Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers

The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations. Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters. Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r² =0.2 and r²= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.对遗传多样性（Genetic Diversity, GD）、种群结构与连锁不平衡（Linkage Disequilibrium, LD）的研究，可深化对种群内个体间遗传关系的认知，该类研究成果可应用于作物研究与品种改良。本研究采用测序分型（Genotyping-by-sequencing, GBS）技术，对74份优质蛋白玉米（Quality Protein Maize, QPM）种质的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）进行检测与分型，并以此为基础解析其遗传多样性、种群结构与连锁不平衡特征。共获得235,214个高质量SNPs用于除种群结构分析外的各类遗传分析，而种群结构分析则采用其中11,950个SNPs。基于上述SNPs的分子方差分析（Analysis of Molecular Variance, AMOVA）结果显示，5个种群间存在较高的遗传杂合度，总遗传变异中仅1%来自亚种群间，剩余99%的变异均来源于种群内个体间。基于贝叶斯聚类（Bayesian-based clustering）的种群结构分析表明，74份种质可划分为4个类群；然而邻接树分析结果则显示供试材料可被分为3个主要类群。进一步采用主成分分析（Principal Component Analyses, PCA）可将供试基因型划分为5个类群，该分类结果与基于系谱信息的类群划分结果一致。种群1的遗传多样性水平最高，GD值为0.484；种群5的遗传多样性最低，仅为0.396；所有种群的平均遗传多样性值为0.434。本研究还解析了优质蛋白玉米的LD模式，发现在r²=0.2与r²=0.1的阈值下，LD衰减距离分别为3.53kb与10.66kb，衰减速度相对较快。本研究结果可为后续玉米连锁作图研究、全基因组关联分析、标记辅助选择育种，以及热带种质（tropical germplasm）的基因组预测选择育种提供重要的理论依据与数据支撑。