Discovery of novel genetic networks associated with 19 economically important traits in beef cattle

Abstract

Quantitative or complex traits are determined by the combined effects of many loci, and are affected by genetic networks or molecular pathways. In the present study, we genotyped a total of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a Wagyu x Limousin reference population. Two hundred forty six F2 animals were measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280 single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed from the analysis due to the small number of animals (≤ 9) in one genotype group or absence of one genotype among three genotypes. The remaining 94 single-trait associations were then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and overdominant effects. All significant markers and their QTMs associated with each of these 19 traits were involved in a linear regression model analysis, which confirmed single-gene associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high correlations between predicted and actual values of performance, thus providing evidence that the classical Mendelian principles of inheritance can be applied in understanding genetic complexity of complex phenotypes. Our present study also indicated that carcass, eating quality and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted selection for improvement of one category of these traits would not interfere with improvement of another.

A single nucleotide polymorphism possibly associated with fat deposition is methylated in the bovine TFAM promoter

“…H1299 cell line was selected as a highly proliferative cell line, which is widely used in research due to its high rate of transgene expression, whereas HEK293 cell line was selected because of its propensity for transfection. In the Wagyu × Limousin F 2 population, we found that C/C/C and A/T/T are the two major haplotypes (Jiang et al, 2009). In general, the former haplotype had lower promoter activity compared to the latter haplotype and the difference among cell lines was more pronounced in the A/T/T haplotype.…”

Complicated Relationships: A Review of Biological Interaction Networks and Pathways in Animal Science

“…Jiang et al [36] described a candidate gene association and gene network analysis for 19 traits related to carcass quality and eating quality in Wagyu 9 Limousin crosses. These traits included phenotypic measurements for carcass weight, carcass rib eye area, subcutaneous fat, pelvic and heart fat, and marbling; and taste panel measurements for tenderness, juiciness, and flavor.…”

Genome wide association study on beef production traits in Marchigiana cattle breed

“…Genomewide association studies (GWAS) represent a first step towards the understanding of molecular and cellular mechanisms underlying phenotypic expression of complex traits (Jiang et al . ).…”

“…Recent GWAS studies have detected associations between SNPs and beef traits, suggesting myostatin , DGAT1 and leptin receptor as candidate genes (Jiang et al . ).…”