Bayes factors revealed selection signature for time to market body weight in chicken: a genome-wide association study using BayesCpi methodology
Bayes Cπ methodology due to the simultaneous use of all SNPs in a random regression model is an alternative to overcome the overestimation of SNPs effects and excess of false positives. Hence, the present study was performed to identify causal single nucleotide polymorphisms (SNPs) associated with b...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2021-01-01
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| Series: | Italian Journal of Animal Science |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/1828051X.2021.1965920 |
| Summary: | Bayes Cπ methodology due to the simultaneous use of all SNPs in a random regression model is an alternative to overcome the overestimation of SNPs effects and excess of false positives. Hence, the present study was performed to identify causal single nucleotide polymorphisms (SNPs) associated with body weight (BW) and their pattern of significance over time from 2 to 8 weeks of age, in an F2 crossbred chicken population using Bayes Cπ methodology. Illumina 60 K SNP bead chip was used to genotype 312 F2 chicks. Sixteen SNPs distributed over 8 chromosomes had a Bayes Factor (BF) greater than 150 for BW in different ages. 14 different genes harbouring these SNPs (±250 kb), of which 12 were protein-encoding (DKK2, LEF1, RASGEF1C, FOXP1, LPCAT1, AKR1D1, GPR137C, EIF2AK3, ROR1, AKR1D1, LRFN5 and XPO7) and two were noncoding RNAs (LOC101751953 and LOC101751953). According to the obtained results, GGA1 and GGA4 were the most important chromosomes containing QTLs associated with observed traits. Different genetic regions were responsible for body weight in early and late ages. The various number of significant Bayes factors across different weeks of ages may indicate the artificial selection for market weight in a given age which has driven larger SNPs effects in intended weeks for desired market weight for the two groups.Highlights My research outputs resulted in discovering associated genes and pathways related to gain growth and body weight in chicken. The identified genes in this study can be used in poultry breeding programs. Therefore, this leads to reduced feed costs and increase revenue. |
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| ISSN: | 1594-4077 1828-051X |