基于重测序的关联分析剖析黄麻纤维素含量的遗传基础

Jute (Corchorus sp.) has more than 100 species, but only Corchorus olitorius and Corchorus capsularis are commercially cultivated. Its fiber is one of the most important sources of nature fiber, covering ~80% of global fiber production. Cellulose content, as one of the main components of fiber, has abundant genetic variation, affecting fiber quality and multiple utilizationof Jute. However, the genetic basis of cellulose content remains unclear. Previously, we assembled the whole genomes of C. capsularis and C. olitorius using the third-generation sequencing technology. It is shown that the genome size of C. capsularis and C. olitorius is 333Mb and 393Mb respectively. Previously, 2 Recombined Inbred Lines (RILs) populations were constructed by single-seed descent. This project plans to dissect the genetic basis of cellulose content by characterization of an association population containing 231 accessions as well as 2 RIL populations based on low-coverage resequencing and precisely measurement of cellulose content under multiple environments. The high-density linkage map and genome-wide variation (including SNP, InDel and Structure Variation) map of jute nature population will be constructed through this project. Based on the genome-wide association study and QTL mapping, potential candidate genes responsible for cellulose content variation will be further confirmed by gene expression, bioinformatic and linkage analyses. Favorable alleles will be defined after haploidtype analysis and their genetic effects will be estimated. The high-density linkage map and genome-wide variation map will enhance the genetic research in jute. And the identification of molecular markers linked to favorable alleles of cellulose content will be helpful for the improvement of designed breeding in jute.

黄麻属有100多个种，生产上栽培的有圆果种和长果种，其纤维产量占世界上麻类纤维总产量的80%。纤维素是黄麻纤维的主要组成成分，其含量变异丰富，影响着纤维品质及综合利用，但纤维素含量的遗传基础尚不清楚。我们前期利用三代测序技术得到染色体水平的圆果种与长果种的基因组，其基因组大小分别为333Mb和393Mb；通过单粒传法构建2个重组自交系群体。本研究将利用231份黄麻品种（系）和2个重组自交系群体为基础材料，通过低覆盖度的基因组重测序构建黄麻高密度遗传连锁图谱和全基因组SNP（或变异）图谱；结合多年多点的表型鉴定，采用全基因组关联分析和QTL定位挖掘黄麻纤维素含量的基因位点；对显著关联的位点通过生物信息学进行功能注释，单倍型分析挖掘优异等位基因，表达和连锁分析予以验证。构建的高密度遗传图谱和全基因组SNP图谱将会大大加快黄麻遗传研究的进程，优异等位基因连锁的分子标记将有助于黄麻设计育种。

黄麻是一种重要的韧皮部纤维作物，其纤维产量占世界上麻类纤维总产量的80%，生产上具有栽培价值的有圆果种和长果种黄麻。纤维素含量等纤维品质是黄麻重要的育种目标，但其遗传基础尚不清楚。本研究利用三代测序技术得到染色体水平的圆果种与长果种的基因组，其基因组大小分别为336Mb和361Mb；利用转录组测序系统鉴定了黄麻纤维发育相关基因；以300余份黄麻品种（系）和2个重组自交系群体为材料，通过低覆盖度的基因组重测序构建黄麻高密度遗传连锁图谱和全基因组SNP图谱；结合3年2点的表型鉴定，采用全基因组关联分析和QTL定位鉴定上百个控制纤维品质相关性状（包括纤维素含量、木质素含量和纤维细度）的基因位点；利用竞争性等位基因特异性PCR、qRT-PCR和转基因技术等方法验证了重要候选基因 CcCOBRA1 和 CcC4H1 的功能。研究结果推动了黄麻基因组学研究和纤维品质分子标记辅助育种，为探索植物次生细胞壁发育研究提供一定理论基础。