Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)

Abstract

Background: Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

“…In total, 218 alleles were scored by the analysis of 103 accessions with 22 SSR primer combinations, corresponding to an average of 9.9 alleles per locus. This confirms the value of SSR markers as a tool to detect intraspecific polymorphism in chickpea (Hüttel et al 1999;Singh et al 2003;Upadhyaya et al 2008;Hajibarat et al 2015). For most markers, observed heterozygosity (H o ) was considerably lower than expected heterozygosity (H e ), leading to high values of inbreeding coefficients.…”

“…Our work, showing a statistic correlation between NDC and either PD or Rp, supports the conclusion of previous studies reporting a linear relationship between the efficacy of a primer combination to distinguish accessions (NDC) and the two parameters Rp and PD (Prevost and Wilkinson 1999;Fernandez et al 2002). A common conclusion from previous studies on chickpea genetic diversity was the distinction of two cultivated gene pools, corresponding to the two main commercial types desi and kabuli (Upadhyaya et al 2008). Accordingly, structure analysis performed in this work led to the identification of two subpopulations, K1 and K2, which were largely composed by desi and kabuli accessions, respectively.…”

“…Genetic similarity between some desi and kabuli genotypes was reported by previous studies. For example, following the SSR analysis of a chickpea composite collection, Upadhyaya et al (2008) generated a Neighbour-Joining tree in which a small cluster of desi was included in major branch containing kabuli accessions and vice versa. In addition, the recent work of Penmetsa et al (2016), evaluating the genetic structure of a representative set of cultivated chickpea, also questioned the strict dichotomy of a desi and kabuli genetic subdivision within cultivated chickpea.…”

Genomic tools and germplasm diversity for chickpea improvement

“…Genotypebased reference set on 48 SSR markers captured 1,315 alleles where as the reference set based on seven qualitative traits captured 1,237 alleles (Upadhyaya, 2008). Mining allelic variation in the mini core collection and reference set will facilitate identification of diverse germplasm with beneficial traits for enhancing the genetic potential of chickpea globally and broaden the genetic base of cultivars.…”

“…Furthermore, based on allelic diversity data of global composite collection of chickpea, a 'reference set' of most diverse 300 accessions was selected (Upadhyaya et al, 2008). Genotypebased reference set on 48 SSR markers captured 1,315 alleles where as the reference set based on seven qualitative traits captured 1,237 alleles (Upadhyaya, 2008).…”