Association of predicted deleterious single nucleotide polymorphisms with carcass traits in meat-type chickens

Abstract

Association of predicted deleterious single nucleotide polymorphisms with carcass traits 44 in meat-type chickens 45 46 Phone number: +55 19 3429 4434 54 55 ABSTRACT 56 57In previous studies, we used genome wide association (GWAS) to identify 58 quantitative trait loci (QTL) associated with weight and yield of abdominal fat, 59 drumstick, thigh and breast traits in chickens. However, this methodology assumes that 60 the studied variants are in linkage disequilibrium with the causal mutation and 61 consequently do not identify it. In an attempt to identify causal mutations in candidate 62 genes for carcass traits in broilers, we selected 20 predicted deleterious SNPs within 63QTLs for association analysis. Additive, dominance and allele substitution effects were 64 tested. From the 20 SNPs analyzed, we identified six SNPs with significant association 65 (p-value <0.05) with carcass traits, and three are highlighted here. The SNP 66 rs736010549 was associated with drumstick weight and yield with significant additive 67 and dominance effects. The SNP rs739508259 was associated with thigh weight and 68 yield, and with significant additive and allele substitution effects. The SNP 69 rs313532967 was associated with breast weight and yield. The three SNPs that were 70 associated with carcass traits (rs736010549, rs739508259 and rs313532967) are 71 respectively located in the coding regions of the WDR77, VWA8 and BARL genes. These 72 genes are involved in biological processes such as steroid hormone signaling pathway, 73 estrogen binding, and regulation of cell proliferation. Our strategy allowed the 74 identification of putative casual mutations associated with muscle growth. 75 76 BACKGROUND 77 Chicken is an important source of protein for human nutrition and a model system in 78 growth and developmental biology (Ellegren 2005). The complete genome sequence of 79 a Red Jungle Fowl female (Gallus gallus gallus), that is considered the ancestor of 80 domestic chicken (G. g. domesticus) (Abplanalp 1992; Cassoli 2007; Dodgson et al. 81 2011), was completed in 2004 (Hillier et al. 2004) and opened the opportunity to 82 explore the molecular control of complex phenotypes such as growth and muscle 83 deposition among other traits. 84 High throughput sequencing of several chicken lines allowed the identification 85 of millions of single nucleotide polymorphisms (SNPs) in the chicken genome (Rubin et 86 al. 2010; Boschiero et al. 2018) and develop high density SNP panels (Kranis et al. 87 2013). SNPs are the most common and frequent DNA variant, with approximately 5 88 SNPs per kilobase (kb) in chicken (Rubin et al. 2010). When located in coding and 89 regulatory regions of genes, they may affect traits of economic interest in animal models 90 and livestock species (Roux et al. 2014).91High-density SNP panels were used in genome wide association studies 92 (GWAS) to identify genomic regions associated with quantitative traits such as body 93

Genetic polymorphism in core promoter sequence of ACTRIIB gene and association analysis with growth traits in chicken

“…Likewise, Bhattacharya et al, () found that exons 2 and 4 of activin receptor 2A and activin receptors 2B were polymorphic and strongly associated with certain carcass traits in chicken population. Congruent with our findings, earlier studies reported significant association between single nucleotide polymorphisms and growth traits in innumerable genes among various chicken breeds (Bhattacharya, Chatterjee, Dange, & Bhanja, ; Li et al, ; Trevisoli et al, ).…”