Sequence-tagged microsatellite site markers for chickpea (Cicer arietinumL.)

Abstract

Two small-insert genomic libraries of chickpea (Cicer arietinum L.) were screened with a set of microsatellite-specific oligonucleotide probes. A total of 121 positive clones were identified among 13,000 plated colonies. Thirty-nine clones were recognized by (TAA)5, 26 by (GA)8, 18 by (GT)8, 27 by a pool of AT-rich trinucleotide repeats [(CAA)5, (CAT)5, and (GAA)5], and 11 by a pool of GC-rich trinucleotides [(TCC)5, (CAC)5, (CAG)5, and (CGA)5]. Of 53 clones selected for sequencing, 43 carried a microsatellite. Flanking primer pairs were designed for 28 loci, and used on a small test-set comprising one C. reticulatum and four C. arietinum accessions. Separation of the PCR products on agarose or polyacrylamide gels revealed single bands of the expected size with 22 of the primer pairs. Sixteen of these "Cicer arietinum sequence-tagged microsatellite site" (CaSTMS) markers were polymorphic at an intraspecific level, detecting 2-4 alleles within the four accessions examined. Primer pairs CaSTMS10 and CaSTMS15 revealed 25 and 16 alleles among 63 C. arietinum accessions from different geographic locations, reflecting gene diversity values of 0.937 and 0.922, respectively. Mendelian inheritance of CaSTMS markers was demonstrated using a set of recombinant inbred lines and their parents.

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.…”

“…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).…”

Chickpea Improvement: Role of Wild Species and Genetic Markers

“…The codominant markers such as isozymes, RFLPs and SSR markers have distinct advantages over dominant markers: a) they allow plant breeders to identify individuals homozygous for the desired alleles in the F 2 generation of a cross, without need for F 3 progeny testing (Yu et al, 1991), and b) codominant nature permits easy transfer of markers between genetic maps of different crosses (Thomas and Scott, 1993). RFLP markers have been used in development of genetic linkage map of chickpea using mapping population from an inter-specific cross , whereas SSRs are the marker of choice for the development of genetic maps and tagging of genes Huttel et al, 1999), inter and intra-specific variabibity (Choudhary et al, 2005;Sethy et al, 2006b) and phylogenetic study (Sethy et al, 2006a).…”

“…The relatively simple interpretation and genetic analysis of single locus markers make them superior to multi-locus DNA markers, especially for map construction and DNA fingerprinting (Thomas and Scott, 1993). The ability of SSRs in detecting intra-specific variation in chickpea has been demonstrated by Huttel et al (1999). Sixteen SSR loci detected 2-4 alleles at intra-specific level out of 22 loci tested.…”

“…Desi chickpeas are characterized by angular seed shape, dark seed coat, pink flowers, anthocyanin pigmentation of stem, rough seed surface and either semi-erect or semi-spreading growth habit, whereas kabuli types generally have owl shaped seeds, beige coloured seeds, white flowers, smooth seed surface, lack of anthocyanin pigmentation and semi-spreading growth habit (Pundir et al, 1985). ~700 Winter et al, 1999Huttel et al, 1999Sethy et al, 2006aand 2006bLichtenzveig et al, 2005Choudhary et al, 2005 …”