Prospecting candidate SNPs for backfat in Canchim beef cattle

Abstract

ABSTRACT. Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.

A SNP in ASAP1 gene is associated with meat quality and production traits in Nelore breed

“…We have to considerate that the SNP effect on trait variation could be biased by the small sample size analyzed, so including more animals in these analyses can help to confirm the results obtained here. Although this gene is located in a QTL for backfat thickness and had been associated with this trait in other studies (Veneroni et al, 2010), association between this SNP in ASAP1 gene and BFT was not confirmed in the Nelore population used in the present study. For REA a P-value near to the significance level (P≤ 0.01) after Bonferroni correction was observed.…”

“…The SNP in intron 13 of the ASAP1 gene was genotyped by an adapted ARMS methodology described by Veneroni et al (2010).…”

Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

“…In attempts to improve meat quality, previous studies have focused on the identification of candidate markers associated with meat quality traits, as well as backfat thickness, in Canchim and other Bos indicus × Bos taurus crosses in Brazil [20-24]. However, these have had limited success, particularly in response to markers on the DDEF1 and LEP genes [20,23].…”

Association of CSSM066 and ILSTS011 microsatellite markers and thyroglobulin gene SNP with backfat in Canchim cattle

“…The development and differentiation enhancing factor 1 gene (DDEF1) located at 9.7 Mb on BTA14 is related to adipogenesis (King et al, 1999). King et al (1999) purified and cloned the DDEF1 protein of bovine brain cells and observed that the expression of this protein resulted in the differentiation of fibroblasts in adipocytes in vitro and Veneroni et al (2010) found a effect (p ≤ 0.05) of allele substitution of an SNP in the DDEF1 gene on backfat thickness in Canchim cattle. Several works reported the existence of a QTL for backfat thickness in centromeric region of BTA14 (Moore et al, 2003;Casas et al, 2000) and the present study found association of this trait with the CSSM066 and ILSTS011 markers, but not with Tg5.…”