title: Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
abstract: Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Rachit K
authors.initials: RK
authors.lastname: Saxena
authors.affiliation: Department of Biological Sciences, Florida International University, Miami, Florida, United States of America ; Fairchild Tropical Botanic Garden, Kushlan Institute for Tropical Science, Miami, Florida, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: von Wettberg
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: Florida International University, Department of Earth and Environment, Miami, Florida, United States of America.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Sanchez
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India ; Egerton University, Egerton, Kenya.
authors.forename: Serah
authors.initials: S
authors.lastname: Songok
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Kulbhushan
authors.initials: K
authors.lastname: Saxena
authors.affiliation: Egerton University, Egerton, Kenya.
authors.forename: Paul
authors.initials: P
authors.lastname: Kimurto
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D000465:Algorithms; D036561:Cajanus / Q000235:genetics*; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D005828:Genetics, Population; D005843:Geography; D007194:India; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012984:Software
chemical_list: D005819:Genetic Markers