Activin receptor 2A and activin receptor 2B genes in chicken: effect on carcass traits

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach

BACKGROUND

Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations.

RESULTS

Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1-4, 6-7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens.

CONCLUSIONS

The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.

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

Molecular breeding exploiting candidate genes is burgeoning reproductive approach to improve growth traits in poultry. The activin type IIB receptor (ACTRIIB) is a negative growth regulator, modulating action of many muscle growth regulators. PCR-single-strand conformation polymorphism was employed to unravel polymorphism in promoter region of the ACTRIIB gene and delineate its association with growth traits in Aseel and control broiler (CB). Analysis of 5' promoter region (1122bp) of ACTRIIB gene identified five SNPs, that is g. [56 G > C (SNP1), 352A > C (SNP2), 580G > A (SNP3), 625C > T (SNP4) and 962C > T (SNP5)] at SMAD, paired box 7 homeodomain binding motif, GC box and bHLH-PAS type transcription factors in CB and Aseel. CB had significantly higher body weight (BW) and average daily gain (ADG) at all SNP sites, except at SNP 1. The haplotype construction resulted 8 haplotypes in CB and Aseel population. The BW and ADG differed significantly (p < .05) at all ages in CB and Aseel. The diplotypes H1H8 and H1H4 manifested higher BW and ADG, while diplotypes H3H8 and H3H7 displayed BW and ADG at each age in both lines (p < .05). Aseel exhibited higher expression of ACTRIIB gene than CB by 70.17, 4.83, 1.41, 2.38, 5.13, 1.20, 2.90, 6.53 and 11.75 times for h1h2, h1h3, h1h4, h1h6, h1h7, h1h8 h3h4, h3h7 and h3h8, respectively. The H3H8 and H3H7 diplotypes exhibited higher level of mRNA and protein than H1H8 and H1H4. The regulatory upstream region of ACTRIIB gene demonstrates high degree of genetic diversity and can be harnessed as potential marker in genetic selection programmes for increasing meat production.

Gene Expression and Polymorphism of Myostatin Gene and its Association with Growth Traits in Chicken

Myostatin is a member of TGF-β super family and is directly involved in regulation of body growth through limiting muscular growth. A study was carried out in three chicken lines to identify the polymorphism in the coding region of the myostatin gene through SSCP and DNA sequencing. A total of 12 haplotypes were observed in myostatin coding region of chicken. Significant associations between haplogroups with body weight at day 1, 14, 28, and 42 days, and carcass traits at 42 days were observed across the lines. It is concluded that the coding region of myostatin gene was polymorphic, with varied levels of expression among lines and had significant effects on growth traits. The expression of MSTN gene varied during embryonic and post hatch development stage.