• Breed- and trait-specific associations define the genetic architecture of calving performance traits in cattle

      Purfield, Deirdre C; Evans, Ross D; Berry, Donagh; European Union; Science Foundation Ireland; 727213; 14/IA/2576); 16/RC/3835 (Oxford University Press (OUP), 2020-05-04)
      Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10−8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10−6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10−8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.
    • Feed and production efficiency of young crossbred beef cattle stratified on a terminal total merit index1

      Kelly, David N; Conroy, Stephen B; Murphy, Craig P; Sleator, Roy D; Berry, Donagh; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 17/S/235; 16/RC/3835 (Oxford University Press (OUP), 2020-07-01)
      Few studies have attempted to quantify the association between a terminal total merit index with phenotypic feed and production efficiency in beef cattle, particularly when feed efficiency is itself explicitly absent as a goal trait in the index. The objective of the present study was to quantify the differences in phenotypic performance for feed intake, feed efficiency, and carcass traits of crossbred bulls, steers, and heifers differing in a terminal total merit index. A validation population of 614 bulls, steers, and heifers that were evaluated for feed intake and efficiency in the same feedlot and subsequently slaughtered at the end of their test period was constructed. The Irish national genetic evaluations for a terminal index of calving performance, docility, feed intake, and carcass traits were undertaken with the phenotypic records of animals present in the validation population masked. The validation population animals were subsequently stratified into four groups, within sex, according to their terminal index value. Mixed models were used to quantify the association between terminal genetic merit and phenotypic performance; whether the associations differed by sex were also investigated. The regression coefficient of phenotypic feed intake, carcass weight, carcass conformation, or carcass fat on its respective estimated breeding values was 0.86 kg dry matter 0.91 kg, 1.01 units, and 1.29 units, respectively, which are close to the expectation of one. On average, cattle in the very high terminal index stratum had a 0.63 kg DM/d lower feed intake, a 25.05 kg heavier carcass, a 1.82 unit better carcass conformation (scale 1 to 15), and a 1.24 unit less carcass fat score (scale 1 to 15), relative to cattle in the very low terminal index stratum. Cattle of superior total genetic merit were also more feed efficient (i.e., had a lower energy conversion ratio, lower residual feed intake, and greater residual gain), had a greater proportion of their live-weight as carcass weight (i.e., better dressing percentage) and were slaughtered at a younger age relative to their inferior total genetic merit counterparts. This study provides validation of an all-encompassing total merit index and demonstrates the benefits of selection on a total merit index for feed and production efficiency, which should impart confidence among stakeholders in the contribution of genetic selection to simultaneous improvements in individual animal performance and efficiency.
    • On-farm net benefit of genotyping candidate female replacement cattle and sheep

      Newton, J.E.; Berry, Donagh; Science Foundation Ireland; Department of Agriculture, Food and the Marine; European Union; 16/RC/3835; 727213 (Elsevier BV, 2020-12-07)
      The net benefit from investing in any technology is a function of the cost of implementation and the expected return in revenue. The objective of the present study was to quantify, using deterministic equations, the net monetary benefit from investing in genotyping of commercial females. Three case studies were presented reflecting dairy cows, beef cows and ewes based on Irish population parameters; sensitivity analyses were also performed. Parameters considered in the sensitivity analyses included the accuracy of genomic evaluations, replacement rate, proportion of female selection candidates retained as replacements, the cost of genotyping, the sire parentage error rate and the age of the female when it first gave birth. Results were presented as an annualised monetary net benefit over the lifetime of an individual, after discounting for the timing of expressions. In the base scenarios, the net benefit was greatest for dairy, followed by beef and then sheep. The net benefit improved as the reliability of the genomic evaluations improved and, in fact, a negative net benefit of genotyping was less frequent when the reliability of the genomic evaluations was high. The impact of a 10% point increase in genomic reliability was, however, greatest in sheep, followed by beef and then dairy. The net benefit of genotyping female selection candidates reduced as replacement rate increased. As genotyping costs increased, the net benefit reduced irrespective of the percentage of selection candidates kept, the replacement rate or even the population considered. Nonetheless, the association between the genotyping cost and the net benefit of genotyping differed by the percentage of selection candidates kept. Across all replacement rates evaluated, retaining 25% of the selection candidates resulted in the greatest net benefit when genotyping cost was low but the lowest net benefit when genotyping cost was high. Genotyping breakeven cost was non-linearly associated with the percentage of selection candidates retained, reaching a maximum when 50% of selection candidates were retained, irrespective of replacement rate, genomic reliability or the population. The genotyping breakeven cost was also non-linearly associated with replacement rate. The approaches outlined within provide the back-end framework for a decision support tool to quantify the net benefit of genotyping, once parameterised by the relevant population metrics.
    • Phenotypic relationships between milk protein percentage and reproductive performance in three strains of Holstein Friesian cows in Ireland

