Abstract
BackgroundIn a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were also associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine LAP3, NCAPG, and LCORL genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, with potential to identify functional variation.ResultsAnimals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the NCAPG-LCORL locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P ≤ 005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the LCORL gene locus remained significant for ADG (P ≤ 0.04).ConclusionsSeveral markers within the NCAPG-LCORL locus were significantly associated with feed intake and body weight gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle.
Highlights
In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle
A polymorphism in the NCAPG gene identified previously by Setoguchi et al [8] (p.I442M) was detected in our population of animals. In addition to this polymorphism, we identified a second non-synonymous alteration in NCAPG (p.L877M)
A 3 base pair deletion resulting in an in-frame deletion of a glutamic acid (p.E47del) and a non-synonymous alteration (p.D92E) were detected in leucine aminopeptidase 3 (LAP3) (Table 1)
Summary
In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (P ≤ 0.003) with average daily gain (ADG) and 3 of these were associated (P ≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. Feed intake and average daily gain are economically important phenotypes in beef cattle. Quantitative trait loci (QTL) for cattle growth traits such as birth weight, body length, carcass weight, and longissimus muscle area (LMA) have been detected on bovine chromosome 6 in several different populations of animals. Body length at birth and birth weight QTL were identified by Gutiérrez-Gil et al [2] at 38 and 39 Mb, respectively, in a Charolais × Holstein crossbred population. There is clear evidence that the region on BTA6 between 30 and 42 cM is involved in growth and size phenotypes across multiple breeds of cattle
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