核农学报2026，Vol.40Issue(7)：1331-1341,11.DOI:10.11869/j.issn.1000-8551.2026.07.1331
基于全基因组SNP构建核桃种质资源指纹图谱
Constructing a Fingerprint Map of Walnut Germplasm Resources Based on Whole Genome SNPs
摘要
Abstract
Walnuts are important woody oil economic tree species in China,and their kernels have high nutritional and economic value.In order to quickly and accurately distinguish and identify walnut germplasm resources in southern Xinjiang,improve the efficiency of their collection and management,and strengthen the protection of variety rights,this study selected 12 representative main cultivars(lines)of walnuts from the Alar region in southern Xinjiang as experimental materials.Through Illumina HiSeq 150 bp double ended resequencing,a total of 95.92 Gb of high-quality data(Q20≥97％,Q30≥93％)were obtained.Using the BWA-GATK process,3.036×107 SNPs were identified at the whole genome level.Based on the six principles-including uniform distribution on chromosomes(no less than 1 marker per Mb),coefficient of variation(CV)less than 15％,no genotype deletion,allele frequency(MAF)not less than 10％,polymorphic information content(PIC)not less than 0.35,Hardy Weinberg equilibrium(P＞0.01),and low degree of linkage disequilibrium within the 60 bp range(r2＜0.2),-281 core single nucleotide polymorphism(SNP)loci were ultimately screened out.Among these,the 7 strains of the Bingta series shared 61.2％of SNP loci,with a genetic similarity ranging from 0.82 to 0.94,indicating that they may originate from the same hybrid combination or have close pedigree relationships.Using this set of core SNP markers,genotyping was performed on the 12 walnut germplasms,and a phylogenetic tree was constructed.The 12 germplasms could be divided into three groups with significant genetic differences:Shaanhe 5 formed an independent branch(exogenous variety),Xinzaofeng and Bingta 7 were clustered together(possibly sharing parental lines),and the remaining 9 varieties(lines)were classified as local breeding populations in southern Xinjiang.Furthermore,the 281 SNPs were converted into binary codes(0/1/2)to form unique 281-bit digital fingerprint code;A 12 digit product code was generated based on 11 agronomic and quality traits,and a dual module walnut molecular ID card with"product code+fingerprint code"was developed for the first time.For the 12 main cultivars in southern Xinjiang included in this study,the system achieved complete differentiation with a resolution index(DP)of 1.000.This study provides a standardized technical framework for DUS(Distinctiveness,Uniformity and Stability)testing,rapid identification of germplasm resources,and molecular breeding of new walnut cultivars in southern Xinjiang.关键词
核桃/SNP分子标记/DNA指纹图谱/分子身份证Key words
walnut/SNP molecular markers/DNA finger printing/molecular ID card引用本文复制引用
夏邱浩,王阳,赵靖钰,张锐,王新汇,高瑞霞,郭众仲..基于全基因组SNP构建核桃种质资源指纹图谱[J].核农学报,2026,40(7):1331-1341,11.基金项目
新疆维吾尔自治区重点研发计划项目(2024B02017),"天山英才"培养计划项目(2022TSYCCX0120),南疆重点产业创新发展支撑计划项目(2022DB022),兵团指导性科技计划项目(2024ZD113) （2024B02017）
