Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

Plekhanova, Elena; Vishnyakova, M. A.; Bulyntsev, S. V.; Chang, Peter L.; Carrasquilla‐Garcia, Noelia; Negash, Kassaye; Wettberg, Eric J. B. von; Noujdina, Nina; Cook, Douglas R.; Samsonova, Maria; Nuzhdin, Sergey V.

doi:10.1038/s41598-017-05087-5

Cited by 26 publications

(26 citation statements)

References 75 publications

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“…The ICRISAT has the largest collection: 19,959 accessions (http://www.icrisat.org, https://www.genesys-pgr.org) of cultivated chickpea and 308 accessions of 18 wild Cicer species from 60 countries. Other major gene banks holding chickpea germplasm include the NBPGR (16,881 accessions, http://www.nbpgr.ernet.in), New Delhi, India; ICARDA (13,818 accessions, http://www.icarda.org, https://www.genesys-pgr.org), Rabat, Morocco; AGG (8,655 accessions, https://grdc.com.au), Horsham, Victoria; and Western Regional Plant Introduction Station (WRPIS), USDA‐Agricultural Research Service (USDA‐ARS) (6,789 accessions, https://www.ars-grin.gov), Pullman, and VIR, Russia (2,091 accessions, http://www.vir.nw.ru) (Plekhanova et al, 2017). Most accessions within these collections are cultivated material.…”

Section: Chickpeamentioning

confidence: 99%

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Coyne¹,

Kumar²,

Wettberg

et al. 2020

Legume Science

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Legumes represent the second most important family of crop plants after grasses, accounting for approximately 27% of the world's crop production. Past domestication processes resulted in a high degree of relatedness between modern varieties of crops, leading to a narrower genetic base of cultivated germplasm prone to pests and diseases. Crop wild relatives (CWRs) harbor genetic diversity tested by natural selection in a range of environments. To fully understand and exploit local adaptation in CWR, studies in geographical centers of origin combining ecology, physiology, and genetics are needed. With the advent of modern genomics and computation, combined with systematic phenotyping, it is feasible to revisit wild accessions and landraces and prioritize their use for breeding, providing sources of disease resistances; tolerances of drought, heat, frost, and salinity abiotic stresses; nutrient densities across major and minor elements; and food quality traits. Establishment of hybrid populations with CWRs gives breeders a considerable benefit of a prebreeding tool for identifying and harnessing wild alleles and provides extremely valuable long-term resources. There is a need of further collecting and both ex situ and in situ conservation of CWR diversity of these taxa in the face of habitat loss and degradation and climate change. In this review, we focus on three legume crops domesticated in the Fertile Crescent, pea, chickpea, and lentil, and summarize the current state and potential of their respective CWR taxa for crop improvement.

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Section: Chickpeamentioning

confidence: 99%

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Coyne¹,

Kumar²,

Wettberg

et al. 2020

Legume Science

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“…C. reticulatum and its sister species Cicer echinospermum occur in contiguous but ecologically distinct ranges in modern-day southeastern Turkey (38). After domestication, chickpea was distributed throughout the Middle East and Mediterranean basin, reaching the Indian subcontinent a minimum of 4,000 y ago (37,39) and Ethiopia between 2,000 and 3,000 y ago (37), with ensuing continuous cultivation. Genome analyses reveal a primary domestication bottleneck at the center or origin (38), and additional unique genetic bottlenecks and secondary diversification in both India and Ethiopia (39,40).…”

Section: Significancementioning

confidence: 99%

“…After domestication, chickpea was distributed throughout the Middle East and Mediterranean basin, reaching the Indian subcontinent a minimum of 4,000 y ago (37,39) and Ethiopia between 2,000 and 3,000 y ago (37), with ensuing continuous cultivation. Genome analyses reveal a primary domestication bottleneck at the center or origin (38), and additional unique genetic bottlenecks and secondary diversification in both India and Ethiopia (39,40). In the past century, chickpea cultivation was established in countries where modern, intensive agricultural practices predominate, including Canada, the United States, and Australia (37).…”

Section: Significancementioning

confidence: 99%

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria

Greenlon

Chang

Damtew

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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135

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Although microorganisms are known to dominate Earth’s biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome—tripartite and monopartite—with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.

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“…Classically, crop relatives were the source of individual traits, most commonly disease resistance,20 but with recent advances in genome‐scale approaches the stage is set for a more systematic characterization and use of crop wild relatives. Such an approach is being undertaken for chickpea to improve a range of agronomic traits, including tolerance to climatic extremes 21, 22, 23. Similar approaches are feasible to improve the nutritional content of crops, as has been done, for example, in corn for provitamin A.…”

Section: Farmingmentioning

confidence: 99%

“…Such an approach is being undertaken for chickpea to improve a range of agronomic traits, including tolerance to climatic extremes. [21][22][23] Similar approaches are feasible to improve the nutritional content of crops, as has been done, for example, in corn for provitamin A. Modern plant breeding is leveraging knowledge of genome content and function, in order to precisely select for genes that underlie high-value traits.…”

Section: Plant Sciencementioning

confidence: 99%

Healthy and sustainable diets for future generations

et al. 2018

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Global food systems will face unprecedented challenges in the coming years. They will need to meet the nutritional needs of a growing population and feed an expanding demand for proteins. This is against a backdrop of increasing environmental challenges (water resources, climate change, soil health) and the need to improve farming livelihoods. Collaborative efforts by a variety of stakeholders are needed to ensure that future generations have access to healthy and sustainable diets. Food will play an increasingly important role in the global discourse on health. These topics were explored during Nestlé's second international conference on ‘Planting Seeds for the Future of Food: The Agriculture, Nutrition and Sustainability Nexus’, which took place in July 2017. This article discusses some of the key issues from the perspective of three major stakeholder groups, namely farming/agriculture, the food industry and consumers. © 2018 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

Cited by 26 publications

References 75 publications

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Potential and limits of exploitation of crop wild relatives for pea, lentil, and chickpea improvement

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria

Healthy and sustainable diets for future generations

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