Research Article: Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers

Date Published: December 24, 2009

Publisher: Public Library of Science

Author(s): Jianbing Yan, Trushar Shah, Marilyn L. Warburton, Edward S. Buckler, Michael D. McMullen, Jonathan Crouch, Xiaoyu Zhang.

Abstract: 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.

Partial Text: Globally, maize is one of the most important food, feed, and industrial crops. Continued improvement and cultivar release with new target traits will require the most precise manipulation possible of the estimated 59,000 genes in the maize genome [1]. Targeted plant breeding must find the right combination of alleles at these genes using new technology and the more traditional “art” of the plant breeder, a process facilitated in maize by the wide range of genetic diversity available in the species [2]. Over 47,000 accessions of maize exist in genebanks around the world, about 27,000 of which are stored at the International Maize and Wheat Improvement Center (CIMMYT) [3]. This includes inbred lines, improved populations, traditional farmer’s populations (landraces) and wild relatives. The majority of accessions are landraces, and to date, much of this germplasm has not been extensively characterized, and most of the landraces have yet to have been utilized in modern plant breeding. It is estimated that less than 5% of the germplasm available in the species is used in commercial breeding programs in the world, and in the U.S. less than 1% [2]. Lack of characterization data for the germplasm stored in the genebanks seems to be one of the impediments to increased use.



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