%A Jia-Yu YAO,Li-Wu ZHANG,Jie ZHAO,Yi XU,Jian-Min QI,Lie-Mei ZHANG %T Evaluation and characteristic analysis of SSRs from the whole genome of jute (Corchorus capsularis) %0 Journal Article %D 2019 %J Acta Agronomica Sinica %R 10.3724/SP.J.1006.2019.84072 %P 10-17 %V 45 %N 1 %U {https://zwxb.chinacrops.org/CN/abstract/article_6604.shtml} %8 2018-09-14 %X

Jute is one of the most important natural bast fiber crops worldwide. However, the lack of SSR markers limits the genetic improvement of jute. In this study, simple sequence repeats (SSRs) were identified from the genome, genes, CDS and cDNA of CVL-1, a sequenced variety in Corchorus capsularis. SSR loci was called using SSR Primer software and the characteristics of SSR loci were analyzed. The 153,242 genomic SSRs were called based on the genomic sequence with an average density of 467.20 SSRs Mb -1. Based on the cDNA sequence, we called 10,747 SSRs were developed with an average density of 260.85 SSRs Mb -1. The majority of repeat types were di- to tetra-nucleotides, accounting for 76.91%. Among them, the tri-nucleotide repeat types were the highest abundance repeat types in the cDNA_SSRs while the di-nucleotide repeat types were the highest abundance repeat types in the genomic SSRs. For different SSR repeat types, the genomic and cDNA-SSR frequency decreased dramatically as repeat times increased. Identification of SSR markers in the whole genome can not only enrich the number of molecular markers, but also lay a foundation for the analysis of genetic basis of important agronomic traits in jute.