Related Experiment Video
Updated: May 29, 2026

Imaging and Analysis for Quantifying Maize (Zea mays) Abiotic Stress Phenotypes
Published on: March 28, 2025
Comparative SNP and haplotype analysis reveals a higher genetic diversity and rapider LD decay in tropical than
Yanli Lu1, Trushar Shah, Zhuanfang Hao
1Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.
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.
More Related Videos
10:27Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria
Published on: November 10, 2015
07:26Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy
Published on: July 29, 2019
Related Concept Videos
Single Nucleotide Polymorphisms-SNPs
Genetic Variation
Genes exist in different versions called alleles, which...
Evolutionary Relationships through Genome Comparisons
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Gene Evolution - Fast or Slow?
In contrast, regions which code...