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.

尽管在过去几十年中为开发黄麻微卫星或 SSR（简单序列重复）标记做出了巨大努力，但仍然迫切需要额外的 SSR 标记来进行遗传和育种研究。两种二倍体栽培黄麻物种的参考基因组序列的可用性使我们能够从C. capsularis和C. olitorius 中鉴定出总共 154,715 和 160,173 个 SSR基因组，分别。在编码序列 (CDS) 中还开采了 6,337 和 7,012 个总 SSR，密度分别为 187.6 和 185.01 SSR/Mb。12bp 是基因组和 CDS 中最常见的重复长度。二核苷酸和四核苷酸基序在基因组序列中占主导地位，而在 CDS 中则是三核苷酸。SSR 频率随着两个物种中重复单元的增加而下降。ATT 和 AT 基序是基因组中最常见的。AG 和 CTT 在两个物种的 CDS 中都很普遍，而 GC 和 CGC 基序很少见。此外，我们使用已鉴定的 SSR（来自两个物种）的侧翼序列来设计总共 1,117 个 SSR 引物对。基于 24 个基因型的 110 个采样 SSR 的遗传多样性分析显示出高多态性。第一个包含 535 个基于 PCR 的多态性 SSR 的物理图谱是通过取C. capsularis作为参考基因组。这些资源将推动黄麻遗传学和育种研究。