基于基因组重测序的GWAS发掘辣椒抗南方根结线虫新位点及候选基因鉴定

Pepper (Capsicum spp.) is the most important seasoning crop in the world, the production of which ranks the first among all the vegetable crops in China. The sustainable development of pepper is severely hindered by Meloidigyne incognita. Breeding of resistant cultivar is the most economical and efficient way of preventing and combating this disease. However, there are few M. incognita resistant genes which are already identified in pepper. Along with the continuously appearance of new races of M. incognita, those resistance genes are losing efficiency gradually. In order to explore new resistance genes to assist the breeding of resistant cultivars, a primary core collection with 250 pepper materials (including immune and highly resistant lines）will be employed to construct genetic variation database through whole genome resequencing. Companioned with the resistance phenotype data, genome-wide association study (GWAS) is employed to explore the new resistance linkage regions. Gene annotation is then applied to confer the candidate genes in the linkage regions. And the resistance phenotype of candidate genes will be validated by differential expression technique. In the end, functional molecular markers of candidate genes will be developed based on the genetic variation among materials with various resistance phenotypes. The findings of this project will widen the M. incognita resistance gene pool, accelerate the marker assist breeding of resistance cultivars, and lay critical foundations for in-depth exploring of the mechanism of M. incognita resistance.

辣椒（Capsicum spp.）是世界最大的调味料作物，在我国，辣椒的产值和效率居蔬菜作物之首。南方根结线虫（Meloidigyne incognita）对辣椒种植业的危害日益严重。抗病育种是防治该病害最为经济有效的办法。然而，辣椒中已知的南方根结线虫抗性基因数量极少，遗传背景狭窄，随着根结线虫新种群的不断出现，其抗病性正在逐渐丧失。急需发掘新的抗病基因位点来开展育种工作。本项目拟以250份辣椒初级核心种质（包含免疫或高抗资源）为对象，基因组重测序构建核心种质遗传变异数据库；结合抗感表型开展GWAS研究，发掘与抗性紧密关联的区段；对抗性关联区段进行基因功能注释，再利用基因差异表达鉴定候选基因；最后，依据候选基因在不同抗性表型材料中的遗传变异信息开发功能标记。本项目研究成果将有助于充实辣椒南方根结线虫抗性基因库，加快抗性分子辅助育种的进程，将为深入解析南方根结线虫抗性机理奠定重要基础。

根结线虫对辣椒种植业的危害日益严重。基于抗病基因的育种工作是防治该病害最为经济有效的办法。为挖掘新的抗病基因位点，充实辣椒抗根结线虫基因库，本项目通过高通量测序对272份辣椒初级核心种质构建遗传变异数据库，明确了试验材料的群体结构和亲缘关系，为种质资源的高效利用提供了依据；将遗传变异数据库的基因型数据结合抗性表型开展GWAS研究，挖掘出92个QTLs位点；利用基因功能注释及代谢途径分析，从中鉴定出了5个与根结线虫抗性紧密关联的QTLs区段，其中4个可能是新的抗性基因区段；从5个抗性QTLs区段注释出9个候选基因，其中位于2号染色体上的PHT91154.1被验证出接种根结线虫后在抗感种质间有差异表达；对PHT91154.1开发了dCAPS标记，为后续分子标记辅助育种提供了前提；挑选抗、感极端表型种质，研究这些种质在根结线虫侵染前后活性酶及根系内二龄幼虫侵染和发育情况，结合相关转录组数据，从生理生化、组织学及分子层面初步探索了辣椒抗根结线虫机理。本项目研究结果对辣椒的根结线虫抗性育种和抗性机理研究具有重要的理论及实践意义。

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