利用QTL-seq鉴定猴头菌子实体大小相关基因

Hericium erinaceus is an important edible mushroom with compelling medicinal properties. As the main determinants of commercial value of H. erinaceus, the fruiting body size is a quantitative trait controlled by multiple genes or quantitative trait loci (QTLs). It is difficult to improve this trait with traditional breeding methods such as selection based on phenotypes. The dissection of genetic architectures of fruiting body size through QTL mapping lays a foundation for breeding high-quality varieties of H. erinaceus. In this proposal, we utilize a simple and rapid approach (QTL-seq) to map QTLs underlying fruiting body size of H. erinaceus. Based on the extreme phenotype of dikaryons in the segregating population, corresponding monokaryons are selected to produce two pools. Then, next generation sequence technology (NGS) are used to resequencing the two pools and the genome-wide SNP (single nucleotide polymorphism) loci are screened. QTLs are mapped by comparing the SNP-index of the two pools. Then, combined with the transcriptome analysis, we uncover the genetic architecture of fruiting body size in H. erinaceus. In this project, it is the first time to utilize QTL-seq in genetic improvement of H. erinaceus. Rapid identification the loci responsible for fruiting body size by QTL-seq is of great value for performing marker assisted selection, which lays a foundation for breeding high-quality varieties of H. erinaceus. This project also possesses important reference significance for genetic improvement of other edible mushrooms.

猴头菌是一种重要的食药用菌，而子实体大小是决定猴头菌商品价值的关键因素。猴头菌子实体大小是受多基因控制的数量性状，难以进行遗传改良。鉴定控制子实体大小的数量性状位点（QTLs），解析其遗传基础是选育优质猴头菌菌株的基础。本课题利用一种简单快速的定位方法QTL-seq，鉴定控制猴头菌子实体大小的遗传位点。在构建分离群体的基础上，根据双核体菌株极端表型，选取相对应的单核体菌株构建混合池。对混合池进行基因组重测序，开发全基因组范围内的SNP标记，利用混合池之间SNP位点的频率差异来进行QTL定位。再结合转录组分析，解析猴头菌子实体大小形成的遗传基础。本项目将QTL-seq引入猴头菌遗传改良研究，快速定位控制子实体大小的遗传位点，有助于建立分子标记辅助育种的技术体系。这既为选育优质的猴头菌品种奠定基础，亦对其它食用菌遗传改良研究具有重要的借鉴意义。

猴头菌子实体大小是决定其商品价值的关键因素，是遗传基础复杂的数量性状。本研究解析了猴头菌子实体大小性状的遗传基础，主要研究结果如下：（1）建立了一种简单高效的菌刺洗脱法分离孢子单核体，构建了一个包含127个F1代孢子单核体的作图群体和一个双核体群体。（2）对猴头菌菌株CS-4进行de novo 测序，组装了高质量的基因组。获得了45个scaffolds，覆盖长度为41.2 Mb，N50的长度为3.2 Mb，鉴定了10620个预测基因。对127个单核体进行了基因组重测序，开发了全基因组的 SNPs 标记，构建了一张高精度遗传图谱M，并对重组交换进行了表征。M 图谱包含1174个bin标记（37, 082 SNPs），15个连锁群，总的覆盖长度为1,096.5 cM。CS-4基因组与M 图谱表型出良好的共线性关系。（3）通过栽培试验，测定了猴头菌子实体直径、鲜重、菇数、产量、出菇期等农艺性状。结合表型、基因型数据，采用QTL定位鉴定18个与表型性状关联的位点，贡献率为6.9%-20.1%，其中4个与单核体菌丝生长速度相关，8个与双核体农艺性状关联，6个调控重组交换变异。位于菌丝生长速度QTLs里的同源域转录因子、锌指转录因子和糖基转移酶编码基因可能参与菌丝生长的调控。在子实体相关性状的QTLs筛选到一些候选基因（例如CSN8蛋白、HMG box转录因子、几丁质合成酶、FunK1、WD40蛋白、BAR结构域蛋白、P450酶等编码基因），可能参与猴头菌子实体大小形成的调控。在重组交换的QTLs里亦鉴定到一些调控同源重组的基因，包括Spo11, Msh5和Smc5。项目研究结果解析猴头菌子实体大小形成的遗传基础提供重要参考价值，亦为猴头菌生物学和遗传改良研究奠定了基础。