Population structure of Nepali spring wheat ( Triticum aestivum L.) germplasm
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RESEARCH ARTICLE
Open Access
Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm Kamal Khadka1* , Davoud Torkamaneh1,2,3, Mina Kaviani1, Francois Belzile2,3, Manish N. Raizada1 and Alireza Navabi1
Abstract Background: Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and population structure of Nepali spring wheat have not been reported. This study aims to improve the exploitation of more diverse and under-utilized genetic resources to contribute to current and future breeding efforts for global food security. Results: We used genotyping-by-sequencing (GBS) to characterize a panel of 318 spring wheat accessions from Nepal including 166 landraces, 115 CIMMYT advanced lines, and 34 Nepali released varieties. We identified 95 K high-quality SNPs. The greatest genetic diversity was observed among the landraces, followed by CIMMYT lines, and released varieties. Though we expected only 3 groupings corresponding to these 3 seed origins, the population structure revealed two large, distinct subpopulations along with two smaller and scattered subpopulations in between, with significant admixture. This result was confirmed by principal component analysis (PCA) and UPGMA distance-based clustering. The pattern of LD decay differed between subpopulations, ranging from 60 to 150 Kb. We discuss the possibility that germplasm explorations during the 1970s–1990s may have mistakenly collected exotic germplasm instead of local landraces and/or collected materials that had already cross-hybridized since exotic germplasm was introduced starting in the 1950s. Conclusion: We suggest that only a subset of wheat “landraces” in Nepal are authentic which this study has identified. Targeting these authentic landraces may accelerate local breeding programs to improve the food security of this climate-vulnerable nation. Overall, this study provides a novel understanding of the genetic diversity of wheat in Nepal and this may contribute to global wheat breeding initiatives. Keywords: Nepal, Landraces, Genotype-by-sequencing (GBS), Genetic diversity, Population structure, Linkage disequilibrium
Key message The study explores the population structure and genetic diversity of spring wheat germplasm in Nepal, not reported previously. The findings were unexpected and provide a novel understanding of the germplasm.
* Correspondence: [email protected] 1 Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2W1, Canada Full list of author information is available at the end of the article
Background A significant challenge faced by modern plant breeders is the need to improve crop yield in the wake of the ever-increasing human population while combating the consequences posed by climate change on crop productivity [1].
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