Discovery and characterization of functional modules associated with body weight in broilers

Abstract

Aim of the present study was to investigate whether body weight (BW) in broilers is associated with functional modular genes. To this end, first a GWAS for BW was conducted using 6,598 broilers and the high density SNP array. The next step was to search for positional candidate genes and QTLs within strong LD genomic regions around the significant SNPs. Using all positional candidate genes, a network was then constructed and community structure analysis was performed. Finally, functional enrichment analysis was applied to infer the functional relevance of modular genes. A total number of 645 positional candidate genes were identified in strong LD genomic regions around 11 genome-wide significant markers. 428 of the positional candidate genes were located within growth related QTLs. Community structure analysis detected 5 modules while functional enrichment analysis showed that 52 modular genes participated in developmental processes such as skeletal system development. An additional number of 14 modular genes ( GABRG1, NGF, APOBEC2, STAT5B, STAT3, SMAD4, MED1, CACNB1, SLAIN2, LEMD2, ZC3H18, TMEM132D, FRYL and SGCB ) were also identified as related to body weight. Taken together, current results suggested a total number of 66 genes as most plausible functional candidates for the trait examined.

A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens

“…The association signal on GGA27 at ~ 4.96 Mb) (a gene dense region) was located near the STAT3 (signal transducer and activator of transcription 3; ~ 4.90-4.91 Mb) gene, and more precisely is within an intron of the ATP6V0A1 (ATPase, H+ transporting, lysosomal V0 subunit a1; ~ 4.93-4.96 Mb) gene (Table 3). The association between the STAT3/STAT5B locus and BW in chicken confirms the findings of [13]. We also detected several other genes related to reproduction.…”

“…In a recent GWAS on a F2 chicken population, TXNRD1 and IGF1 have been associated with BW35 and BW41, respectively [52]. Moreover, the IGFBP4 (insulin like growth factor binding protein 4) gene has been identified as a candidate gene for broiler BW in a study that analysed a subset of the population used in our work [13]. This gene is in close proximity (~ 0.5 Mb) to the signal we detected on GGA27.…”

“…Several GWAS have been conducted in broilers for a variety of carcass and growth traits, using commercial lines [9,13], birds from experimental stations [7,37,40], or field data [41], and a variety of SNP array densities that ranged from ~ 44,000 [7][8][9] to 470,486 [41]. In spite of this, previous GWAS that scanned the entire genome, were still limited in terms of statistical power because the size of the samples was usually only a few hundreds of birds.…”

“…Furthermore, the populations used were often F 2 or advanced inter-crosses between lines of chicken that have been selected for egg laying, which are relatively slow growing, and fast growing broiler lines [4,10,11]. Relatively few publications on GWAS of body weight are available for commercially relevant lines [9,12,13].…”

Influence of meat and bone meal, phytase, and antibiotics on broiler chickens challenged with subclinical necrotic enteritis: 2. intestinal permeability, organ weights, hematology, intestinal morphology, and jejunal gene expression

“…It also appeared that phytase supplementation at a lower concentration in the absence of AB upregulated the expression of CACNB1 and TPCN3. The CACNB1 has also been reported to be associated with growth ( Chen et al., 2011 , Tarsani et al., 2019 ).…”