Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm
<i>Pleurotus pulmonarius</i> is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for <i>P. pulmonarius</i>, only a limited number of cultivars are commercially available. A comprehensive eva...
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MDPI AG
2024-11-01
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| author | Qian Li Xuebing Ying Yashu Yang Wei Gao |
| author_facet | Qian Li Xuebing Ying Yashu Yang Wei Gao |
| author_sort | Qian Li |
| collection | DOAJ |
| description | <i>Pleurotus pulmonarius</i> is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for <i>P. pulmonarius</i>, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of <i>P. pulmonarius</i> germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 <i>P. pulmonarius</i> strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of <i>P. pulmonarius</i> germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials. |
| format | Article |
| id | doaj-art-c111e030f74b402ab098f8c256ec8569 |
| institution | OA Journals |
| issn | 2077-0472 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
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| series | Agriculture |
| spelling | doaj-art-c111e030f74b402ab098f8c256ec85692025-08-20T02:08:04ZengMDPI AGAgriculture2077-04722024-11-011411202310.3390/agriculture14112023Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> GermplasmQian Li0Xuebing Ying1Yashu Yang2Wei Gao3Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaLin’an District Agricultural and Forestry Technology Extension Center, Hangzhou 311300, ChinaInstitute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China<i>Pleurotus pulmonarius</i> is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for <i>P. pulmonarius</i>, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of <i>P. pulmonarius</i> germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 <i>P. pulmonarius</i> strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of <i>P. pulmonarius</i> germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials.https://www.mdpi.com/2077-0472/14/11/2023<i>Pleurotus pulmonarius</i>genetic diversitygenome-wide association study |
| spellingShingle | Qian Li Xuebing Ying Yashu Yang Wei Gao Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm Agriculture <i>Pleurotus pulmonarius</i> genetic diversity genome-wide association study |
| title | Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm |
| title_full | Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm |
| title_fullStr | Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm |
| title_full_unstemmed | Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm |
| title_short | Genetic Diversity and Genome-Wide Association Study of <i>Pleurotus pulmonarius</i> Germplasm |
| title_sort | genetic diversity and genome wide association study of i pleurotus pulmonarius i germplasm |
| topic | <i>Pleurotus pulmonarius</i> genetic diversity genome-wide association study |
| url | https://www.mdpi.com/2077-0472/14/11/2023 |
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