Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.)

Abstract

The paucity of sequence information flanking the simple sequence repeat (SSR) motifs identified especially in the transcript sequences has been limiting factor in the development of SSR markers for plant genome analysis as well as breeding applications. To overcome this and enhance the genic SSR marker repertoire in chickpea, the draft genome sequence of kabuli chickpea (CDC Frontier) and publicly available transcript sequences consisting of in silico identified SSR motifs were deployed in the present study. In this direction, the 300 bp sequence flanking the SSR motifs were retrieved by aligning 566 SSR containing transcripts of ICCV 2 available in public domain on the reference chickpea genome. A set of 202 novel genic SSRs were developed from a set of 507 primer pairs designed, based on in silico amplification of single locus and having no similarity to the publicly available SSR markers. Further, 40 genic SSRs equally distributed on chickpea genome were validated on a select set of 44 chickpea genotypes (including 41 Cicer arietinum and 3 Cicer reticulatum), out of which 25 were reported to be polymorphic. The polymorphism information content (PIC) value of 25 polymorphic genic SSRs ranged from 0.11 to 0.77 and number of alleles varied from 2 to 9. Clear demarcation among founder lines of multi-parent advanced generation inter-cross (MAGIC) population developed at ICRISAT and near-isogenic nature of JG 11 and JG11 ? demonstrates the usefulness of these markers in chickpea diversity analysis and breeding studies. Further, genic polymorphic SSRs reported between parental lines of 16 different mapping populations along with the novel SSRs can be deployed for trait mapping and breeding applications in chickpea.

Microsatellite markers: what they mean and why they are so useful

“…PAGE genotyping is more labor intensive but provides better resolution, allowing identification of given polymorphisms for a single base pair (Penha et al ., 2013; Mason, 2015). Alternatively, marked SSR primers can be synthesized with fluorescent markers for genotyping by capillary electrophoresis using conventional sequencers (Araújo et al ., 2007; Csencsics et al ., 2010; Agarwal et al ., 2015). In this case, each DNA sample is loaded into a capillary containing a polyacrylamide matrix in which the electrophoresis is performed.…”

High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

“…Moreover, basic molecular biology lab equipment is sufficient to genotype SSRs [11,12]. As a result, SSR markers remain extensively utilized molecular genetic tools in plant genetics and breeding [13][14][15].…”

The Chickpea Genome

“…usefulness for trait dissection and implementing them in breeding programs. During last decade, efforts of chickpea research community especially at ICRISAT in collaboration with several partners across the globe developed >3,000 SSRs (Nayak et al 2010;Thudi et al 2011;Agarwal et al 2015), transcriptomic resources (Hiremath et al 2011;Kudapa et al 2014), millions of SNPs and structural variations (Varshney et al 2013a;Thudi et al 2016a, b). Both desi and kabuli draft genomes have been decoded (Varshney et al 2013a;Jain et al 2013).…”