Abstract
BackgroundGenetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. This paper presents a genome-wide association approach utilizing single nucleotide polymorphisms (SNP) in the Illumina BovineSNP50 BeadChip to seek genomic regions that potentially harbor genes or QTN underlying variation in carcass quality of beef cattle.This study used 747 genotyped animals, mainly crossbred, with phenotypes on twelve carcass quality traits, including hot carcass weight (HCW), back fat thickness (BF), Longissimus dorsi muscle area or ribeye area (REA), marbling scores (MRB), lean yield grade by Beef Improvement Federation formulae (BIFYLD), steak tenderness by Warner-Bratzler shear force 7-day post-mortem (LM7D) as well as body composition as determined by partial rib (IMPS 103) dissection presented as a percentage of total rib weight including body cavity fat (BDFR), lean (LNR), bone (BNR), intermuscular fat (INFR), subcutaneous fat (SQFR), and total fat (TLFR).ResultsAt the genome wide level false discovery rate (FDR < 10%), eight SNP were found significantly associated with HCW. Seven of these SNP were located on Bos taurus autosome (BTA) 6. At a less stringent significance level (P < 0.001), 520 SNP were found significantly associated with mostly individual traits (473 SNP), and multiple traits (47 SNP). Of these significant SNP, 48 were located on BTA6, and 22 of them were in association with hot carcass weight. There were 53 SNP associated with percentage of rib bone, and 12 of them were on BTA20. The rest of the significant SNP were scattered over other chromosomes. They accounted for 1.90 - 5.89% of the phenotypic variance of the traits. A region of approximately 4 Mbp long on BTA6 was found to be a potential area to harbor candidate genes influencing growth. One marker on BTA25 accounting for 2.67% of the variation in LM7D may be worth further investigation for the improvement of beef tenderness.ConclusionThis study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting carcass quality traits in beef cattle. It also revealed many SNP that acted pleiotropically to affect carcass quality. This knowledge is important in selecting subsets of SNP to improve the performance of beef cattle.
Highlights
Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers
Yield grade had strong positive genetic correlations to fat related traits (0.65 and 0.66, back fat thickness (BF) and marbling scores (MRB) respectively), and a slight negative correlation with ribeye area (REA) (−0.18), because yield grade is a function of BF, MRB and REA
Genetic correlations between shear force at 7 days of post-mortem aging and other traits varied from almost null to low. This suggests that selection for back fat thickness and yield grade may not affect beef tenderness; while selection to increase carcass weight or ribeye area will potentially increase shear force at 7 days, whereas an increase in marbling score will improve beef tenderness
Summary
Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. Real-time ultrasound imaging has been used on live animals to measure a number of traits, such as Longissimus dorsi muscle area, and backfat, it evaluates marbling through ultrasound intramuscular fat, and cannot measure tenderness. Selection programs that incorporate either subsets of markers on select regions of the genome, for instance markers for growth and feed efficiency, as well as carcass quality [5], or double-muscling DNA test [6], or a large number of markers covering the whole genome in genomic selection that has been reported to result in a 32% improvement in accuracy compared to parental average breeding values [7], have drawn the attention of both beef researchers and producers. American Angus Association has started incorporating genetic marker information from a 50,000 marker panel into their weekly carcass EPD evaluation program [8], American Simmental Association has applied marker assisted EPD for beef tenderness [9], and North American Limousin Foundation announced its commencement of genomic-enhanced EPDs as of December 2012 [10]
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