基于全基因组SNP构建核桃种质资源指纹图谱OA

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.