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.）是全球最为关键的粮食作物之一，年产量高达7.65亿吨，用以滋养约占世界40%的人口。对现有种质资源中的农艺形态性状和遗传多样性进行研究，对于可持续的春小麦改良至关重要，以确保全球粮食安全。本研究采用基于高通量测序技术的基因分型方法（GBS），利用123,596个高质量的基于单核苷酸多态性（SNP）标记对184个巴基斯坦春小麦基因型进行基因分型，其中42%的SNP标记定位在B亚基因组，36%定位在A亚基因组，22%定位在D亚基因组。2B染色体含有最多的SNP标记（9,126个），而4D染色体含有最少的（2,660个）。种群结构分析将种群划分为两个亚种群。该群体的平均多态信息含量（PIC）、遗传多样性（GD）和主要等位基因频率（MAF）分别为0.157、0.1844和0.87。分子方差分析（AMOVA）显示，亚种群内的遗传多样性（80%）高于亚种群间（20%）。全基因组连锁不平衡（LD）衰减值为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），其次是A亚基因组（2.88 cM）和B亚基因组（2.03 cM）。本研究结果将为春小麦的标记辅助选择（MAS）、关联作图（AM）、全基因组关联研究（GWAS）和基因组选择（GS）等育种程序提供基础。关键词：基因分型测序（GBS）、遗传多样性（GD）、种群结构（PS）、多态信息含量（PIC）、主要等位基因频率（MAF）。参与者：Shabbir Hussain1, Madiha Habib1, Amy Bernardo2, Paul St. Amand2, Guihua Bai2, Nida Ghori2, Azeem Iqbal Khan1, Faisal Saeed Awana1。1 中心农业生物化学与生物技术（CABB），巴基斯坦费萨拉巴德农业大学，38000；2 美国农业部，硬质冬小麦遗传学研究单位，美国堪萨斯州曼哈顿，66506。