Data_Sheet_3_Establishment and application of a SNP molecular identification system in Grifola frondosa.PDF

Germplasm resources of edible mushrooms are essential for the breeding of varieties with improved traits. Analysis of the genetic diversity of Grifola frondosa germplasm resources and clarification of the genetic relationships among strains can provide valuable information for the selection of breeding parents. A total of 829,488 high-quality SNP loci were screened from 2,125,382 SNPs obtained by sequencing 60 G. frondose. Phylogenetic analysis, PCA, and population structure analysis based on the high-quality SNPs showed that the 60 strains could be divided into five subgroups, and the clustering results were consistent with the geographical distributions of these strains. Based on high-quality SNP loci, a core collection containing 18 representative germplasm resources was constructed, and 1,473 Kompetitive Allele-Specific PCR markers were obtained. A total of 722 SNP markers in the exonic regions were screened using KASP-genotyping experiments, and 50 candidate SNP markers and 12 core SNP markers were obtained. Genetic fingerprints of G. frondosa germplasm resources were constructed based on the selected SNP markers; these fingerprints provide an accurate, rapid, convenient, and efficient method for the identification of G. frondosa germplasm resources. The results of this study have important implications for the preservation and utilization of G. frondosa germplasm resources and the identification of varieties.

食用蕈菌种质资源是培育优良性状品种的关键基础。对灰树花（Grifola frondosa）种质资源开展遗传多样性分析并明确菌株间的遗传关系，可为育种亲本的遴选提供重要参考依据。本研究对60株灰树花进行测序，共获得2125382个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，最终筛选得到829488个高质量SNP位点。基于上述高质量SNP位点开展系统发育分析、主成分分析（Principal Component Analysis, PCA）以及群体结构分析，结果显示60株供试菌株可划分为5个亚群，且聚类结果与菌株的地理分布高度吻合。基于高质量SNP位点，本研究构建了包含18份代表性种质资源的核心种质库，并开发得到1473个竞争性等位基因特异性PCR（Kompetitive Allele-Specific PCR, KASP）标记。通过KASP基因分型实验，从外显子区域筛选得到722个SNP标记，最终获得50个候选SNP标记与12个核心SNP标记。基于筛选得到的SNP标记，本研究构建了灰树花种质资源的遗传指纹图谱，该图谱可为灰树花种质资源的鉴定提供准确、快速、便捷且高效的技术手段。本研究结果对于灰树花种质资源的保存与利用以及品种鉴定均具有重要指导意义。