ORCID Profile
0000-0002-2724-0317
Current Organisation
University of Vermont
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Publisher: Wiley
Date: 2021
DOI: 10.1002/AGG2.20211
Abstract: A major agronomic challenge for chickpea ( Cicer arietinum L.) production is temperatures above 35 °C, which causes reduced fertility and seed development. This study was aimed at assessing the phenotypic variation of chickpea genotypes under variable heat stress conditions. Chickpea genotypes were grown in heat‐stressed locations in both Ethiopia and India to assess phenotypic variation for heat tolerance. In addition, genomic relationships among the genotypes were assessed using genome‐wide single nucleotide polymorphism (SNP) markers. A total of 121 genotypes were assessed at three field sites in Ethiopia, under heat stress and nonstress conditions, and 57 genotypes were assessed under high‐heat‐stress conditions at the International Crops Research Institute for the Semiarid Tropics (ICRISAT) in Hyderabad, India. Data for five phenological and seven agromorphological traits were recorded. The results showed that the chickpea genotypes were severely affected by excessive heat at Hyderabad as compared with those planted under non‐heat‐stress conditions in Debre Zeit, Ethiopia. At extremely high temperatures, chickpea plants exhibited reduced floral initiation, arrested seed and pod development, shortened life cycles, and reduced plant height, seed size, grain yield, and yield‐related traits. Across stressed and nonstressed environments, there were highly significant differences among the genotypes for most of the traits (ANOVA, P ≤ .001). Under heat‐stressed environments, DZ‐Cr‐0034 was found to be a highly tolerant, whereas DZ‐Cr‐0026 was found to be a highly sensitive genotype. Genetic relationships among the genotypes were determined using 5,722 SNPs, revealing a single group of Ethiopian genotypes with small number of cultivars showing introgression from Middle Eastern germplasm. This study clearly demonstrated that there is genetic variability in chickpea for heat tolerance that can be harnessed to meet expected shifts towards warmer climatic conditions.
Publisher: MDPI AG
Date: 10-11-2022
Abstract: In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple in iduals and at the species level using ‘pangenome analysis.’ This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.
Publisher: eLife Sciences Publications, Ltd
Date: 19-05-2023
DOI: 10.7554/ELIFE.85725
Abstract: While the domestication process has been investigated in many crops, the detailed route of cultivation range expansion and factors governing this process received relatively little attention. Here, using mungbean ( Vigna radiata var. radiata ) as a test case, we investigated the genomes of more than 1000 accessions to illustrate climatic adaptation’s role in dictating the unique routes of cultivation range expansion. Despite the geographical proximity between South and Central Asia, genetic evidence suggests mungbean cultivation first spread from South Asia to Southeast, East and finally reached Central Asia. Combining evidence from demographic inference, climatic niche modeling, plant morphology, and records from ancient Chinese sources, we showed that the specific route was shaped by the unique combinations of climatic constraints and farmer practices across Asia, which imposed ergent selection favoring higher yield in the south but short-season and more drought-tolerant accessions in the north. Our results suggest that mungbean did not radiate from the domestication center as expected purely under human activity, but instead, the spread of mungbean cultivation is highly constrained by climatic adaptation, echoing the idea that human commensals are more difficult to spread through the south-north axis of continents.
Publisher: Public Library of Science (PLoS)
Date: 29-12-2010
Publisher: Public Library of Science (PLoS)
Date: 22-06-2012
Publisher: MDPI AG
Date: 07-11-2019
DOI: 10.3390/IJMS20225562
Abstract: “Stay-green” crop phenotypes have been shown to impact drought tolerance and nutritional content of several crops. We aimed to genetically describe and functionally dissect the particular stay-green phenomenon found in chickpeas with a green cotyledon color of mature dry seed and investigate its potential use for improvement of chickpea environmental adaptations and nutritional value. We examined 40 stay-green accessions and a set of 29 BC2F4-5 stay-green introgression lines using a stay-green donor parent ICC 16340 and two Indian elite cultivars (KAK2, JGK1) as recurrent parents. Genetic studies of segregating populations indicated that the green cotyledon trait is controlled by a single recessive gene that is invariantly associated with the delayed degreening (extended chlorophyll retention). We found that the chickpea ortholog of Mendel’s I locus of garden pea, encoding a SGR protein as very likely to underlie the persistently green cotyledon color phenotype of chickpea. Further sequence characterization of this chickpea ortholog CaStGR1 (CaStGR1, for carietinum stay-green gene 1) revealed the presence of five different molecular variants (alleles), each of which is likely a loss-of-function of the chickpea protein (CaStGR1) involved in chlorophyll catabolism. We tested the wild type and green cotyledon lines for components of adaptations to dry environments and traits linked to agronomic performance in different experimental systems and different levels of water availability. We found that the plant processes linked to disrupted CaStGR1 gene did not functionality affect transpiration efficiency or water usage. Photosynthetic pigments in grains, including provitaminogenic carotenoids important for human nutrition, were 2–3-fold higher in the stay-green type. Agronomic performance did not appear to be correlated with the presence/absence of the stay-green allele. We conclude that allelic variation in chickpea CaStGR1 does not compromise traits linked to environmental adaptation and agronomic performance, and is a promising genetic technology for biofortification of provitaminogenic carotenoids in chickpea.
