New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]

Abstract

Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations (K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility (Rf) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable genomic resource for pigeonpea research community, particularly in South Asia and East Africa where pigeonpea is primarily grown.

Introgression of Shoot Fly (Atherigona soccata L. Moench) Resistance QTLs into Elite Post-rainy Season Sorghum Varieties Using Marker Assisted Backcrossing (MABC)

“…In the present study, the SSRs are found to be highly polymorphic exhibiting different alleles among closely related individuals for each marker in relatively lesser time and minute quantity of DNA which is in agreement with recent reports in pigeonpea ( Bohra et al, 2015 , 2017 ). The SSR has been employed extensively in sorghum to study genetic diversity, linkage mapping and QTL analysis ( Njung’e et al, 2016 ).…”

Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes

“…Notably, resistance to wilt is an essential prerequisite for variety identification and release in pigeonpea. Several pigeonpea varieties such as Asha (ICPL , 1998;Castillo et al, 2003 Chickpea Andoum 1 and Ayala (race 0) - Halila and Harrabi, 1990;Landa et al, 2006 Chickpea Surutato-77, Sonora-80, Tubutama, UC-15 and UC-27, Gavilan Mexico Morales, 1986;Buddenhagen et al, 1988;Helms et al, 1992;Sharma et al, 2005 Chickpea (Singh I. P. et al, 2016;Bohra et al, 2017).…”

Grain Fe and Zn Contents Linked SSR Markers Based Genetic Diversity Reveal Perspective for Marker Assisted Biofortification Breeding in Rice

“…Like other crop plants, molecular markers have been proved to be most effective in evaluating genetic diversity, structure analysis and phylogenetic relatedness among rice accessions too [10,36]. During recent years, SSR markers based genotyping has proven to be very useful for exploring a variety of surreptitious information in plants, ranging from domestication traits to crop improvement through marker-assisted breeding [37][38][39][40]. Although, individual reports on micronutrient density and SSR based genetic diversity in rice have been recently published [10,12,13,36,41], however, to date, a combined study of grain Fe and Zn contents and trait linked SSR markers based genetic diversity is obscure.…”