| 130 | 0 | 188 |
| 下载次数 | 被引频次 | 阅读次数 |
本研究利用全基因组重测序(whole-genome sequencing, WGS)技术对35份来源广泛的紫苏(Perilla frutescens)种质资源进行深度测序分析,挖掘全基因组水平的单核苷酸多态性(single nucleotide polymorphism,SNP)和插入/缺失(insertion/deletion,In Del)变异位点,分析紫苏种质资源的遗传多样性与群体结构,并构建SNP分子身份证,以期系统全面地评价紫苏资源多样性并开发种质鉴别技术。本研究通过高深度全基因组重测序,累计获得462.95 Gb高质量数据,筛选鉴定出14 337 811个SNP和2 551 899个In Del变异位点。系统发育树、主成分分析(principal component analysis, PCA)及群体结构分析(k=3)结果一致将供试材料划分为三个遗传亚群:北方亚群、南方亚群及混合亚群,揭示了紫苏种质资源存在显著的“南-北”地理分化格局。遗传多样性分析显示,总群体的核苷酸多样性(π)为0.001 8,观测杂合度(Ho=0.154)显著低于期望杂合度(He=0.308),平均近交系数(F)高达0.507,表明群体内等位基因分布不平衡,存在显著的杂合子缺失,符合紫苏自花授粉的遗传特性。群体间遗传分化与连锁不平衡(linkage disequilibrium, LD)分析表明,南、北亚群间存在极大的遗传分化(Fst>0.20),与南方亚群相比,北方亚群表现出较慢的LD衰减速度,说明该群体在驯化过程中可能经历了强烈的人工定向选择,基因组连锁程度高。此外,本研究筛选出124个核心SNP位点,构建了包含紫苏种质遗传信息的DNA分子身份证,可实现紫苏种质的数字化鉴定。本研究发现紫苏种质资源遗传多样性丰富,群体间分化显著,研究结果为后续的种质创新、分子育种及资源保护提供了重要的理论依据。
Abstract：In this study, whole-genome resequencing( WGS) technology was employed to conduct deep sequencing analysis on 35 widely collected Perilla frutescens germplasm resources. Genome-wide single nucleotide polymorphism( SNP) and insertion/deletion( InDel) variation sites were mined to analyze the genetic diversity and population structure of Perilla frutescens germplasm resources, and SNP molecular identity cards were constructed. These efforts aimed to comprehensively evaluate the diversity of P. frutescens germplasm resources and develop germplasm identification technologies. Through high-depth whole-genome resequencing, a total of 462. 95 Gb of high-quality data was generated, resulting in the identification of 14 337 811 SNPs and 2 551 899 In Dels. Phylogenetic tree, principal component analysis( PCA), and population structure analysis(k= 3) consistently classified the tested materials into three genetic subgroups: the northern group, the southern group and the mixed group revealing a significant "north-south" geographical differentiation pattern in P. frutescens germplasm resources. Genetic diversity analysis showed that the nucleotide diversity(π) of the total population was 0. 001 8. The observed heterozygosity(Ho= 0. 154) was significantly lower than the expected heterozygosity(He= 0. 308), and the average inbreeding coefficient(F) was as high as 0. 507. These results indicate an unbalanced distribution of alleles and a significant heterozygote deficiency within the population, which corresponds to the self-pollinating genetic characteristic of P. frutescens. Analysis of inter-population genetic differentiation and linkage disequilibrium( LD) revealed substantial genetic differentiation between the northern group and the southern group(Fst>0. 20). Furthermore, the northern group exhibited the slower LD decay rate than the southern group, indicating that the population might have undergone strong artificial directional selection during domestication, resulting in a high degree of genomic linkage. In addition, 124 core SNP loci were selected to construct DNA molecular identity cards containing germplasm genetic information of P. frutescens accessions, enabling digital identification of the P. frutescens germplasm. This study demonstrates that P. frutescens germplasm resources possess rich genetic diversity and significant inter-population differentiation. These findings provide an important theoretical basis for future germplasm innovation, molecular breeding, and resource conservation.
蔡顺顺，张兴翠，2013.四川、 重庆不同紫苏遗传多样性的SRAP研究.西南师范大学学报(自然科学版),38(3):101-106.[CAI S S,ZHANG X C,2013.On genetic diversity of Perilla frutescens (linn).Britt in Sichuan and Chongqing by SRAP marker.Journal of Southwest China Normal University (Natural Science Edition),38(3):101-106.]
国家药典委员会，2025.中华人民共和国药典-一部：2025年版.北京：中国医药科技出版社.[Chinese Pharmacopoeia Commission,2025.People’s republic of China (PRC) pharmacopoeia-part I:2025 edition.Beijing:China Medical Science Press.]
沈奇，商志伟，徐静，等，2018.紫苏属植物研究进展及发展潜力.中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会论文集：91-99.
谭美莲，严明芳，汪磊，等，2012.国内外紫苏研究进展概述.中国油料作物学报，34(2):225-231.[TAN M L,YAN M F,WANG L,et al.,2012.Research progress on Perilla frutescens.Chinese Journal of Oil Crop Sciences,34(2):225-231.]
王仕玉，郭凤根，2012.基于ISSR标记的云南紫苏资源的遗传多样性研究.中国油料作物学报，34(4):372-376.[WANG S Y,GUO F G,2012.Genetic diversity of Perilla frutescens from Yunnan based on ISSR.Chinese Journal of Oil Crop Sciences,34(4):372-376.]