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2022
DOI: 10.1101/2022.09.08.506689
Abstract: Domestication and improvement are two crucial processes underlying the evolution of crops. Domestication transformed wild plants into a utilizable form for humans improvement refined cultivars adapting to distinct environments and local preferences. Using whole-genome re-sequencing of Vigna radiata , we investigated the demographic history and compared the genetic footprints of domestication and improvement. The Asian wild population migrated to Australia at about 50 kya, and domestication happened in Asia about 9 kya selecting for non-shattering pods. The key candidate gene for this trait, VrMYB26a , has lower expression in cultivars, consistent with the reduced polymorphism in the promoter region reflecting hard selective sweep. The determinate stems were later selected as an improvement phenotype and associated with the gene VrDet1 . Two ancient haplotypes reducing gene expression exhibit intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in soft selective sweep. Our results suggest domestication and improvement may leave different genomic signatures of selection, reflecting the fundamental differences in the two processes and highlighting the limitations of genome-scan methods relying on hard selective sweep.
Publisher: Public Library of Science (PLoS)
Date: 12-02-2014
Publisher: Wiley
Date: 19-05-2016
DOI: 10.1111/NPH.14010
Abstract: Chickpea ( Cicer arietinum ) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so‐called kabuli type, has white flowers and light‐colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms ( SNP s) and examined patterns of molecular ersity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic ersity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix–loop–helix ( bHLH ) transcription factor at chickpea's B locus that conditions flower and seed colors, orthologous to Mendel's A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic ersification after initial domestication of cultivated chickpea.
Publisher: Oxford University Press (OUP)
Date: 19-06-2023
Abstract: Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pattern expected under the standard selective sweep model remains unclear. With whole-genome resequencing of mungbean (Vigna radiata), we investigated this issue by resolving its global demographic history and targeted dissection of the molecular footprints of genes underlying 2 key traits representing different stages of domestication. Mungbean originated in Asia, and the Southeast Asian wild population migrated to Australia about 50 thousand generations ago. Later in Asia, the cultivated form erged from the wild progenitor. We identified the gene associated with the pod shattering resistance trait, VrMYB26a, with lower expression across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found that 2 ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of 2 important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.
Publisher: Springer Science and Business Media LLC
Date: 10-11-2021
DOI: 10.1038/S41586-021-04066-1
Abstract: Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources 1 . So far, few chickpea ( Cicer arietinum ) germplasm accessions have been characterized at the genome sequence level 2 . Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic ersity across cultivated chickpea and its wild progenitor accessions. A ergence tree using genes present in around 80% of in iduals in one species allowed us to estimate the ergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic ersity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic ersity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.
Publisher: Springer Science and Business Media LLC
Date: 22-05-2017
DOI: 10.1038/NG.3872
Abstract: Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding. Using genome-wide association analysis, we identify associations between several candidate genes and agronomically important traits. Candidate genes for these traits in pigeonpea have sequence similarity to genes functionally characterized in other plants for flowering time control, seed development and pod dehiscence. Our findings will allow acceleration of genetic gains for key traits to improve yield and sustainability in pigeonpea.
Publisher: Springer Science and Business Media LLC
Date: 25-03-2022
Publisher: eLife Sciences Publications, Ltd
Date: 16-05-2023
Publisher: Springer Science and Business Media LLC
Date: 29-04-2019
DOI: 10.1038/S41588-019-0401-3
Abstract: We report a map of 4.97 million single-nucleotide polymorphisms of the chickpea from whole-genome resequencing of 429 lines s led from 45 countries. We identified 122 candidate regions with 204 genes under selection during chickpea breeding. Our data suggest the Eastern Mediterranean as the primary center of origin and migration route of chickpea from the Mediterranean/Fertile Crescent to Central Asia, and probably in parallel from Central Asia to East Africa (Ethiopia) and South Asia (India). Genome-wide association studies identified 262 markers and several candidate genes for 13 traits. Our study establishes a foundation for large-scale characterization of germplasm and population genomics, and a resource for trait dissection, accelerating genetic gains in future chickpea breeding.
Publisher: Public Library of Science (PLoS)
Date: 10-07-2014
No related grants have been discovered for Eric von Wettberg.