Genome-Wide Association Study Reveals Genetic Loci, Candidate Genes and Favorable Haplotypes for Important Agronomic Traits in Auricularia cornea

TL;DR

This study identifies genetic loci and favorable haplotypes in Auricularia cornea that influence key agronomic traits, aiding in breeding for higher yield and quality.

Contribution

The study provides a systematic genetic analysis of A. cornea traits, identifying candidate genes and superior haplotypes for molecular breeding.

Findings

1178 and 821 SNPs were associated with agronomic traits in two years, with yield-related loci on chromosome 9.

42 candidate genes were identified, involved in processes like polysaccharide modification and pigment biosynthesis.

Six superior haplotypes were found to enhance traits like yield and morphology.

Abstract

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 ±5kb 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.

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