| 1. |
- Batte, Michael, et al.
(författare)
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Crossbreeding East African Highland Bananas: Lessons Learnt Relevant to the Botany of the Crop After 21 Years of Genetic Enhancement
- 2019
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- East African highland bananas (EAHB) were regarded as sterile. Their screening for female fertility with "Calcutta 4" as male parent revealed that 37 EAHB were fertile. This was the foundation for the establishment of the EAHB crossbreeding programs by the International Institute of Tropical Agriculture (IITA) and the National Agricultural Research Organization (NARO) in Uganda in the mid-1990s. The aim of this study was to assess the progress and efficiency of the EAHB breeding program at IITA, Sendusu in Uganda. Data on pollinations, seeds generated and germinated, plus hybrids selected between 1995 and 2015 were analyzed. Pollination success and seed germination percentages for different cross combinations were calculated. The month of pollination did not result in significantly different (P = 0.501) pollination success. Musa acuminata subsp. malaccensis accession 250 had the highest pollination success (66.8%), followed by the cultivar "Rose" (66.6%) among the diploid males. Twenty-five EAHB out of 41 studied for female fertility produced up to 305 seeds per pollinated bunch, and were therefore deemed fertile. The percentage of seed germination varied among crosses: 26% for 2x x 4x, 23% for 2x x 2x, 11% for 3x x 2x, and 7% for 4x x 2x. Twenty-seven NARITA hybrids (mostly secondary triploids ensuing from the 4x x 2x) were selected for further evaluation in the East African region. One so far -"NARITA 7"- was officially released to farmers in Uganda. Although pollination of EAHB can be conducted throughout the year, the seed set and germination is low. Thus, further research on pollination conditions and optimization of embryo culture protocols should be done to boost seed set and embryo germination, respectively. More research in floral biology and seed germination as well as other breeding strategies are required to increase the efficiency of the EAHB breeding program.
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| 2. |
- Batte, Michael, et al.
(författare)
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Significant progressive heterobeltiosis in banana crossbreeding
- 2020
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundHeterobeltiosis is the phenomenon when the hybrid's performance is superior to its best performing parent. Banana (Musa spp. AAA) breeding is a tedious, time-consuming process, taking up to two decades to develop a consumer acceptable hybrid. Exploiting heterobeltiosis in banana breeding will help to select breeding material with high complementarity, thus increasing banana breeding efficiency. The aim of this study was therefore to determine and document the level of heterobeltiosis of bunch weight and plant stature in the East African highland bananas, in order to identify potential parents that can be used to produce offspring with desired bunch weight and stature after a few crosses.ResultsThis research found significant progressive heterobeltiosis in cross-bred 'Matooke' (highland cooking) banana hybrids, also known as NARITAs, when grown together across years with their parents and grandparents in Uganda. Most (all except 4) NARITAs exhibited positive heterobeltiosis for bunch weight, whereas slightly more than half of them had negative heterobeltiosis for stature. The secondary triploid NARITA 17 had the highest heterobeltiosis for bunch weight: 249% versus its 'Matooke' grandparent and 136% against its primary tetraploid parent. Broad sense heritability (across three cropping cycles) for yield potential and bunch weight were high (0.84 and 0.76 respectively), while that of plant stature was very low (0.0035). There was a positive significant correlation (P < 0.05) between grandparent heterobeltiosis for bunch weight and genetic distance between parents (r=0.39, P=0.036), bunch weight (r=0.7, P<0.001), plant stature (r=0.38, P=0.033) and yield potential (r=0.59, P<0.001). Grandparent heterobeltiosis for plant stature was significantly, but negatively, correlated to the genetic distance between parents (r=-0.6, P<0.001).ConclusionsSuch significant heterobeltiosis exhibited for bunch weight is to our knowledge the largest among main food crops. Since bananas are vegetatively propagated, the effect of heterobeltiosis is easily fixed in the hybrids and will not be lost over time after the release and further commercialization of these hybrids.
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| 3. |
- Batte, Michael, et al.
