ABSTRACT

Kenaf (Hibiscus cannabinus L.) is one of the most important crops, which is grown for natural fiber production. However, the deficiency of SSR markers limits the genetic improvement of kenaf. In this study, SSRs (simple sequence repeats) were identified from the reference genome and coding sequence (CDS) of Fuhong952, a sequenced variety of kenaf. SSR loci were mined using the Seiners 2.0 software and the characteristics of SSR loci were analyzed. A total of 301, 505 and 14, 269 SSRs with an overall density of 279.70 SSRs/Mb and 182.70 SSRs/Mb were identified from whole-genome and CDS, respectively. 12bp was the predominant repeat in the entire genome and CDS, trinucleotide repeats were the most abundant among both types of sequences. For different SSR repeat types, the SSR frequency decreased dramatically as repeat times increased. AT was the most frequent single motif across the entire genome, while AG was the most abundant motif in CDS. The homologous genes in kenaf were obtained from the 71 genes associated with photoperiodic flowering-time. As such, 115 primer pairs were designed and synthesized using these homologous genes in kenaf. The amplification of 108 pairs revealed stable and clear bands, and two pair of primers located in HcFCA and HcVIN3 were significantly associated with photoperiodic flowering-time using one-way ANOVA and regression analysis. The detailed results of the SSR markers in this study provides valuable information about the frequency distribution of SSRs in the whole genome and will expedite genomic research for improvement in kenaf.

摘要

红麻（木槿大麻L.) 是最重要的作物之一，是为生产天然纤维而种植的。然而，SSR标记的缺乏限制了红麻的遗传改良。在本研究中，从已测序的洋麻品种 Fuhong952 的参考基因组和编码序列 (CDS) 中鉴定了 SSR（简单序列重复）。利用Seiners 2.0软件挖掘SSR位点，分析SSR位点的特征。从全基因组和 CDS 中分别鉴定出 301、505 和 14、269 个 SSR，总密度分别为 279.70 SSR/Mb 和 182.70 SSR/Mb。12bp 是整个基因组和 CDS 中的主要重复序列，三核苷酸重复序列在这两种类型的序列中最为丰富。对于不同的 SSR 重复类型，随着重复次数的增加，SSR 频率急剧下降。AT 是整个基因组中最常见的单一基序，而 AG 是 CDS 中最丰富的基序。红麻中的同源基因来自与光周期开花时间相关的71个基因。因此，使用洋麻中的这些同源基因设计并合成了 115 对引物。108对扩增条带稳定清晰，两对引物位于使用单向方差分析和回归分析，HcFCA和HcVIN3与光周期开花时间显着相关。本研究中 SSR 标记的详细结果提供了有关 SSR 在整个基因组中的频率分布的宝贵信息，并将加速基因组研究以改进红麻。