利用永久F2群体和高密度遗传图谱剖析短季棉杂种优势遗传机理

Short-season cotton (G. hirsutum) hybrids can exhibit strong heterosis in important economic traits especially yield and fiber quality, the research on genetic mechanism of heterosis in short-season cotton, however, has not been reported. Baimian 3 is a short-season cotton hybrid with strong heterosis bred by Cotton Research Institute of Henan Institute of Science and Technology (HIST). In this project, the following three contents will be carried out about Baimian 3: (1) Taking on an immortalized F2 population from Baimian 3 as material, a high-density genetic linkage map based on whole-genome SSR, SNP molecular markers will be constructed; (2) Using an immortalized F2 population and a high density genetic map, the QTLs for the traits including yield and its components, and fiber quality will be identified, and the genetic effects of major QTLs, interaction between QTL and interaction between QTLs and environment will also be analysed; (3) Using an immortalized F2 population and a high density genetic map, the QTLs for heterosis of yield and quality traits will be detected and all genetic effects of these heterosis QTLs will be analysed. Comparing the QTLs for traits with the QTLs for heterosis, we would dissect deeply the genetic mechanism of heterosis of short-season cotton. The results is of great significance in accelerating the steps of short-season cotton heterosis utilization, alleviating the contradiction presented when occupying farmlands with either cotton or cereals, and optimization of agricultural industry structure.

短季棉杂交种在重要性状特别是产量和纤维品质性状上能够表现出较强的优势，然而对短季棉杂种优势遗传机理的研究目前未见报道。百棉3号是河南科技学院棉花研究所培育的强优势短季棉杂交种。本项目围绕百棉3号开展三方面工作：（1）构建百棉3号永久F2群体的基于棉花全基因组SSR、SNP分子标记的高密度遗传图谱；（2）利用百棉3号永久F2群体和高密度遗传图谱，鉴定产量及其构成因素、纤维品质性状QTL，分析主效QTL、QTL间互作、QTL与环境互作等遗传效应；（3）利用百棉3号永久F2群体和高密度遗传图谱，鉴定产量及其构成因素、纤维品质性状杂种优势QTL，分析杂种优势QTL的各种遗传效应。比较性状QTL与杂种优势QTL，剖析短季棉杂种优势遗传机理。研究结果对加快短季棉杂种优势利用步伐、缓解我国粮棉争地矛盾和优化农业产业结构具有重要意义。

陆地棉中的短季棉在育种目标性状特别是产量和纤维品质性状上能够表现出较强的杂种优势，然而目前对短季棉杂种优势遗传机理的研究未见报道。本项目开展的研究内容包括（1）利用基因组重测序技术构建短季棉百棉3号高密度遗传图谱；（2）利用高密度遗传图谱鉴定产量、纤维品质QTL，及其目标性状杂种优势QTL；（3） 陆地棉产量、纤维品质、早熟性相关的分子标记发掘；（4）陆地棉DNA指纹图谱构建；（5）百棉3号及其亲本的转录组测序分析。对百棉3 号及其亲本进行了基因组重测序，构建了短季棉高密度遗传图谱，上图SNP标记为72599个，Bin标记为4960个；26条染色体（连锁群）总图距3971.08cM，平均图距0.80cM。利用高密度遗传图谱对棉花产量、纤维品质QTL及其杂种优势QTL进行了检测，共检测到5个产量性状42个QTL和94对上位性QTL，5个纤维品质性状36个QTL和87对上位性QTL，以及41个产量杂种优势QTL、43个纤维品质杂种优势QTL；同时检测到若干目标性状稳定表达的QTL。使用CottonSNP80K芯片对育种目标性状进行了分子标记发掘，在四个环境中共检测到23个产量（子棉和皮棉）SNP，342个纤维品质SNP，74个早熟性SNP；这些性状均检测到至少在2个环境中稳定表达的分子标记。从至少与棉花两个育种目标性状（产量、纤维品质、早熟等）关联的78对SSR引物中筛选26对引物为核心引物，扩增陆地棉基因组DNA，获得168份棉花材料的指纹图谱及数字指纹代码。通过转录组测序发掘到新基因10,484个，其中8,946个得到功能注释；基于比对结果，进行基因表达量分析；根据基因在不同样品中的表达量识别差异表达基因，并对其进行了功能注释和富集分析。本项目获得的稳定表达QTL和分子标记，为棉花重要性状的标记辅助选择、杂种优势遗传机理解析及杂种优势分子育种奠定了重要基础。