Overview of Genomic Insights into Chicken Growth Traits Based on Genome-Wide Association Study and microRNA Regulation

Abstract

Over the two past decades, a significant number of studies have observed animal growth traits to examine animal genetic mechanisms due to their ease of measurement and high heritability. Chicken which has a significant impact on fundamental biology is a major source of protein worldwide, making it an ideal model for examining animal growth trait development. The genetic mechanisms of chicken growth traits have been studied using quantitative trait loci mapping through genome-scan and candidate gene approaches, genome-wide association studies (GWAS), comparative genomic strategies, microRNA (miRNA) regulation of growth development analysis, and epigenomic analysis. This review focuses on chicken GWAS and miRNA regulation of growth traits. Several recently published GWAS reports showed that most genome-wide significant single nucleotide polymorphisms are located on chromosomes 1 and 4 in chickens. Chicken growth, particularly skeletal muscle growth and development, is greatly regulated by miRNA. Using dwarf and normal chickens, let-7b was found to be involved in determining chicken dwarf phenotypes by regulating growth hormone receptor gene expression.

Keywords: Chicken; Genome-wide association study (GWAS); Growth traits; Quantitative trait loci (QTL); Single nucleotide polymorphisms (SNPs).; microRNA (miRNA) regulation.

Fig. (1)

MicroRNAs regulating myogenesis via PI3K/Akt signaling. This schematic diagram is a reference for [60-63]. The dash arrows indicates the favorable pathway has not been well clarified. IGF-1: insulin-like growth factor 1; IGF-1R: insulin-like growth factor 1 receptor; AKT^P: phospho-AKT; Foxo1a: forkhead box O1; Foxo3a: forkhead box O3; MEF2: myocyte enhancer factor-2; MRTF-A: myocardin-related transcription factor-A; SRF: serum response factor; PTEN: phosphatase and tensin homolog; PI3K: phosphoinositide-3-kinase; MyoD: myogenic differentiation 1.

Fig. (2)

Differentially expressed miRNAs in chickens with different growth performance and target validation. A: Expression pattern of 23 miRNAs in breast muscles of White Recessive Rock (WRR) and Qingyuan Partridge chickens (QYP) based on microarray experiments. The bars represent the fold change in WRR/QYP. B: Relative abundance of 22 miRNAs in the livers of normal and RSS chickens based on Solexa sequencing data. The bars represent the fold change of RSS/normal. C: Schema of gga-miR-221 binding sites in chicken wide-type and mutated TAB2 (TGF-beta activated kinase 1/MAP3K7 binding protein 2) 3'-UTR sequence. Seed binding sites and mutated bases are highlighted in red. Target prediction was performed using TargetScan 5.0 software (http://targetscan.org/). D: To verify whether gga-miR-221 targets TAB2, a luciferase reporter assay was conducted. A gga-miR-221 overexpression plasmid was constructed using pcDNA3.1 (Promega, Fitchburg, WI, USA). Wild-type (WT) or mutated TAB2 3'-UTR sequence (MUT) was cloned into the pmirGLO luciferase reporter vector at downstream of Renilla luciferase, the internal Firefly luciferase gene was used to normalize for transfection efficiency. DF-1 cells were used for transfection, and 600 ng of the gga-miR-221 overexpression plasmid was co-transfected with 200 ng of WT or MUT reporter plasmid (221-WT/-MUT). A parallel inhibition or negative control experiment was conducted using30 ng IN or NC vector plasmid cotransfected with 200 ng of WT reporter plasmid (221-IN/-NC). Dual-luciferase assays were conducted in triplicate in 24-well plates. Cells were lysed and assayed for luciferase activity 36h after transfection. Error bars represent the standard error of three independent experiments per group.