[Evaluation of genetic diversity and screening of high-quality germplasms in Codonopsis based on phenotypic traits and whole-genome resequencing].

Abstract

Using phenotyping and whole-genome resequencing, this study analyzed the genetic diversity of Codonopsis and screened high-quality core germplasms, thereby providing support for germplasm innovation, variety improvement, and industrial standardization. Twenty-seven Codonopsis germplasms were collected from Gansu, Shanxi, Guizhou, and other provinces. After planting in a unified environment, 21 agronomic traits and 6 quality traits were determined. Comprehensive evaluation was conducted using methods such as correlation analysis, cluster analysis, and principal component analysis(PCA) to screen out excellent Codonopsis germplasms. Total DNA was extracted from young leaves by the magnetic bead method, and whole-genome resequencing was performed on the MGIDL-T7 platform. After quality control with FASTP, the sequences were aligned to the reference genome to detect single nucleotide polymorphism(SNP). Subsequently, linkage disequilibrium analysis was carried out using the sliding window method, and population structure was analyzed with the Admixture software to clarify the population genetic characteristics and germplasm genetic background. The 27 Codonopsis germplasms exhibited rich phenotypic and genetic diversity, with the coefficient of variation of the 27 traits ranging from 5.1% to 130.6%. Among them, yield(130.6%), root branch number(87.4%), and atractylenolide Ⅲ content(68.2%) showed significant variation, while traits such as seed germination rate(5.1%) and corolla tube diameter(6.0%) had relatively small variation. Correlation analysis revealed that yield was significantly positively correlated with the number of fruits per plant and the number of primary branches; root weight per plant was significantly positively correlated with root diameter; lobetyolin content was significantly positively correlated with lobetyolinin content; tangshenoside Ⅰ content was significantly positively correlated with polysaccharide content. PCA extracted 8 principal components(with a cumulative contribution rate of 82%), and 5 high-quality germplasms were screened out through comprehensive evaluation. Cluster analysis divided the germplasms into 6 groups, and the group characteristics were related to geographical origin and original plants. Whole-genome resequencing yielded 334.49 Gb of clean data(average Q30=95.70%), and 32 429 491 SNP loci were detected. Population structure analysis could clearly distinguish 3 original plants, PC1 significantly differentiated Codonopsis pilosula from C. tangshen, and when K=3, C. pilosula var. modesta showed an independent genetic component. In conclusion, the tested Codonopsis germplasms have rich phenotypic and genetic diversity, and whole-genome SNP markers can clearly resolve their genetic structure. The screened high-quality core germplasms possess both excellent agronomic and quality traits, which can provide a material basis and technical support for Codonopsis variety breeding and high-quality industrial development.