accumulation. In view of this, the complete lack of starch in sugar beet tap-roots is enigmatic.
39.	Willforss, J, et al. (författare) Interactive proteogenomic exploration of response to Fusarium head blight in oat varieties with different resistance 2020 Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 218, s. 103688-103688 Tidskriftsartikel (refereegranskat)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.
40.	Zhu, Tianqing (författare) Regulation of embryo development in Norway spruce by WOX transcription factors 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract In seed plants, the apical-basal axis of the plant body is established during early embryogenesis. Major regulatory genes of the apical-basal axis formation belong to the WUSCHEL-RELATED HOMEOBOX (WOX) gene family of transcription factors. The spatiotemporal expression pattern and the molecular role of the WOX genes has mainly been studied in the angiosperm model plant Arabidopsis (Arabidopsis thaliana). Similar information in conifers is limited. The aim of my thesis has been to characterize WOX genes in Norway spruce (Picea abies) and to elucidate the function of WOX genes expressed during embryo development. We cloned 11 WOX homologs from Norway spruce and examined their phylogenetic relationship to WOX genes from other species. The phylogenetic analyses showed that the major diversification within the WOX gene family took place before the gymnosperm-angiosperm split. PaWOX8/9, PaWOX2 and PaWOX3, which are expressed in embryos, were selected for further studies. PaWOX8/9 and PaWOX2 are highly expressed in early and late embryos, and PaWOX3 is highly expressed in mature embryos. Functional studies were performed in RNAi lines where the genes were down-regulated. Embryos in PaWOX8/9 RNAi lines showed a disturbed apical-basal patterning caused by abnormal orientation of the cell division plane at the basal part of the embryonal mass. In PaWOX2 RNAi lines, vacuolated cells differentiated on the surface of the embryonal mass and the embryos failed to form a proper protoderm. Down-regulation of PaWOX3 disturbed lateral margin outgrowth in cotyledons and needles. Taken together, our results indicate that WOX8/9, WOX2 and WOX3 exert evolutionarily conserved functions during embryo development. We can therefore conclude that the regulatory networks of embryo development are at least partly conserved between angiosperms and gymnosperms.
41.	Åhman, Inger (författare) Regulation of barley (Hordeum vulgare L.) defense against the bird cherry-oat aphid (Rhopalosiphum padi L.) 2013 Ingår i: IOBC-WPRS Bulletin. - 1027-3115. ; 88, s. 100- Annan publikation (övrigt vetenskapligt/konstnärligt)
42.	Åhman, Inger (författare) Transcript profiling of plant-aphid interactions in barley as an approach to identifying resistance genes 2012 Ingår i: IOBC-WPRS Bulletin. - 1027-3115. ; 83, s. 84-84 Konferensbidrag (övrigt vetenskapligt/konstnärligt)
43.	Ahmadi Afzadi, Masoud (författare) Genetic variation in resistance to fungal storage diseases in apple : inoculation-based screening, transcriptomics and biochemistry 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Apple is one of the economically and culturally most important fruit crops and has many health-related benefits. Apple production is, however, sensitive to several fungal diseases including blue mold, caused by Penicillium expansum. Problems are more pronounced in organic production or in countries where postharvest application of fungicides is prohibited. To limit or overcome this problem, many studies have been focused on investigations of the mechanism of resistance/tolerance. No major gene(s) have as yet been identified, but quantitatively inherited traits, some of which are related to fruit texture and content of chemical compounds, have been shown to affect the ability of cultivars to withstand storage diseases. In the present thesis, inter-cultivar variation in terms of resistance to fungal storage diseases was investigated at two locations, i.e. Balsgård in Sweden and Njøs in Norway. The association of harvest date, fruit firmness and softening with lesion decay was investigated on large sets of cultivars. The contribution of four fruit texture-related genes (Md-ACO1, Md-ACS1, Md-Exp7 and Md-PG1) in explaining the fruit texture characteristics was examined. Fruit content of chemical compounds with a potential impact on disease resistance was also investigated, and finally the regulation of apple genes upon fungal infection was studied in order to identify candidate genes responsible for disease resistance. Inoculation-based screening indicated large variation across the investigated cultivars in terms of blue mold and bitter rot susceptibility. Harvest date and softening rate of fruits during storage had a large impact on resistance to fungal diseases, thus cultivars with moderate to firm fruits that soften comparatively little during storage could withstand the fungal infection comparatively well. Softening rate is, in its turn, closely associated with harvest date whereas four fruit texture-related genes had lower predictive power than expected. Quantifying the chemical compounds in the fruit samples revealed that some of these compounds, especially flavonols and procyanidin B2, could contribute to resistance against blue mold, whereas contents of malic acids or total titratable acidity had considerably less impact. Differential expression of FLS, LDOX, and CHS genes involved in biosynthesis of flavonoids and PGIP, TT10, WAK1 and CTL1 genes related to cell wall structure indicate the importance of fruit characteristics and biochemical compounds in the resistance mechanism.
44.	Brandt, Monika, et al. (författare) Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci 2017 Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 7:1, s. 119-128 Tidskriftsartikel (refereegranskat)abstract The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.
