Abstract
Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436–0.566) were generally much higher than individual SNPs (0.247–0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2–100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10–100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5–10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.
Highlights
Maize has adapted to different environments with its spread from the center of origin in Mexico to various parts of the world and its evolution into a cultivated and productive plant for food, feed, and industrial products
Based on the sequence annotation analysis performed on the maize B73 filtered gene set, 273 single nucleotide polymorphism (SNP) are from intergenic regions, while the remaining 1670 SNPs are from intragenic regions which involve 1180 genes
This study showed a much higher polymorphism information content (PIC) estimated by SNP haplotypes than by single SNPs
Summary
Maize has adapted to different environments with its spread from the center of origin in Mexico to various parts of the world and its evolution into a cultivated and productive plant for food, feed, and industrial products. Understanding of the contribution of genic and intergenic diversity to genetic and functional variation at the genome level needs to use whole genome sequences or marker chips containing a large number of SNPs from different regions of genes. With the advent of generation sequencing technology, maize inbreds can be resequenced and large allelic regions from many germplasm accessions can be compared [10] Such studies indicate that the nature of observed allelic differences within genes and their immediate vicinity is different from those within intergenic regions [11,12,13]. The SNP chips developed recently in maize contain a large proportion of markers from genic regions [16,17], providing a unique opportunity for understanding the contribution of genic and intergenic variation to genetic diversity and population structure
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