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Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using
A H Khaltabadi Farahani1, H Mohammadi2, M H Moradi1
1Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University , Arak, Iran.
British Poultry Science
|February 4, 2020
Summary
Haplotype analysis using Bayesian methods identified genomic regions associated with egg weight in laying hens. Fixed-length haplotypes explained significant genetic variance, revealing candidate genes for improved egg production traits.
Area of Science:
- Animal Genetics
- Quantitative Genetics
- Genomic Prediction
Background:
- Single nucleotide polymorphism (SNP) genotypes are commonly used in genome-wide association studies.
- Haplotype blocks may offer advantages in capturing multi-allelic quantitative trait loci (QTL) effects.
- Identifying genetic regions influencing egg weight is crucial for poultry breeding programs.
Purpose of the Study:
- To identify genomic regions associated with egg weight traits in laying hens.
- To compare the effectiveness of different Bayesian methods (BayesA, BayesB, BayesN) using fixed-length haplotypes.
- To pinpoint candidate genes influencing egg weight.
Main Methods:
- Genotyping 1,063 laying hens with 294,705 SNPs using an Affymetrix chip.
- Phasing SNP genotypes to create haplotypes.
- Applying Bayesian regression models (BayesA, BayesB, BayesN) within the GenSel software.
- Analyzing first egg weight (FEW) and average egg weight across multiple weeks.
Main Results:
- Fitting 1 Mb haplotypes with BayesB explained the highest proportion of genetic variance for egg weight traits (27%–76%).
- Specific haplotype windows explained a smaller percentage of genetic variance, with the top 1-Mb window on GGA1 explaining 4.05% of FEW variance.
- Candidate genes (e.g., PRKAR2B, HMGA2, LEMD3) were identified for egg weight traits.
- Several genomic regions associated with egg weight were identified, some overlapping with known genes and QTLs for egg production.
Conclusions:
- Haplotype analysis, particularly with BayesB and 1 Mb windows, is effective for dissecting the genetic architecture of egg weight traits.
- The identified genomic regions and candidate genes provide valuable targets for marker-assisted selection in poultry breeding.
- This study highlights the utility of haplotype-based genomic prediction for complex traits in livestock.
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