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Linkage disequilibrium and haplotype block patterns in popcorn populations
Andréa Carla Bastos Andrade1, José Marcelo Soriano Viana1, Helcio Duarte Pereira1
1Federal University of Viçosa, Department of General Biology, Viçosa, MG, Brazil.
Plos One
|September 26, 2019
Summary
Linkage disequilibrium (LD) analysis in popcorn revealed varied patterns across populations. While LD decay was rapid, the limited number of SNPs in haplotype blocks suggests limited utility for genomic selection.
Area of Science:
- Population Genetics
- Genomics
- Evolutionary Biology
Background:
- Linkage disequilibrium (LD) analysis is crucial for understanding population evolution.
- Haplotype blocks enhance quantitative trait loci detection and genomic selection accuracy.
- Popcorn populations exhibit distinct evolutionary characteristics influencing genetic studies.
Purpose of the Study:
- Compare LD degree, decay, and extent in popcorn populations.
- Characterize haplotype block number and length.
- Investigate recombination patterns across maize chromosomes.
Main Methods:
- Utilized biparental, synthetic, and breeding popcorn populations.
- Genotyped ~75,000 single nucleotide polymorphisms (SNPs) across 190-192 plants.
- Performed whole-genome and intragenic LD and haplotype block analyses using a 500 kb window.
Main Results:
- Biparental populations showed higher frequencies of significant LD (|D'| > 0.75) compared to breeding populations.
- LD decay was rapid (5-10 kb), with extent up to 300 kb, consistent with maize inbred lines.
- Limited SNPs per haplotype block suggest minimal advantage for haplotype-based association studies or genomic selection.
Conclusions:
- Maize chromosomes display regions of varying LD, potentially reflecting allele frequency differences rather than recombination rates.
- Haplotype block structure in these popcorn populations may not significantly benefit genomic selection.
- Further research can explore the implications of observed LD patterns for breeding strategies.
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