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.
Highlights
Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain-legume crop grown in 7.03 mha area with a total production of 4.89 mt from tropical and subtropical regions of the world (FAOSTAT, 2014)
A set of 23,410 primer pairs was designed out of 309,052 simple sequence repeat (SSR) identified in pigeonpea genome (Varshney et al, 2012)
These 421 SSR markers were assayed on eight pigeonpea genotypes viz. Type 7, ICP 8863, PA 163A, ICPA 2089, AK 261322R, AK 261354R, AK 250189R, AK 250173R that are parents of different mapping populations (F2 and backcross) segregating for important traits such as Fusarium wilt and fertility restoration
Summary
Pigeonpea [Cajanus cajan (L.) Millspaugh] is an important grain-legume crop grown in 7.03 mha area with a total production of 4.89 mt from tropical and subtropical regions of the world (FAOSTAT, 2014). India is the largest producer of pigeonpea, contributing 67.3% to the global production, followed by Myanmar, Malawi, and Kenya (FAOSTAT, 2014). The breeding efforts aimed at improving pigeonpea led to the development and release of more than 100 improved varieties during last 50 years in India (Singh I. et al, 2016). The genetic gains from conventional breeding remained limited over same period of time (Varshney et al, 2013). This implies toward an urgent need to strengthen pigeonpea breeding program with the modern tools to improve their efficacy
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