Genotyping by Sequencing (GBS) based Molecular Genetic Diversity, Population Structure, Linkage Disequilibrium and Kinship Analysis of Pakistani Bread Wheat Genotypes

Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops with annual production of 765 million tons globally to feed ~ 40% world population. Studying agro-morphological traits and genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat genotypes was genotyped using 123,596 high quality based single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS) with 42% of the SNPs mapped on B, 36% on A and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126) and 4D has the least (2,660). Population structure analysis divided the population into two subpopulations. The mean polymorphic information content (PIC), genetic diversity (GD), and major allele frequency (MAF) of the population were 0.157, 0.1844 and 0.87, respectively. Analysis of molecular variance (AMOVA) revealed the higher genetic diversity (80%) within the subpopulation than among the subpopulations (20%). The genome-wide linkage disequilibrium (LD) decay was 3.38 cM. Among the three subgenomes, D has the highest LD decay value (7.45 cM), followed by A (2.88 cM) and B (2.03 cM). Results of this study will be a baseline to start marker-assisted selection (MSA), association mapping (AM), genome wide association studies (GWAS) and genome selection (GS) related breeding programs of wheat.Keywords. Genotyping by Sequencing (GBS), Genetic Diversity (GD), Population Structure (PS), Polymorphic Information Content (PIC), Major Allele Frequency (MAF).Participants: Shabbir Hussain1, Madiha Habib1, Amy Bernardo2, Paul St. Amand2, Guihua Bai2, Nida Ghori2, Azeem Iqbal Khan1, Faisal Saeed Awana1.1 Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad-38000, Pakistan;2 USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA

春小麦（Triticum aestivum L.）是全球最重要的主食作物之一，全球年产量达7.65亿吨，可供养全球约40%的人口。针对现有种质资源开展农艺形态性状与遗传多样性研究，对于推进小麦可持续改良、保障全球粮食安全具有关键意义。本研究利用测序分型（genotyping-by-sequencing, GBS）技术生成的123,596个高质量单核苷酸多态性（single nucleotide polymorphism, SNP）标记，对由184份巴基斯坦小麦基因型组成的多样性群体进行基因分型；其中42%的SNP定位至小麦B亚基因组、36%定位至A亚基因组、22%定位至D亚基因组。2B染色体携带的SNP数量最多（9,126个），4D染色体携带的SNP数量最少（2,660个）。群体结构分析将该供试群体划分为两个亚群。该群体的平均多态性信息含量（polymorphic information content, PIC）、遗传多样性（genetic diversity, GD）及主等位基因频率（major allele frequency, MAF）分别为0.157、0.1844和0.87。分子方差分析（analysis of molecular variance, AMOVA）结果显示，亚群内的遗传多样性占比达80%，显著高于亚群间的20%。全基因组连锁不平衡（linkage disequilibrium, LD）衰减距离为3.38 cM；在三个亚基因组中，D亚基因组的LD衰减值最高（7.45 cM），其次为A亚基因组（2.88 cM）与B亚基因组（2.03 cM）。本研究结果可作为开展小麦标记辅助选择（MSA）、关联作图（AM）、全基因组关联研究（GWAS）及基因组选择（GS）相关育种项目的基础依据。关键词：测序分型（GBS）、遗传多样性（GD）、群体结构（PS）、多态性信息含量（PIC）、主等位基因频率（MAF）。作者：Shabbir Hussain¹, Madiha Habib¹, Amy Bernardo², Paul St. Amand², Guihua Bai², Nida Ghori², Azeem Iqbal Khan¹, Faisal Saeed Awana¹。¹ 巴基斯坦费萨拉巴德农业大学农业生物化学与生物技术中心（CABB），费萨拉巴德-38000；² 美国农业部硬冬小麦遗传学研究室，美国堪萨斯州曼哈顿市66506