Matthew Kelly

Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle

Linkage disequilibrium (LD) and the persistence of its phase across populations are important for genomic selection as well as fine scale mapping of quantitative trait loci (QTL). However, knowledge of LD in beef cattle, as well as the persistence of LD phase between crossbreds (C) and purebreds, is limited. The objective of this study was to understand the patterns of LD in Angus (AN), Charolais (CH), and C beef cattle based on 31,073, 32,088, and 33,286 SNP in each population, respectively. Amount of LD decreased rapidly from 0.29 to 0.23 to 0.19 in AN, 0.22 to 0.16 to 0.12 in CH, 0.21 to 0.15 to 0.11 in C, when the distance range between markers changed from 0–30 kb to 30–70 kb and then to 70–100 kb, respectively. Breeds and chromosomes had significant effects (P < 0.001) on LD decay. There was significant interaction between breeds and chromosomes (P < 0.001). Correlations of LD phase were high between C and AN (0.84), C and CH (0.81), as well as between AN and CH (0.77) for distances less than or equal to 70 kb. These dropped when the distance increased. Estimated effective population sizes for AN and CH were 207 and 285, respectively, for 10 generations ago. Given a useful LD of at least 0.3 between pairs of SNPs, the LD phase between any pair of the three breed groups was highly persistent. The current SNP density would allow the capture of approximately 49% of useful LD between SNP and marker QTL in AN, and 38% in CH. A higher density SNP panel or redesign of the current panel is needed to achieve more of useful LD for the purpose of genomic selection beef cattle.

Genome-wide association analyses for carcass quality in crossbred beef cattle.

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.

Heritability of beef tenderness at different aging times and across breed comparisons

Zwambag, A., Kelly, M., Schenkel, F., Mandell, I., Wilton, J. and Miller, S. 2013. Heritability of beef tenderness at different aging times and across breed comparisons. Can. J. Anim. Sci. 93: 307-312. The heritability of shear force at 7, 14 and 21 d was estimated from a crossbred population of beef cattle. The population consisted of approximately 1400 crossbred cattle that were predominantly the offspring of Angus, Simmental, Gelbvieh and Piedmontese sires bred to predominantly Angus and Simmental females. Significant breed effects on tenderness were found within each aging time and no effect of heterosis was detected. The heritability of shear force declined from 0.194 to 0.048 as aging time increased from 7 to 21 d, highlighting the effectiveness of aging as a tool to improve tenderness. The repeatability of shear force was also found to be moderate (0.53). However, as energy prices increase it may be attractive to reduce aging times, thus breeding animals that are more tender at shorter aging times would be beneficial. The heritability of tenderness found at shorter aging times would indicate that improvement in this trait would be possible within a population where phenotypes are available.

Effect of crop residues in haylage-based rations on the performance of pregnant beef cows

Seventy-one individually fed multiparous, pregnant crossbred beef cows [body weight (BW) ± SD; 730 ± 77.9 kg] were used to examine the effects of including crop residues in alfalfa/grass haylage-based rations on BW gain, fat deposition/loss and plasma metabolites. The haylage control ration (CON; n = 23) was modified to include either 40% (dry matter basis) wheat straw (WS; n = 24) or 40% corn stalklage (CS; n = 24). Cows were blocked by calving date and randomly assigned to each treatment and fed for 82 d leading up to the earliest calving date. On days 1, 40, and 82, cows were weighed, ultrasounded to measure subcutaneous backfat (BF) over the ribs, body condition scored (BCS) and plasma was collected. Calves from cows fed WS had greater (P = 0.02 ) weaning weights than cows fed CS, but did not differ (P = 0.23) from CON. CS cows had the lowest ADG (P < 0.03), lost the most body condition (P < 0.04), and had the lowest dry matter intake (P ≤ 0.001). These data indicate that diets containing crop residue...