EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera

Abstract

A total of 12,080 sequences, including 5,851 transcriptome contigs developed at NBRI and 5,002 singlets and 1,227 contigs assembled from 13,201 expressed sequence tags (ESTs) of Jatropha curcas from National Center for Biotechnology Information database were used to search for simple sequence repeats (SSRs). Seven hundred and two sequences containing 786 SSRs with 93.4% simple and 7.6% compound repeat motifs were identified. Dinucleotide repeats (DNRs) were most abundant, followed by trinucleotide and tetranucleotide repeats. AG/CT was the most common motif (50.0%) followed by AT/AT (38.8%) and AC/GT (10.0%) among the DNRs. Four hundred and six primer pairs were designed out of the 702 SSR-containing sequences. Fifty randomly selected EST-SSR markers were amplified in 25 accessions collected from different geographical regions of India. Twenty-one SSR markers were polymorphic and with allele variation from two to four. Polymorphic information content value ranged between 0.04 and 0.61 with an average of 0.25 ± 0.16, indicating low to moderate level of informativeness within these EST-SSRs. The polymorphic markers showed 57.0% to 95.6% transferability among five species of Jatropha and 47.0% transferability across genera in Ricinus communis. Fifty-one alleles detected by the 21 polymorphic EST-SSRs were used to determine genetic relationships among 25 J. curcas accessions. Genetic similarity coefficient ranged from 0.44 to 0.94. The 25 accessions got grouped to three main clusters, comprising 10, 11, and four accessions. This is the first report of development of EST-SSRs in J. curcas and will be valuable resource for future genetical studies, like construction of linkage maps, diversity analysis, quantitative trait locus/association mapping, and molecular breeding of J. curcas.