{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T15:25:12Z","timestamp":1791559512036,"version":"4.3.4"},"reference-count":53,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T00:00:00Z","timestamp":1772668800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research and Development Program of China","award":["2023YFD1201604-4"],"award-info":[{"award-number":["2023YFD1201604-4"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JoF"],"abstract":"<jats:p>Auricularia cornea is rich in nutrients and bioactive compounds, and with the continuous expansion of its industrial cultivation, elucidating the genetic basis of key agronomic traits is essential for marker-assisted breeding and cultivar improvement. In this study, 140 A. cornea germplasm accessions representing diverse geographic origins were subjected to a comprehensive two-year phenotypic evaluation of ten agronomic traits, including FBL, FBW, FBT, Yield, MGR, GP, and fruiting body color. The results showed that all traits exhibited substantial genetic variation across the population, and most traits displayed high heritability. Genome-wide association studies (GWAS) identified 1178 and 821 SNPs significantly associated with agronomic traits in the two respective years, with yield-related loci predominantly located on chromosome 9. Based on an integrated significance threshold, ten core SNPs were ultimately retained, and 42 putative candidate genes were identified within \u00b15kb flanking regions of these SNPs. These candidate genes were mainly involved in cell wall polysaccharide modification, redox regulation, pigment biosynthesis, metabolic processes, and signal transduction. Furthermore, haplotype analysis identified six superior haplotypes associated with ear morphology, yield, MGR, and GP, and accessions carrying these superior haplotypes exhibited significantly enhanced phenotypic performance. Overall, this study provides a systematic dissection of the genetic architecture of important agronomic traits in A. cornea and offers a solid theoretical foundation for high-yield and high-quality molecular breeding and genetic improvement.<\/jats:p>","DOI":"10.3390\/jof12030186","type":"journal-article","created":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T10:31:14Z","timestamp":1772706674000},"page":"186","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genome-Wide Association Study Reveals Genetic Loci, Candidate Genes and Favorable Haplotypes for Important Agronomic Traits in Auricularia cornea"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-4867-6598","authenticated-orcid":false,"given":"Xu","family":"Sun","sequence":"first","affiliation":[{"name":"Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixin","family":"Lu","sequence":"additional","affiliation":[{"name":"Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangjie","family":"Yao","sequence":"additional","affiliation":[{"name":"Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China"},{"name":"Lab of Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Fang","sequence":"additional","affiliation":[{"name":"Lab of Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxu","family":"Ma","sequence":"additional","affiliation":[{"name":"Lab of Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuling","family":"Cui","sequence":"additional","affiliation":[{"name":"Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Sun","sequence":"additional","affiliation":[{"name":"Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-8277-1966","authenticated-orcid":false,"given":"Xianqi","family":"Shan","sequence":"additional","affiliation":[{"name":"Lab of Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Liu","sequence":"additional","affiliation":[{"name":"Lab of Genetic Breeding of Edible Mushroom, College of Horticulture, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1016\/j.ijbiomac.2018.08.160","article-title":"Purification, chemical characterization and antioxidant activities of a novel polysaccharide from Auricularia polytricha","volume":"120","author":"Chen","year":"2018","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_2","unstructured":"Wu, C., and Chen, Q. (1992). Effects of Auricularia polytricha polysaccharides on hypoxia tolerance and heart and blood pressure. Chin. J. Biochem. Pharm., 21\u201323."},{"key":"ref_3","first-page":"164","article-title":"Anticoagulation and Antihyperlipidemia Action of the Polysaccharide from Auricularia polytricha","volume":"3","author":"Wu","year":"1991","journal-title":"J. China Pharm. Univ."