(författare)
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Suitability of existing Musa morphological descriptors to characterize East African highland 'matooke' bananas
- 2018
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Ingår i: Genetic Resources and Crop Evolution. - : Springer Science and Business Media LLC. - 0925-9864 .- 1573-5109. ; 65, s. 645-657
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Tidskriftsartikel (refereegranskat)abstract
- Morphological traits are commonly used for characterizing plant genetic resources. Germplasm characterization should be based on distinctly identifiable, stable and heritable traits that are expressed consistently and are easy to distinguish by the human eye. Characterization and documentation of a representative sample of East African highland bananas (Lujugira-Mutika subgroup) was carried out following an internationally accepted standard protocol for bananas. Eleven cultivars were characterized using an existing set of minimum descriptors (31 qualitative and quantitative traits) with the aim of determining stable descriptors and the ability of these descriptors to distinguish among East African highland banana cultivars. There was variation in stability of these descriptors within cultivars and across the 11 cultivars. Only 10 (32%) out of 31 descriptors studied were stable in the 11 cultivars. However, they had similar scores and therefore are not suitable to distinguish between cultivars within this group. Nonetheless, these 10 descriptors may be useful for distinguishing the East African highland bananas as a group from other groups of bananas. A few descriptors were unique to the cultivar 'Tereza' and may be used to distinguish this cultivar from other 'matooke' cultivars. None of the quantitative descriptors were stable.
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| 4. |
- Batte, Michael, et al.
(författare)
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Traits that define yield and genetic gain in East African highland banana breeding
- 2021
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Ingår i: Euphytica. - : Springer Science and Business Media LLC. - 0014-2336 .- 1573-5060. ; 217
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Tidskriftsartikel (refereegranskat)abstract
- East African highland bananas (Musa spp. AAA group) are an important staple in the Great Lakes region of East Africa. Their production has declined due to pests and diseases. Breeding for host plant resistance is a sustainable option for addressing this challenge. Understanding the relationships between growth parameters and bunch weight (i.e., yield) is crucial to guide breeding efforts for this crop. We investigated cause-effect relationships, through path analysis, in bunch weight of East African highland banana derived hybrids, their parents and grandparents. These family structures were planted in a 7 × 8 rectangular lattice design, replicated twice. Genetic gains for bunch weight (kg plant−1) and yield potential (t ha−1 year−1) were estimated. Significant increases of bunch weight and yield potential were noted from the landrace triploid germplasm, their derived primary tetraploid hybrids and secondary triploid bred-germplasm. Path analysis revealed that fruit length, circumference and number, number of hands and plant cycle number had a direct positive effect on the bunch weight. Days to fruit filling, days to maturity and index of non-spotted leaves had indirect effects on bunch weight. The average genetic gains for bunch weight and yield potential were 1.4% and 1.3% per year, respectively. This is the first report about genetic gains in banana breeding. Our findings may be useful for assessing progress and directing future breeding efforts in banana breeding.
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| 5. |
- Brhanie Mesfin, Haftom, et al.
