Abstract
Jute, comprising white and dark jute, is the second important natural fiber crop after cotton worldwide. However, the lack of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers has resulted in a large gap in the improvement of jute. Previously, de novo 48,914 unigenes from white jute were assembled. In this study, 1,906 EST-SSRs were identified from these assembled uingenes. Among these markers, di-, tri- and tetra-nucleotide repeat types were the abundant types (12.0%, 56.9% and 21.6% respectively). The AG-rich or GA-rich nucleotide repeats were the predominant. Subsequently, a sample of 116 SSRs, located in genes encoding transcription factors and cellulose synthases, were selected to survey polymorphisms among12 diverse jute accessions. Of these, 83.6% successfully amplified at least one fragment and detected polymorphism among the 12diverse genotypes, indicating that the newly developed SSRs are of good quality. Furthermore, the genetic similarity coefficients of all the 12 accessions were evaluated using 97 polymorphic SSRs. The cluster analysis divided the jute accessions into two main groups with genetic similarity coefficient of 0.61. These EST-SSR markers not only enrich molecular markers of jute genome, but also facilitate genetic and genomic researches in jute.
Highlights
Jute (Corchorus spp.) is a diploid plant of the Tiliaceae family (2n = 14) and has about 60 species under the genus, out of which white jute (C. capsularis) and dark jute (C. olitorius) are two commercially cultivated species [1,2,3]
A total of 48,914 jute unigenes' sequences derived from the transcription sequence, representing a total length of 44.35Mb, were analyzed for Simple sequence repeat (SSR)-containing sequences. 1,906 SSRs, designated as CcES markers hereafter, with repeat lengths of at least12 nucleotides were identified in 1,410 of the 48,914 unigenes
Few expressed sequence tag-derived simple sequence repeat (EST-SSR) markers derived from jute have been reported in addition to the development of expressed sequence tags (ESTs)-SSR from Genbank database in our group [13]
Summary
Jute (Corchorus spp.) is a diploid plant of the Tiliaceae family (2n = 14) and has about 60 species under the genus, out of which white jute (C. capsularis) and dark jute (C. olitorius) are two commercially cultivated species [1,2,3]. It is the second important crop for natural fiber production after cotton in the word. Jute mainly cultivated in India, China, Bangladesh, Malaysia, South Africa, Thailand, United States and southeast Europe [1]. Jute has received much attention in China, India, Malaysia, the United States, Mexico, Italy and so on
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