Molecular Characterization of 170 New gDNA-SSR Markers for Genetic Diversity in Button Mushroom (Agaricus bisporus)

Abstract

We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (M AF) and the average number of alleles (N A) were 0.50 and 5.47, respectively. The average number of genotypes (N G), observed heterozygosity (H O), expected heterozygosity (H E), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson's correlation coefficient showed that M AF was negatively correlated with N G (À0.683), N A (À0.600), H O (À0.584), and PIC (À0.941). N G , N A , H O, and PIC were positively correlated with other polymorphic parameters except for M AF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

Development of CAPS Markers for Evaluation of Genetic Diversity and Population Structure in the Germplasm of Button Mushroom (Agaricus bisporus)

“…To assess whether the CAPS markers developed in this study were suitable for evaluating diversity and population structures, diversity was determined using the SSR diversity index, a widely used metric in population genetic studies [ 9 , 10 , 11 , 35 ]. GD, a representative diversity index, is influenced by the allele frequency.…”

“…Polymorphism frequencies were lower than average GD values of 0.548, 0.619, and 0.6807 from previously developed SSR markers. However, polymorphism levels were higher than the average GD value of 0.395 from monospores of limited accessions [ 9 , 10 , 11 , 35 ].…”

“…Previous studies of mushroom diversity and population structures using SSR and SNP markers focused on differences in the diversity index for the same marker [ 9 , 10 , 11 , 12 , 13 , 14 , 44 ]. However, direct comparison of diversity was difficult because of differences in the target loci of the two marker types.…”

“…In this study, 10 SNP markers were sufficient to distinguish 41 A. bisporus accessions. Previous research also developed minimum marker sets for accession differentiation: SSR markers were used to distinguish all accessions by using 4 of 26 accessions [ 10 ] and 6 of 171 accessions [ 11 ]. Discrimination using SNP markers tends to require more markers, and distinguish fewer accessions, than SSR markers.…”

“…Polymerase chain reaction (PCR)-based molecular markers, such as simple sequence repeats (SSR) and single nucleotide polymorphisms (SNPs), can be used for molecular genetic studies of culture collections. Genetic diversity in A. bisporus has been examined using several similar approaches, including analysis with restriction fragment length polymorphisms (RFLP) [ 7 ], discrimination analysis with random amplified polymorphic DNA (RAPD) [ 8 ], genetic diversity analysis using SSR markers [ 9 , 10 , 11 ], phylogenetic analysis using SNP markers [ 12 ], SNP genotyping [ 13 , 14 ], and quantitative trait locus (QTL) mapping using SNP markers [ 15 , 16 ]. However, molecular markers that can be used for the analysis of population structure and diversity of accession collections are biased toward SSR markers, and new SNP genotyping markers are needed.…”