(författare)
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Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources
- 2022
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Eleusine coracana, finger millet, is a multipurpose crop cultivated in arid and semi-arid regions of Africa and Asia. RNA sequencing (RNA-seq) was used in this study to obtain valuable genomic resources and identify genes differentially expressed between Al-tolerant and Al-susceptible genotypes. Two groups of finger millet genotypes were used: Al-tolerant (215836, 215845, and 229722) and Al-susceptible (212462, 215804 and 238323). The analysis of the RNA-seq data resulted in 198,546 unigenes, 56.5% of which were annotated with significant hits in one or more of the following six databases: NR (48.8%), GO (29.7%), KEGG (45%), PlantTFDB (19.0%), Uniprot (49.2%), and NT (46.2%). It is noteworthy that only 220 unigenes in the NR database had significant hits against finger millet sequences suggesting that finger millet’s genomic resources are scarce. The gene expression analysis revealed that 322 genes were significantly differentially expressed between the Al-tolerant and Alsusceptible genotypes, of which 40.7% were upregulated while 59.3% were downregulated in Al-tolerant genotypes. Among the significant DEGs, 54.7% were annotated in the GO database with the top hits being ATP binding (GO:0005524) and DNA binding (GO:0003677) in the molecular function, DNA integration (GO:0015074) and cell redox homeostasis in the biological process, as well as cellular anatomical entity and intracellular component in the cellular component GO classes. Several of the annotated DEGs were significantly enriched for their corresponding GO terms. The KEGG pathway analysis resulted in 60 DEGs that were annotated with different pathway classes, of which carbohydrate metabolism and signal transduction were the most prominent. The homologs of a number of significant DEGs have been previously reported as being associated with Al or other abiotic stress responses in various crops, including carboxypeptidase SOL1, HMA3, AP2, bZIP, C3H, and WRKY TF genes. A more detailed investigation of these and other DEGs will enable genomic-led breeding for Al tolerance in finger millet RNA-seq data analysis also yielded 119,073 SNP markers, the majority of which had PIC values above 0.3, indicating that they are highly informative. Additionally, 3,553 single-copy SSR markers were identified, of which trinucleotide SSRs were the most prevalent. These genomic resources contribute substantially to the enrichment of genomic databases for finger millet, and facilitate future research on this crop.
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| 6. |
- Brhanie Mesfin, Haftom, et al.
(författare)
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Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses
- 2022
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13
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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.
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| 7. |
- Campbell, Bruce M., et al.
(författare)
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Agriculture production as a major driver of the Earth system exceeding planetary boundaries
- 2017
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Ingår i: Ecology and Society. - 1708-3087. ; 22:4
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Tidskriftsartikel (refereegranskat)abstract
- We explore the role of agriculture in destabilizing the Earth system at the planetary scale, through examining nine planetary boundaries, or safe limits: land-system change, freshwater use, biogeochemical flows, biosphere integrity, climate change, ocean acidification, stratospheric ozone depletion, atmospheric aerosol loading, and introduction of novel entities. Two planetary boundaries have been fully transgressed, i.e., are at high risk, biosphere integrity and biogeochemical flows, and agriculture has been the major driver of the transgression. Three are in a zone of uncertainty i.e., at increasing risk, with agriculture the major driver of two of those, land-system change and freshwater use, and a significant contributor to the third, climate change. Agriculture is also a significant or major contributor to change for many of those planetary boundaries still in the safe zone. To reduce the role of agriculture in transgressing planetary boundaries, many interventions will be needed, including those in broader food systems.
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| 8. |
- Desta, Zeratsion Abera, et al.
(författare)
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Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Field cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F-2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that similar to 57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.
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| 9. |
- Desta, Zeratsion Abera, et al.
(författare)
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Molecular mapping and identification of quantitative trait loci for domestication traits in the field cress (Lepidium campestre L.) genome
- 2020
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Ingår i: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540.
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Tidskriftsartikel (refereegranskat)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.
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| 10. |
- Dida, Mulatu Geleta, et al.
(författare)
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Analysis of Genetic Diversity of Fescue Populations from the Highlands of Bolivia Using EST-SSR Markers
- 2022
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- In the highlands of Bolivia, native Festuca species are an important source of feed for animals due to their high tolerance to low temperatures and drought. Using simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs), the genetic diversity of 43 populations of Festuca species from Oruro, La Paz, Potosi and Cochabamba departments was evaluated for the purpose of providing information for effective conservation and breeding. In total, 64 alleles were detected across the 43 populations. SSR locus NFA 142 (with 12 alleles) had the highest number of detected alleles, while locus FES 13 (with eight alleles) had the highest polymorphism information content (PIC) at 0.55. Based on Nei’s genetic distance between populations, the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis revealed two major clusters, each consisting of populations from the four departments. However, the analysis of molecular variance (AMOVA) revealed that only 5% of the total variation separated these two groups, indicating low genetic differentiation between the populations. It was also found that there was a low but significant differentiation (0.08%) between the population groups of the four departments (p = 0.01). The newly developed EST-SSR markers are highly valuable for evaluating the genetic diversity of Bolivian fescues and other related species.
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