Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource

Abstract

Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16–94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

“…In contrast, trinucleotide P-SSRs were less abundant than tetranucleotide P-SSRs, and hexanucleotide P-SSRs was the least in the primate genomes. The presence of abundant di- and tetranucleotide SSRs with their features of higher replication slippage than trinucleotide SSRs, especially in the upstream regulatory regions, introns and intergenic regions might be contributing to their high polymorphic potential [29]. Mayer et al (2010) detected that there was weak correlation between the genome sizes and SSR densities [30].…”

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

“…The perfect SSRs exhibiting repeat-length variations flanked by conserved genomic sequences (against Nipponbare reference genome) at least between any two of 11 rice accessions were screened and defined as ‘ in silico polymorphic perfect SSRs’ in accordance with Khajuria et al (2015) and Parida et al (2015). To develop in silico polymorphic perfect SSR markers at a genome-wide scale, the forward and reverse primer-pairs were designed from the sequences flanking the polymorphic perfect SSR repeats employing the Primer3 interface modules of MISA 6 .…”

“…Furthermore, the degree of in silico repeat-length variations predetermined for these polymorphic SSR markers prior to their experimental validation can assist us to select most-suitable genotyping assay for efficient resolution and accurate detection of fragment length polymorphism as well as allelic discrimination among accessions. The implication of in silico polymorphic SSR markers developed at a genome-wide scale for manifold high-throughput genetic analyses have been well-demonstrated in crop plants including rice (Zhang et al, 2007; Khajuria et al, 2015; Parida et al, 2015). …”

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

“…Simple Sequence Repeat (SSR) markers are widely used due to their high reproducibility, multi-allelic nature and co-dominant inheritance (Tautz 1989). Several SSR markers were developed and used in chickpea (Hüttel et al 1999;Udupa and Baum 2001;Lichtenzveig et al 2005;Sethy et al 2006;Choudhary et al 2006;Saxena et al 2014;Parida et al 2015;Khajuria et al 2015). Most of them have a known genomic localization, following linkage analysis (Winter et al 2000;Nayak et al 2010;Jamalabadi et al 2013;Khajuria et al 2015).…”