Abstract
This study investigated the genetic diversity and genomic variation in wild Cordyceps chanhua populations from four regions in China—Dazhou, Sichuan (ICD); Lu’an, Anhui (ICL); Taizhou, Zhejiang (ICT); and Yixing, Jiangsu (ICY)—to elucidate genetic differentiation patterns and provide a scientific foundation for resource conservation and sustainable utilization. Whole-genome resequencing was performed, yielding high-quality sequencing data (Q20 > 98%, Q30 > 94%, coverage: 93.62–95.79%) and enabling the detection of 82,428 single-nucleotide polymorphisms (SNPs) and 12,517 insertion–deletion markers (InDels). Genomic variations were unevenly distributed across chromosomes, with chromosome chrU05 exhibiting the highest SNP density (5187.86), suggesting a potential hotspot of genetic diversity. Phylogenetic analysis confirmed that all samples belonged to the C. chanhua lineage but revealed significant genetic differentiation among regions. Population structure analysis, supported by structure analysis and PCA, identified two distinct subgroups (G1 and G2) closely associated with geographic origins, reflecting the influence of both environmental and geographic factors on genetic differentiation. These findings underscore the substantial interregional genetic diversity in C. chanhua populations, highlighting the importance of tailored conservation strategies and region-specific germplasm utilization. The study provides critical genomic insights to support marker-assisted breeding, regional cultivation optimization, and the sustainable development of C. chanhua resources.
Published Version
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