Identification and Characterization of EST‐SSR Markers in Cluster Bean (Cyamopsis spp.)

Abstract

Cluster bean, or guar, [Cyamopsis tetragonoloba (L.) Taub] is an important industrial crop. At present there are no marker resources or linkage maps available for this crop. Development of molecular markers is essential for accelerating genetic studies and breeding in guar. In the present study, mining of simple sequence repeat (SSR) sequences from 16,476 expressed sequence tags (ESTs) of guar was done using the microsatellite (MISA) identification tool. A total of 907 SSR‐containing sequences were identified. Flanking primers were designed for SSR‐containing sequences. Primers were selected on the basis of Tm, guanine‐cytosine (GC) content, and product length. A total of 362 pairs of primers were designed, out of which 224 were synthesized and used for assessment of amplification and polymorphism in five accessions of three Cyamopsis species. Out of 224 primer pairs, 187, 184, and 121 resulted in the amplification of SSR‐containing sequences producing reliable and reproducible DNA bands in C. tetragonoloba, C. serrata, and C. senegalensis, respectively. The analysis of the DNA bands revealed that 44 SSR markers were monomorphic in all the five accessions. Four SSR markers showed polymorphism in all three tested varieties of C. tetragonoloba. Our study gives the preliminary information on types, distribution, and frequencies of various SSRs present in the EST database of guar. The results provide the first set of 187 SSR markers for the guar research community.

RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources

“…A total of 5773 potential SSRs were identified with an average of one SSR per 7.31 kb in the unigenes. This result was consistent with the previous EST-SSR report in guar with occurrence (kb/SSR) of 7.9 (Kumar et al, 2016 ) while, Kuravadi et al reported the occurrence of 4.1 using the same dataset (Kuravadi et al, 2014 ). The occurrence of genic-SSR was also comparable to 8.4 in pigeonpea, 3.4 in rice, 5.4 in wheat, and 7.4 in soybean (Cardle et al, 2000 ; Peng and Lapitan, 2005 ; Dutta et al, 2011 ).…”

“…Marker assisted breeding, especially with SSRs and SNPs, has given excellent results in several other crops (Rafalski, 2002 ; Kesawat and Kumar, 2009 ; Hiremath et al, 2012 ). Such breeding programs have not been possible in guar due to the lack of sufficient number of SSRs (Kuravadi et al, 2014 ; Kumar et al, 2016 ) and the complete absence of SNPs. This has happened due to the limited availability of genetic resources in this crop.…”

“…These markers are a tool to detect genetic polymorphism at specific loci and whole-genome level as they facilitate marker-based gene tagging, genetic mapping, map-based cloning of agronomically important genes, genetic diversity studies, and phylogenetic analysis (Morgante et al, 2002 ; Kesawat and Kumar, 2009 ). Five molecular markers, namely, random amplified polymorphic DNA (RAPD), ribosomal DNA (rDNA), inter simple sequence repeat (ISSR), simple sequence repeat (SSR) and sequence characterized amplified region (SCAR) have been used in the study of molecular diversity in guar (Punia et al, 2009 ; Pathak et al, 2010 , 2011 ; Kuravadi et al, 2013 , 2014 ; Sharma et al, 2014 ; Kumar et al, 2016 ). Among the various molecular markers, SSR and single nucleotide polymorphism (SNP) markers are considered to be very important in genetic and plant breeding applications (Hiremath et al, 2012 ).…”

“…Among the various molecular markers, SSR and single nucleotide polymorphism (SNP) markers are considered to be very important in genetic and plant breeding applications (Hiremath et al, 2012 ). However, limited number of SSR markers are available in guar (Kuravadi et al, 2014 ; Kumar et al, 2016 ) and no SNPs have yet been reported in this crop.…”

Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics

“…No primer pairs were designed for 31,913 (29.02%) SSR loci. An average of one SSR per 5.88kb genome sequence was developed in this study; similar observations were reported by previous authors [32,33]. However, the average size (kbp) may be varied depending upon the size of datasets (genes, contigs, and scaffolds), program or parameters [34].…”