Development of Genome-wide SSR Markers for Physical Map Construction with PCR-based Polymorphic SSRs in Jute (Corchorus Spp.)

Despite substantial efforts in the past decades towards the development of microsatellites or SSR (simple sequence repeat) markers in jute, there is still an urgent necessity for additional SSR markers for performing genetic and breeding investigations. The availability of reference genomic sequences for both diploid cultivated jute species enabled us to identify a total of 154,715 and 160,173 SSRs from the C. capsularis and C. olitorius genomes, respectively. 6,337 and 7,012 total SSRs with a density of 187.6 and 185.01 SSR/Mb were also mined in coding sequences (CDS). 12bp was the most common repeat length in both genomic and CDS. Di- and tetra-nucleotide motifs were prevailed in the genomic sequences, while trinucleotides in the CDS. SSR frequency declined with increasing repeat units in both species. ATT and AT motifs were the most common in the genome. AG and CTT were prevalent in the CDS of both species while GC and CGC motifs were infrequent. Further, we used the flanking sequences of identified SSRs (from both species) to design a total of 1,117 SSR primer pairs. Genetic diversity analysis based on 110 sampled SSRs in 24 genotypes displayed high polymorphism. The first physical map with 535 PCR-based polymorphic SSRs were constructed by taking C. capsularis as the reference genome. These resources will advance genetics and breeding research in jute.