王仙萍，温贺，商志伟，等，2017.基于SSR标记13个紫苏品种(系)的亲缘关系及遗传多样性.贵州农业科学，45(9):103-106.[WANG X P,WEN H,SHANG Z W,et al.,2017.Genetic relationship and genetic diversity of 13 Perilla frutescens varieties based on SSR markers.Guizhou Agricultural Sciences,45(9):103-106.]
温贺，王仙萍，杨森，等，2019.紫苏SSR标记筛选及遗传关系分析.分子植物育种，17(7):2285-2290.[WEN H,WANG X P,YANG S,et al.,2019.Analysis on SSR markers screening and genetic relationship of Perilla frutescens.Molecular Plant Breeding,17(7):2285-2290.]
魏国江，郭梦桥，崔海波，等，2019.紫苏新品种龙紫苏1号的选育.种子，38(7):155-157.[WEI G J,GUO M Q,CUI H B,et al.,2019.The breeding report of a new perilla variety of longzisu No.1.Seed,38(7):155-157.]
向依，潘金卫，李慧琳，等，2024.基于SSR分子标记的紫苏种质资源遗传多样性及群体结构分析.种子，43(5):40-47.[XIANG Y,PAN J W,LI H L,et al.,2024.Genetic diversity and population structure analysis of the Perilla frutescens L.Germplasm resources based on SSR markers.Seed,43(5):40-47.]
ALEXANDER D H,NOVEMBRE J,LANGE K,2009.Fast model-based estimation of ancestry in unrelated individuals.Genome Res.,19(9):1655-1664.
BOTSTEIN D,WHITE R,SKOLNICK M H,et al.,1980.Construction of a genetic linkage map in man using restriction fragment length polymorphisms.Am.J.Hum.Genet.,32(3):314-31.
CHEN S F,ZHOU Y Q,CHEN Y R,et al.,2018.Fastp:an ultra-fast all-in-one FASTQ preprocessor.Bioinformatics,34(17):i884-i890.
DANECEK P,AUTON A,ABECASIS G,et al.,2011.The variant call format and VCFtools.Bioinformatics,27(15):2156-2158.
DOU T Y,WANG C C,MA Y L,et al.,2023.CoreSNP:an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops.BMC Plant Biol.,23(1):580.
EVANNO G,REGNAUT S,GOUDET J,2005.Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study.Mol.Ecol.,14(8):2611-2620.
KENDIG K I,BAHETI S,BOCKOL M A,et al.,2019.Sentieon DNASeq variant calling workflow demonstrates strong computational performance and accuracy.Front.Genet.,10:736.
KIM J I,LEE M H,KIM S W,et al.,2025.Development and application of SNP markers to discriminate Korean Perilla (Perilla frutescens) varieties using genomic sequence variations.Sci.Rep.,16(1):3097.
LEE J K,OHNISHI O,2003.Genetic relationships among cultivated types of Perilla frutescens and their weedy types in East Asia revealed by AFLP markers.Genet.Resour.Crop Evol.,50(1):65-74.
LAM H M,XU X,LIU X,et al.,2010.Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.Nat.Genet.,42(12):1053-1059.
LI H,DURBIN R,2009.Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics,25(14):1754-1760.
LI Z P,CHEN Y Q,LI Y Y,et al.,2023.Whole-genome resequencing reveals the diversity of patchouli germplasm.Int.J.Mol.Sci.,24(13):10970.
MA S J,SA K J,HONG T K,et al.,2019.Genetic diversity and population structure analysis in Perilla crop and their weedy types from northern and southern areas of China based on simple sequence repeat (SSRs).Genes Genom.,41(3):267-281.
MCKENNA A,HANNA M,BANKS E,et al.,2010.The genome analysis Toolkit:a MapReduce framework for analyzing next-generation DNA sequencing data.Genome Res.,20(9):1297-1303.
NITTA M,LEE J K,KANG C W,et al.,2005.The distribution of perilla species.Genet.Resour.Crop Evol.,52(7):797-804.
OH J S,SA K J,HYUN D Y,et al.,2020.Assessment of gene-tic diversity and population structure among a collection of Korean Perilla germplasms based on SSR markers.Genes Genom.,42(12):1419-1430.
PURCELL S,NEALE B,TODD-BROWN K,et al.,2007.PLINK:a tool set for whole-genome association and population-based linkage analyses.Am.J.Hum.Genet.,81(3):559-575.
ZHANG C,DONG S S,XU J Y,et al.,2019.PopLDdecay:a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.Bioinformatics,35(10):1786-1788.
ZHANG Y J,SHEN Q,LENG L,et al.,2021.Incipient diploidization of the medicinal plant Perilla within 10,000 years.Nat.Commun.,12:5508.
基本信息:
DOI：10.13417/j.gab.045.000571
中图分类号:S567.219
引用信息:
[1]谢聪,梁丽华,程宵,等.基于全基因组重测序的紫苏种质资源遗传多样性与群体结构分析[J].基因组学与应用生物学,2026,45(03):571-585.DOI:10.13417/j.gab.045.000571.
基金信息:
国家自然科学基金项目(82373976); 广东省乡村振兴战略专项(2026CXTD24、 2025-NQD-21-001)共同资助
2026-06-25
2026-06-25