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Genetic Diversity and Genome-Wide Association Study of Pleurotus pulmonarius Germplasm

Author

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  • Qian Li

    (Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China
    These authors contributed equally to this work.)

  • Xuebing Ying

    (Lin’an District Agricultural and Forestry Technology Extension Center, Hangzhou 311300, China
    These authors contributed equally to this work.)

  • Yashu Yang

    (Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China)

  • Wei Gao

    (Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, Beijing 100081, China)

Abstract

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius , only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius 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 P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials.

Suggested Citation

  • Qian Li & Xuebing Ying & Yashu Yang & Wei Gao, 2024. "Genetic Diversity and Genome-Wide Association Study of Pleurotus pulmonarius Germplasm," Agriculture, MDPI, vol. 14(11), pages 1-19, November.
    • Handle: RePEc:gam:jagris:v:14:y:2024:i:11:p:2023-:d:1518046
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    References listed on IDEAS

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    1. Susanna Atwell & Yu S. Huang & Bjarni J. Vilhjálmsson & Glenda Willems & Matthew Horton & Yan Li & Dazhe Meng & Alexander Platt & Aaron M. Tarone & Tina T. Hu & Rong Jiang & N. Wayan Muliyati & Xu Zha, 2010. "Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines," Nature, Nature, vol. 465(7298), pages 627-631, June.
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