Data from: Genetic diversity among INERA maize inbred lines with single nucleotide polymorphism (SNP) markers and their relationship with CIMMYT, IITA, and temperate lines

Background: Genetic diversity provides the capacity for plants to meet changing environments. It is fundamentally important in crop improvement. Fifty-nine local maize lines developed at INERA and 41 exotic (temperate and tropical) inbred lines were characterized using 1057 SNP markers to (1) analyse the genetic diversity in a diverse set of maize inbred lines; (2) determine the level of genetic diversity in INERA inbred lines and patterns of relationships of these inbred lines developed from two sources; and (3) examine the genetic differences between local and exotic germplasms. Results: Roger’s genetic distance for about 64% of the pairs of lines fell between 0.300 and 0.400. Sixty one per cent of the pairs of lines also showed relative kinship values of zero. Model-based population structure analysis and principal component analysis revealed the presence of 5 groups that agree, to some extent, with the origin of the germplasm. There was genetic diversity among INERA inbred lines, which were genetically less closely related and showed a low level of heterozygosity. These lines could be divided into 3 major distinct groups and a mixed group consistent with the source population of the lines. Pairwise comparisons between local and exotic germplasms showed that the temperate and some IITA lines were differentiated from INERA lines. There appeared to be substantial levels of genetic variation between local and exotic germplasms as revealed by missing and unique alleles. Conclusions: Allelic frequency differences observed between the germplasms, together with unique alleles identified within each germplasm, shows the potential for a mutual improvement between the sets of germplasm. The results from this study will be useful to breeders in designing inbred-hybrid breeding programs, association mapping population studies and marker assisted breeding.

背景：遗传多样性是植物应对多变环境的能力基础，对作物遗传改良具有核心意义。本研究采用1057个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，对59份由INERA育成的本地玉米自交系与41份外来（温带、热带）玉米自交系进行基因型分型，旨在实现三大研究目标：（1）解析多样化玉米自交系群体的遗传多样性；（2）明确INERA自交系的遗传多样性水平，以及两类不同来源自交系的亲缘关系格局；（3）探究本地与外来种质间的遗传差异。结果：约64%的材料对的罗杰遗传距离（Roger's Genetic Distance）介于0.300~0.400区间；另有61%的材料对的相对亲缘系数为0。基于模型的群体结构分析与主成分分析（Principal Component Analysis, PCA）结果表明，供试群体可划分为5个类群，其分类结果在一定程度上与种质来源相契合。INERA自交系群体内部存在遗传多样性，各材料间遗传亲缘关系较远且杂合度水平偏低；该类自交系可进一步划分为3个独立类群与1个混合类群，该分类结果与材料的源群体保持一致。本地与外来种质的两两比对结果显示，温带种质以及部分国际热带农业研究所（International Institute of Tropical Agriculture, IITA）创制的自交系与INERA自交系存在遗传分化；借助缺失等位基因与特有等位基因的分析结果可见，本地与外来种质间存在显著的遗传变异。结论：不同种质间观测到的等位基因频率差异，结合各种质内鉴定得到的特有等位基因，证实了两类种质之间具备相互遗传改良的潜力。本研究结果可为育种工作者设计自交系-杂种育种方案、开展关联作图群体研究以及标记辅助育种（Marker-Assisted Breeding, MAB）提供重要的理论支撑与实践指导。