An Hyejin, Lee Hwa-Yong, Shim Donghwan, Choi Seong Ho, Cho Hyunwoo, Hyun Tae Kyung, Jo Ick-Hyun, Chung Jong-Wook
Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
J Fungi (Basel). 2021 May 11;7(5):375. doi: 10.3390/jof7050375.
is a globally cultivated mushroom with high economic value. Despite its widespread cultivation, commercial button mushroom strains have little genetic diversity and discrimination of strains for identification and breeding purposes is challenging. Molecular markers suitable for diversity analyses of germplasms with similar genotypes and discrimination between accessions are needed to support the development of new varieties. To develop cleaved amplified polymorphic sequences (CAPs) markers, single nucleotide polymorphism (SNP) mining was performed based on the genome and resequencing data. A total of 70 sets of CAPs markers were developed and applied to 41 for diversity, multivariate, and population structure analyses. Of the 70 SNPs, 62.85% (44/70) were transitions (G/A or C/T) and 37.15% (26/70) were transversions (A/C, A/T, C/G, or G/T). The number of alleles per locus was 1 or 2 (average = 1.9), and expected heterozygosity and gene diversity were 0.0-0.499 (mean = 0.265) and 0.0-0.9367 (mean = 0.3599), respectively. Multivariate and cluster analyses of accessions produced similar groups, with -statistic values of 0.134 and 0.153 for distance-based and model-based groups, respectively. A minimum set of 10 markers optimized for accession identification were selected based on high index of genetic diversity (GD, range 0.299-0.499) and major allele frequency (MAF, range 0.524-0.817). The CAPS markers can be used to evaluate genetic diversity and population structure and will facilitate the management of emerging genetic resources.
是一种全球广泛种植且具有高经济价值的蘑菇。尽管其种植广泛，但商业双孢蘑菇菌株的遗传多样性很低，对菌株进行鉴定和育种目的的区分具有挑战性。需要适合对基因型相似的种质进行多样性分析以及区分不同种质的分子标记，以支持新品种的开发。为了开发酶切扩增多态性序列（CAPs）标记，基于基因组和重测序数据进行了单核苷酸多态性（SNP）挖掘。共开发了70组CAPs标记，并应用于41个样本进行多样性、多变量和群体结构分析。在这70个SNP中，62.85%（44/70）为转换（G/A或C/T），37.15%（26/70）为颠换（A/C、A/T、C/G或G/T）。每个位点的等位基因数为1或2（平均=1.9），预期杂合度和基因多样性分别为0.0 - 0.499（平均=0.265）和0.0 - 0.9367（平均=0.3599）。对样本的多变量和聚类分析产生了相似的分组，基于距离的分组和基于模型的分组的F统计值分别为0.134和0.153。基于高遗传多样性指数（GD，范围0.299 - 0.499）和主等位基因频率（MAF，范围0.524 - 0.817），选择了一组最少10个用于样本鉴定的优化标记。CAPs标记可用于评估遗传多样性和群体结构，并将有助于新兴遗传资源的管理。