45.	Chengjiang, Ruan, et al. (författare) Advances in improvement of quality and resistance in a multipurpose crop: sea buckthorn 2013 Ingår i: Critical Reviews in Biotechnology. - : Informa UK Limited. - 0738-8551 .- 1549-7801. ; 33, s. 126-144 Forskningsöversikt (refereegranskat)
46.	Gustavsson, Larisa, et al. (författare) Resistance to Neonectria ditissima in apple : insights from metabolomics and lipidomics analyses 2023 Ingår i: Xxxi international horticultural congress (ihc2022). - : International Society for Horticultural Science. - 9789462613614 ; , s. 329-335, s. 329-336 Konferensbidrag (refereegranskat)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.
47.	Nybom, Hilde, et al. (författare) Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level 2016 Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 16 Tidskriftsartikel (refereegranskat)abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe.Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (F-ST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (F-ST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars.Conclusions: The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
48.	Nybom, Hilde, et al. (författare) Nordiska äpplen – projekt NordApp 2015 Ingår i: LTV-fakultetens faktablad. Annan publikation (populärvet., debatt m.m.)abstract Frukt av många olika slag odlas över hela världen, och utgör en viktig del av den totala livsmedelsförsörjningen. I varmare länder är mångfalden stor – former och färger bildar en förförande palett om man besöker en fruktmarknad, liksom doft och smak hos de frukter man väljer att bekanta sig närmare med. I de nordiska länderna sätter klimatet dessvärre stopp för merparten av dessa frukter – men vi har lyckligtvis några, främst kärn- och stenfrukter inom familjen Rosaceae. Äpple har sålunda odlats i de nordiska länderna sedan början av medeltiden, och detta är numera vår i särklass viktigaste frukt, såväl kulturellt som ekonomiskt. Vissa utländska äpplesorter fungerar ganska bra i odling även på våra breddgrader men för merparten blir den korta vegetationsperioden och de stränga vintrarna övermäktiga hinder. Offentligt finansierade växtförädlingsprogram har därför bedrivits i Finland, Norge och Sverige för att ta fram klimatanpassade sorter. På senare tid har ökad omsorg om miljö och hälsa aktualiserat ytterligare ett förädlingsmål: resistens mot olika skadegörare.
49.	Nybom, Hilde, et al. (författare) Resistens mot grönmögel hos äpple 2015 Ingår i: LTV-fakultetens faktablad. Annan publikation (populärvet., debatt m.m.)abstract Äpple är gott och nyttigt, och allt fler konsumenter frågar efter svensk frukt i affärerna. Men tillgången är inte så stor eftersom svenska odlare endast producerar 20% av de äpplen vi äter i Sverige. Resten importeras från utlandet, där klimatet är gynnsammare, arbetskostnaderna lägre och tillgången på tillåtna växtskyddsmedel större. Konsumenterna är kanske beredda att betala lite extra för svensk frukt men man förväntar sig då att kvaliteten ska vara på topp: vackra, friska och välsmakande frukter!
50.	Ortiz Rios, Rodomiro Octavio (författare) Advances in Transgenic Vegetable and Fruit Breeding 2014 Ingår i: Agricultural Sciences. - : Scientific Research Publishing, Inc.. - 2156-8553 .- 2156-8561. ; 5, s. 1448-1467 Tidskriftsartikel (refereegranskat)abstract Vegetables and fruits are grown worldwide and play an important role in human diets because they provide vitamins, minerals, dietary fiber, and phytochemicals. Vegetables and fruits are also associated with improvement of gastrointestinal health, good vision, and reduced risk of heart disease, stroke, chronic diseases such as diabetes, and some forms of cancer. Vegetable and fruit production suffers from many biotic stresses caused by pathogens, pests, and weeds and requires high amounts of plant protection products per hectare. United States vegetables farmers are benefiting from growing transgenic squash cultivars resistant to Zucchini yellow mosaic virus , Watermelon mosaic virus , and Cucumber mosaic virus , which were deregulated and commercialized since 1996. Bt- sweet corn has also proven effective for control of some lepidopteran species and continues to be accepted in the fresh market in the USA, and Bt- fresh-market sweet corn hybrids are released almost every year. Likewise, transgenic Bt- eggplant bred to reduce pesticide use is now grown by farmers in Bangladesh. Transgenic papaya cultivars carrying the coat-protein gene provide effective protection against Papaya ring spot virus elsewhere. The transgenic “Honey Sweet” plum cultivar provides an interesting germplasm source for Plum pox virus control. Enhanced host plant resistance to Xanthomonas campestris pv. musacearum , which causes the devastating banana Xanthomonas wilt in the Great Lakes Region of Africa, was achieved by plant genetic engineering. There are other vegetable and fruit crops in the pipeline that have been genetically modified to enhance their host plant resistance to insects and plant pathogens, to show herbicide tolerance, and to improve features such as slow ripening that extends the shelf-life of the produce. Consumers could benefit further from eating more nutritious transgenic vegetables and fruits. Transgenic plant breeding therefore provides genetically enhanced seed embedded technology that contributes to integrated pest management in horticulture by reducing pesticide sprays as well as improving food safety by minimizing pesticide residues. Furthermore, herbicide-tolerant transgenic crops can help reducing plough in fields, thereby saving fuel because of less tractor use, which also protects the structure of the soil by reducing its erosion. Transgenic vegetable and fruit crops could make important contributions to sustainable vegetable production and for more nutritious and healthy food. Countries vary, however, in their market standards of acceptance of transgenic crops. Biotechnology products will be successful if clear advantages and safety are demonstrated to both growers and consumers

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