基于全基因组重测序和叶绿体DNA序列的河北魏县梨地方品种资源分析  

Genetic analysis of local pear varieties in Weixian county,Hebei province based on whole-genome resequencing and chloroplast DNA sequences

作　　者：齐丹[1] 董星光[1] 李振江 曹玉芬[1] 路露 田路明[1] 李军喜 张莹[1] 霍宏亮[1] 苗秀晨 徐家玉 刘超 李金岭 朱蕊颖 QI Dan;DONG Xingguang;LI Zhenjiang;CAO Yufen;LU Lu;TIAN Luming;LI Junxi;ZHANGYing;HUO Hongliang;MIAO Xiuchen;XU Jiayu;LIU Chao;LI Jinling;ZHU Ruiying(Research Institute of Pomology,Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops Germplasm Resources Utilization,Ministry of Agriculture and Rural Affairs,Xingcheng 125100,Liaoning,China;Weixian Forestry-Fruit Development Service Center,Weixian 056800,Hebei,China)

机构地区：[1]中国农业科学院果树研究所·农业农村部园艺作物种质资源利用重点实验室,辽宁兴城125100 [2]魏县林果开发服务中心,河北魏县056800

出　　处：《果树学报》2025年第4期707-720,共14页Journal of Fruit Science

基　　金：中国农业科学院科技创新工程(CAAS-ASTIP-2021-RIP-01);财政部和农业农村部:国家现代农业产业技术体系(CARS-28-01)。

摘　　要：【目的】解析河北魏县梨地方品种的遗传背景,探讨魏县梨种质间的亲缘关系。【方法】以20个河北省魏县梨地方品种以及10个河北其他地区代表性梨地方品种为研究试材,基于全基因组重测序数据和叶绿体DNA变异信息开展河北魏县梨地方品种的分子鉴定。【结果】魏县梨地方品种具有明显的群体遗传结构,可分为两大类:类群1由魏县红梨等9份材料组成,与南方梨品种群亲缘关系较近,类群2由小白面等11份材料组成,更接近北方梨品种群。叶绿体DNA非编码区域的测序结果显示,在魏县梨地方品种中检测到3种较进化的单倍型,大部分地方品种的单倍型为H_3,魏县红梨的单倍型为H_2,雪花以及除金丰鸭梨外的鸭梨品种群的单倍型为H_1。分析品种间的亲缘关系和单倍型类别,鉴定金丰鸭梨并非鸭梨的芽变品种,可能为鸭梨的实生后代选育而成。白雪花不是雪花的芽变,白红梨不是魏县红梨的芽变,油秋与武安油秋两者的遗传背景存在显著差异,证实白砘子梨是砘子梨的芽变选育品种。【结论】明确魏县梨地方品种的亲缘关系和遗传背景,为魏县地方梨种质资源的保护和高效利用提供理论基础。【Objective】Weixian has a long pear cultivation history with approximately 20 unique local pear cultivars,including the most famous Weixian Yali.Researchers have made significant progress in the collection,preservation and phenotypic evaluation on pear germplasm resources in Weixian,but the genetic relationship and background of these pears remain largely unexplored.To provide a theory basis for the efficient utilization of Weixian pears and the sustainable development of pear industry,it is needed to elucidate the genetic relationship and background of Weixian pear accessions.【Methods】Twenty local pear cultivars from Weixian and 10 representative local pear cultivars from other regions within Hebei province were selected as research materials.Based on the whole-genome resequencing data and chloroplast DNA variation,we investigated the genetic relationship and background of local pear cultivars in Weixian.The clean reads were aligned to the reference genome Yunhong No.1 using BWA v0.7.15 software for whole-genome alignment;SNP detection and filtering were performed using GATK v4.2.5.0 software;Population structure analysis was conducted using Admixture v1.3.0 and principal component analysis was carried out using GCTA v1.93.2 software;Treebest v1.9.2 software was used to calculate the distance matrix,and a phylogenetic tree was constructed using the neighbor-joining method.The chloroplast DNA sequencing results were aligned and manually corrected using the software MEGA X;the genetic parameters of chloroplast DNA sequence fragments were calculated using the software DnaSP 5.1;the evolutionary relationship between haplotypes was analyzed using the software NetWork 10.【Results】By comparing the resequencing data of 30 materials with the reference genome,a total of 30041,877 SNP loci were identified.We performed principal component analysis,population genetic structure and phylogenetic tree based on these SNPs.The results showed that local pear cultivars in Weixian exhibited a clear population genetic stru

关 键 词：魏县梨 全基因组重测序 叶绿体DNA 亲缘关系 

分 类 号：S661.2[农业科学—果树学]