基于全基因组关联分析确定苎麻纤维细度显著关联分子标记

Ramie fiber is an important raw material in the textile industry. To satisfy the requirements of textile industry development, improvement of fiber fineness has become a key task in ramie breeding. Marker-assisted selection (MAS) can effectively speed up this improvement process. However, so far, MAS for fiber fineness is still stagnant because of the lack of molecular markers related to elite-fineness alleles. In our previous study, the natural population of ramie(108 core collections and 20 bred varieties) exhibited a good association-mapping population, because it had a wide range of variation in fineness(1062-2869m/g), a simple population structure(k=2),and low level of linkage disequilibrium(LD). In this study, genome-wide association analysis will be performed on the association-mapping population to explore the specific molecular markers correlated with superior alleles that control fiber fineness, utilizing whole-genome single nucleotide polymorphism(SNP) markers, which will be obtained using simplified genome sequencing technology, and the fiber fineness, which will be assessed during nine entire seasons across a period of three years. In addition, we will carry out single marker association analyses in the population, which includes 213 ramie accessions, to verify the results from the above research and confirm the distinctly effective molecular markers correlated with superior alleles that control fiber fineness. This study may strengthen the understanding of germplasms and lay the foundation for molecular breeding in ramie. Moreover, the results will benefit follow-up studies on molecular MAS, molecular breeding, and isolation of related genes for fiber fineness of ramie.

苎麻是重要的纺织原料，为更好地满足纺织工业要求，提高纤维细度已成为目前苎麻育种研究的重要任务。通过分子标记辅助选择可有效加速其改良进程，但目前缺乏纤维细度优异等位基因连锁分子标记。我们前期对自然群体（108份核心种质+20份选育品种）的研究表明，其纤维细度变异广泛（1062-2869m/g），群体结构简单(k=2)，连锁不平衡水平低，是一个较好地关联分析群体。本项目拟首先以关联分析群体为研究材料，采用简化基因组测序技术开发其全基因组SNP标记，同时测定其3年9季麻纤维细度；其次通过全基因组关联分析发掘与纤维细度显著关联分子标记，挖掘其优异等位基因候选标记；然后利用验证群体（213份苎麻种质资源）对候选显著关联分子标记通过单标记关联分析确认，最终明确优异等位基因有效分子标记。本研究可深化苎麻种质资源认识，奠定分子育种基础；且将对分子标记辅助选择及设计育种、相关基因分离等后续研究具有重要意义。

纤维细度是衡量苎麻纤维品质的重要指标，直接关系到纤维的纺织价值。挖掘苎麻纤维细度QTLs，对培育高纤维细度苎麻品种具有重要的意义。本研究利用319份苎麻h核心种质构成关联群体，利用全基因组重测序技术开发覆盖全基因组的SNPs；基于2点多年的田间种植试验鉴定得到的纤维细度表型数据，进行表型与基因型的GWAS研究及候选基因的筛选。主要研究结果如下：.1. 鉴定了319份苎麻种质的纤维细度的表型性状。结果表明该319份苎麻种质纤维细度变异广泛，遗传多样性丰富。环境之间纤维细度及纤维直径相关性和广义遗传力分析表明，苎麻纤维细度表型主要受基因型的影响。.2. 过滤后获得3,494,975个高质量的群体SNPs用于亲缘关系和群体结构的分析。进一步过滤后得到用于GWAS分析的1,336,689个SNPs，平均间距为246.80 bp，远小于苎麻LD衰减的平均距离1.27 Kb。利用SPAGeDi软件计算的亲缘关系值表明，大多数苎麻种质亲缘关系在0.3-0.4之间。系统发育分析显示，该群体可以分为4组，不同组间无明显的地域分布特征。群体结构分析表明，该苎麻群体无明显的群体分层。.3. 基于GLM+Q模型分析方法，3个环境分别检测到与纤维细度显著相关的SNPs位点82个（2017Lb）、361个（2018Lb）和18个（2018La）；结合本实验室中苎1号与合江苎麻杂交F1群体定位的结果，检测到4个稳定的纤维细度QTLs区段（Chr.9: 16.16-16.50 Mb, Chr.9: 3.13-3.61Mb, Chr.8: 13.90-14.17 Mb, Chr.8: 15.62-15.86 Mb）。.4. 利用两个纤维细度差异品种，5个时期茎皮的转录组基因表达量数据，对QTLs区段内基因进行了初步筛选分析，并结合荧光定量PCR验证。最终筛选得到6个候选基因。.本研究深化了对苎麻种质资源的认识，奠定了苎麻分子辅助选择育种基础。以上研究结果对分子标记辅助选择、分子设计育种、相关基因分离等后续研究具有重要的指导意义。