      Yang, L; Lopez-Villalobos, N; Berry, Donagh; Parkinson, T (2021-04-11)
      The relationship between milk protein percentage and fertility in seasonal calving, dairy cattle in Ireland was quantified using a total of 584 lactation records, collected over a five-year period from experiments comparing three strains of Holstein-Friesian cows under three different feeding systems. Logistic regression analyses showed that increased protein percentage during early lactation was positively associated with the probability of a cow becoming pregnant to its first service (P <0.05). Similarly, protein percentage during the lactation had a positive (P <0.01) association with overall pregnancy rate. The results suggest that negative energy balance in early lactation or during the whole lactation causes a shortage of glucose to the udder, this restricts the synthesis of milk protein in the udder and causes a lower milk protein percentage. During negative energy balance there is also a concurrent reduction of IGF-І, LH and oestradiol secretion, which consequently delay ovarian follicular development, and hence impairs reproductive performance. In conclusion, cows with higher milk protein percentage during early lactation have a greater likelihood of becoming pregnant earlier in the breeding season, and have a higher conception rate.
    • The use of subjectively assessed muscular and skeletal traits on live cattle to aid in differentiation between animal genetically divergent in carcass kill out metrics

      Berry, Donagh; Coyne, J. M.; Doyle, J.; Evans, R. D.; Science Foundation Ireland; Department of Agriculture, Food and the Marine; 16/RC/3835 (Elsevier BV, 2020-04)
      Subjective linear scoring of live beef cattle is routinely undertaken as part of breed society regulations or as part of national breeding programs; linear scores describe biological extremes of animals for a range of different traits reflecting muscularity, skeletal development, and functionality. The objective of the present study was to quantify the usefulness of these linear scores measured on live growing beef cattle to predict genetic merit for kill out (KO) percent and the difference between live-weight at slaughter and carcass weight (herein known as KO difference). The data used consisted of linear scores for 16 traits on up to 67,167 cattle as well as KO information on 31,827 cattle; 1,166 animals had records for both sets of traits. Variance components were estimated using univariate animal linear mixed models while covariance components between the linear scores and the KO traits were estimated using a series of bivariate sire linear mixed models. In an additional series of analyses, the KO metrics were adjusted phenotypically for differences in live-weight at slaughter through its inclusion as a covariate in the statistical model. Heritability estimates of the linear scores varied from 0.06 (width at pins) to 0.37 (development of hind-quarter); the heritability of KO percent and KO difference were estimated to be 0.53 and 0.37, respectively. Both the phenotypic and genetic correlations between the muscular type traits and KO percent were moderately positive, albeit the genetic correlations were stronger. The phenotypic correlations ranged from 0.27 (development of inner thigh) to 0.37 (development of hind quarter) while the genetic correlations varied from 0.40 (development of inner thigh and development of loin) to 0.60 (development of hind quarter); in all cases, adjusting for differences in live-weight at slaughter had minimal impact on the estimated correlations. With the exception of depth of rump, the phenotypic and genetic correlations between the skeletal traits with KO percent were all close to zero (≤|0.24|) irrespective of whether or not differences in live-weight at slaughter were accounted for. While the genetic correlations between the muscular traits and KO difference not adjusted for differences in live-weight at slaughter were all close to zero (≤|0.30|), the correlations strengthened (≥|0.39|) once adjusted to a common live-weight at slaughter. The opposite was true for the genetic correlations between the skeletal traits and KO difference. In all, the results suggest that the muscular linear scores assessed subjectively on live animals at, on average, 10 months of age are a useful genetic (and phenotypic) predictor of KO percent at, on average, 21 months of age, but also the quantity of live-weight that does not end up as carcass, once adjusted to a common live-weight.