Genetic Resources Program, International Maize and Wheat Improvement Center, Mexico City, Mexico.
PLoS One. 2009 Dec 24;4(12):e8451. doi: 10.1371/journal.pone.0008451.
A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.
一种新开发的玉米Illumina GoldenGate分析方法，使用来自582个位点的1536个单核苷酸多态性（SNP），对来自温带、热带和亚热带公共育种项目的632个自交系组成的高度多样化的全球玉米种质库进行基因分型。利用327个位点内的1229个信息性SNP和1749个单倍型来估计遗传多样性、群体结构和家族亲缘关系。群体结构分析确定了热带和温带亚群，并且在全球种质库中发现了复杂的家族关系。对整个基因组以及各条染色体、等位基因频率组、按地理起源划分的亚群和不同样本量的亚群进行了连锁不平衡（LD）测量。LD衰减距离在各条染色体间有所不同，范围在1至10 kb之间。LD距离随着次要等位基因频率（MAF）的增加而增加，并且样本量越小，在研究中使用过少品系时就越需谨慎。温带品系的LD衰减距离比热带和亚热带品系高得多，因为热带和亚热带品系比温带品系更加多样化，并且包含更多稀有等位基因。基于单倍型定义了一组核心自交系，60个品系捕获了整个群体90%的单倍型多样性。所定义的核心种质库和整个种质库可广泛用于不同的研究目标。