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"8179","DOI":"10.1038\/s41598-024-58208-2","article-title":"M1 macrophages polarized by crude polysaccharides isolated from Auricularia polytricha exhibit anti-tumor effect on human breast cancer cells","volume":"14","author":"Nilkhet","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_5","first-page":"1688","article-title":"Optimization of extraction conditions of melanin from Auricularia polytricha and its antioxidant activities in vitro","volume":"31","author":"Liu","year":"2019","journal-title":"Nat. Prod. Res. Dev."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Khan, A.A., Lu, L.X., Yao, F.J., Fang, M., Wang, P., Zhang, Y.M., Meng, J.J., Ma, X.X., He, Q., and Shao, K.S. (2023). Characterization, antioxidant activity, and mineral profiling of Auricularia cornea mushroom strains. Front. Nutr., 10.","DOI":"10.3389\/fnut.2023.1167805"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1093\/pcp\/pcae140","article-title":"Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression","volume":"66","author":"Hajheidari","year":"2025","journal-title":"Plant Cell Physiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e4","DOI":"10.1017\/S0016672317000027","article-title":"Fine mapping by composite genome-wide association analysis","volume":"99","author":"Casellas","year":"2017","journal-title":"Genet. Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1038\/s41592-023-02133-1","article-title":"GWAS and eQTL disparity","volume":"20","author":"Tang","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Qian, F., Jing, J., Zhang, Z., Chen, S., Sang, Z., and Li, W. (2023). GWAS and Meta-QTL Analysis of Yield-Related Ear Traits in Maize. Plants, 12.","DOI":"10.3390\/plants12223806"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/j.plantsci.2012.08.004","article-title":"Genome-wide association study (GWAS) of resistance to head smut in maize","volume":"196","author":"Wang","year":"2012","journal-title":"Plant Sci."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Muhammad, A., Hu, W., Li, Z., Li, J., Xie, G., Wang, J., and Wang, L. (2020). Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21165649"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Leonova, I.N., Kiseleva, A.A., Berezhnaya, A.A., Orlovskaya, O.A., and Salina, E.A. (2023). Novel Genetic Loci from Triticum timopheevii Associated with Gluten Content Revealed by GWAS in Wheat Breeding Lines. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241713304"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Zhong, H., Liu, S., Meng, X., Sun, T., Deng, Y., Kong, W., Peng, Z., and Li, Y. (2021). Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07391-x"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"9958","DOI":"10.1038\/s41598-020-66604-7","article-title":"Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS","volume":"10","author":"Yuan","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"18573","DOI":"10.1021\/acs.jafc.4c03012","article-title":"Joint GWAS and WGCNA Identify Genes Regulating the Isoflavone Content in Soybean Seeds","volume":"72","author":"Yang","year":"2024","journal-title":"J. Agric. Food Chem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1111\/pbi.12918","article-title":"Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean","volume":"16","author":"Wen","year":"2018","journal-title":"Plant Biotechnol. J."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.jare.2021.09.008","article-title":"Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes","volume":"38","author":"Zhang","year":"2022","journal-title":"J. Adv. Res."},{"key":"ref_19","first-page":"31","article-title":"Screening of DUS Test Characteristics for Auricularia cornea","volume":"30","author":"Cao","year":"2023","journal-title":"Acta Edulis Fungi"},{"key":"ref_20","first-page":"233","article-title":"Genetic Diversity and Comprehensive Evaluation of the Phenotypic Characteristics of Auricularia cornea Germplasm Resources","volume":"39","author":"Cao","year":"2025","journal-title":"J. Nucl. Agric. Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"16815","DOI":"10.1021\/acs.jafc.3c02935","article-title":"Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane","volume":"71","author":"Zhang","year":"2023","journal-title":"J. Agric. Food Chem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"8413","DOI":"10.1021\/acs.jafc.5c00085","article-title":"Identifying Candidate Genes for Grape (Vitis vinifera L.) Fruit Firmness through Genome-Wide Association Studies","volume":"73","author":"Hu","year":"2025","journal-title":"J. Agr. Food Chem."},{"key":"ref_23","unstructured":"Xianghui, K. (2019). Study of Comprehensive Evaluation of Germplasm Resource on Auricularia cornea. [Master\u2019s Thesis, Jilin Agriculture University]."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Bai, Y., Xie, J., Tong, T., Zhou, X., Yuan, Z., Zhang, Y., Li, X., and Wu, C. (2025). Genetic Diversity Analysis of Phenotypic Traits in Jujube Germplasm Resources. Agronomy, 15.","DOI":"10.3390\/agronomy15092063"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.ajhg.2010.11.011","article-title":"GCTA: A tool for genome-wide complex trait analysis","volume":"88","author":"Yang","year":"2011","journal-title":"Am. J. Hum. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Cagirici, H.B., Andorf, C.M., and Sen, T.Z. (2022). Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. BMC Plant Biol., 22.","DOI":"10.1186\/s12870-022-03985-z"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1093\/bioinformatics\/btab710","article-title":"vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA","volume":"38","author":"Vogt","year":"2022","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"8326","DOI":"10.1038\/ncomms9326","article-title":"A transposable element in a gene is associated with drought tolerance in maize seedlings","volume":"6","author":"Mao","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: Analysis and visualization of LD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_30","first-page":"1","article-title":"Genome-wide association study of growth traits in 322 maize germplasms","volume":"43","author":"Chen","year":"2025","journal-title":"J. Zhejiang AF Univ."},{"key":"ref_31","unstructured":"Mao, N., Tang, J., Cao, F., Long, W., Luo, G., Liu, H., Yang, Y., Yang, Z., Chen, J., and Li, L. (2025). Genetic Diversity Analysis of Phenotypic Traits in Sorghum Germplasm Resources. J. Yibin Univ., 1\u20138."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Xie, J., Liu, Z., Chang, H., Zhang, C., Liang, Q., Wang, Z., Cheng, Y., Wang, Q., and Wu, J. (2025). Genetic Diversity Evaluation of 70 Chewing Cane Germplasm Resources Based on Phenotypic Traits. Plants, 14.","DOI":"10.3390\/plants14193111"},{"key":"ref_33","unstructured":"Liu, L., Cao, X., Liu, S., Chen, Y., Yan, S., Wang, Y., Peng, W., and Jie, T. (2026). Analysis and comprehensive evaluation of genetic diversity in phenotypic traits of germplasm resources of four species of Morchella. Mycosystema, 1\u201328."},{"key":"ref_34","first-page":"566","article-title":"Genetic Diversity of Mycelia of Self-bred Strains of Auricularia heimuer","volume":"46","author":"Li","year":"2024","journal-title":"J. Jilin Agric. Univ."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1007\/s11676-020-01124-8","article-title":"Leaf phenotypic variation of endangered plant Tetracentron sinense Oliv. and influence of geographical and climatic factors","volume":"32","author":"Li","year":"2020","journal-title":"J. For. Res."},{"key":"ref_36","first-page":"17","article-title":"Analysis on Genetic Differences of 59 Strains of Auricularia heimuer","volume":"41","author":"Pan","year":"2022","journal-title":"Edible Fungi China"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1017\/S1479262121000526","article-title":"Diversity of white Guinea yam (Dioscorea rotundata Poir.) cultivars from Benin as revealed by agro-morphological traits and SNP markers","volume":"19","author":"Agre","year":"2021","journal-title":"Plant Genet. Resour."},{"key":"ref_38","first-page":"27","article-title":"Study on Phenotypic Diversity of Flowers of 102 Crabapples","volume":"58","author":"Yuan","year":"2026","journal-title":"Shandong Agric. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"111942","DOI":"10.1016\/j.scienta.2023.111942","article-title":"Comprehensive evaluation of agronomic traits and mineral elements of cultivated on corncob substrates","volume":"314","author":"Xu","year":"2023","journal-title":"Sci. Hortic."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Li, F., Xie, J., Zhu, X., Wang, X., Zhao, Y., Ma, X., Zhang, Z., Rashid, M.A.R., Zhang, Z., and Zhi, L. (2018). Genetic Basis Underlying Correlations Among Growth Duration and Yield Traits Revealed by GWAS in Rice (Oryza sativa L.). Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.00650"},{"key":"ref_41","unstructured":"Chuang, L. (2016). Association Analysis of Important Agronomic Traits with Markers in Lentinula edodes Cultivars. [Master\u2019s Thesis, Huazhong Agricultural University]."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Teplova, A.D., Serebryakova, M.V., Galiullina, R.A., Chichkova, N.V., and Vartapetian, A.B. (2021). Identification of Phytaspase Interactors via the Proximity-Dependent Biotin-Based Identification Approach. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms222313123"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Fang, M., Sun, X., Yao, F., Lu, L., Ma, X., Shao, K., and Kaimoyo, E. (2024). A Combination of Transcriptome and Enzyme Activity Analysis Unveils Key Genes and Patterns of Corncob Lignocellulose Degradation by Auricularia heimuer under Cultivation Conditions. J. Fungi, 10.","DOI":"10.3390\/jof10080545"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Perrot, T., Pauly, M., and Ramirez, V. (2022). Emerging Roles of beta-Glucanases in Plant Development and Adaptative Responses. Plants, 11.","DOI":"10.3390\/plants11091119"},{"key":"ref_45","unstructured":"Gaolei, L. (2017). Genome-Wide Association Study of Important Traits in Lentinula Edodes Strains of China. [Master\u2019s Thesis, Huazhong Agricultural University]."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s00294-017-0756-x","article-title":"To finish things well: Cysteine methylation ensures selective GTPase membrane localization and signalling","volume":"64","author":"Cansado","year":"2018","journal-title":"Curr. Genet."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1933","DOI":"10.1023\/B:BILE.0000003989.19657.53","article-title":"Cloning and expression of a putative cytochrome P450 gene that influences the colour of Phalaenopsis flowers","volume":"25","author":"Vincent","year":"2003","journal-title":"Biotechnol. Lett."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Ma, X., Lu, L., Yao, F., Fang, M., Wang, P., Meng, J., Shao, K., Sun, X., and Zhang, Y. (2023). High-quality genome assembly and multi-omics analysis of pigment synthesis pathway in Auricularia cornea. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1211795"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1016\/j.jia.2023.06.030","article-title":"Genome-wide association study of grain micronutrient concentrations in bread wheat","volume":"23","author":"Hao","year":"2024","journal-title":"J. Integr. Agric."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Hu, X., and Zuo, J. (2021). The CCCH zinc finger family of soybean (Glycine max L.): Genome-wide identification, expression, domestication, GWAS and haplotype analysis. BMC Genom., 22.","DOI":"10.1186\/s12864-021-07787-9"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Lujan Basile, S.M., Ramirez, I.A., Crescente, J.M., Conde, M.B., Demichelis, M., Abbate, P., Rogers, W.J., Pontaroli, A.C., Helguera, M., and Vanzetti, L.S. (2019). Haplotype block analysis of an Argentinean hexaploid wheat collection and GWAS for yield components and adaptation. BMC Plant Biol., 19.","DOI":"10.1186\/s12870-019-2015-4"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e02662","DOI":"10.1002\/advs.202502662","article-title":"A Blast-Resistant NLR Gene Confers Drought Resistance by Competitively Interacting with an E3 Ligase to Protect Phenylalanine Ammonia-Lyase in Rice","volume":"12","author":"Xiang","year":"2025","journal-title":"Adv. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Guo, Y., Liu, Z., Fu, Y., Li, Y., Dai, Y., and Xiao, S. (2022). Pan-Genomes Provide Insights into the Genetic Basis of Auricularia heimuer Domestication. J. Fungi, 8.","DOI":"10.3390\/jof8060581"}],"container-title":["Journal of Fungi"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/3\/186\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T05:15:33Z","timestamp":1772860533000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2309-608X\/12\/3\/186"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,5]]},"references-count":53,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["jof12030186"],"URL":"https:\/\/doi.org\/10.3390\/jof12030186","relation":{},"ISSN":["2309-608X"],"issn-type":[{"value":"2309-608X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,5]]}}}