基于全基因组重测序的陈皮及其近缘种遗传多样性研究OA

Objective:To analyze the population structures and phylogenetic relationships of Citrus reticulata(the original plant of Citri Reticulatae Pericarpium)and its related species using whole-genome resequencing,providing a basis for the identification and development of C.reticulata germplasm resources.Methods:DNA was extracted from young leaves of 45 major cultivated varieties of C.reticulata and its closely related species listed in the Pharmacopoeia of the People's Republic of China(hereinafter referred to as the Chinese Pharmacopoeia)(1985-2025 editions)and then sequenced for library construction.Raw sequencing data were aligned and variants were detected via Sentieon 202503.Plink 1.90b6.21 was used to construct the phylogenetic tree and principal component analysis(PCA).Admixture 1.3.0 was employed to examine the population structure of C.reticulata.SweeD 4.0.0 was used for selection signal analysis,and VCFtools 0.1.16 for calculating nucleotide polymorphism(π).Results:A total of 11 274 136 single nucleotide polymorphism(SNP)sites,1 843 256 insertion-deletion(InDel)sites,and 38 881 structural variation(SV)sites were detected.The phylogenetic analysis,PCA,and genetic structure analysis collectively indicated that the germplasm resources of C.reticulata were classified into four distinct groups(group1 to group4).The primary cultivated varieties of Citri Reticulatae Pericarpium listed in the Chinese Pharmacopoeia(1985-2025 editions)originated from two populations.C.reticulata'Chachiensis',C.reticulata'Dahongpao'and C.reticulata'Tangerina'shared close genetic relationships and belonged to group2,along with C.reticulata'Ponkan'and C.reticulata'Shiyue Ju'.C.reticulata'Unshiu'belonged to group3.Population selection signals were detected in all the four groups,with group4 exhibiting the strongest selection signals.The SNP data of the whole genome revealed that group4 possessed the highest nucleotide polymorphism.Conclusion:Whole-genome resequencing provides technical support for the original plant identification of Citri Reticulatae Pericarpium and the genetic diversity research of C.reticulata.C.reticulata'Ponkan'and C.reticulata'Shiyue Ju'are genetically closer to C.reticulata'Chachiensis',C.reticulata'Dahongpao'and C.reticulata'Tangerina'specified in the Chinese Pharmacopoeia(1985-2025 editions).They can serve as potential resources of Citri Reticulatae Pericarpium for further research.