S.R. Davis

Accuracy of genomic predictions of residual feed intake and 250-day body weight in growing heifers using 625,000 single nucleotide polymorphism markers

Feed makes up a large proportion of variable costs in dairying. For this reason, selection for traits associated with feed conversion efficiency should lead to greater profitability of dairying. Residual feed intake (RFI) is the difference between actual and predicted feed intakes and is a useful selection criterion for greater feed efficiency. However, measuring individual feed intakes on a large scale is prohibitively expensive. A panel of DNA markers explaining genetic variation in this trait would enable cost-effective genomic selection for this trait. With the aim of enabling genomic selection for RFI, we used data from almost 2,000 heifers measured for growth rate and feed intake in Australia (AU) and New Zealand (NZ) genotyped for 625,000 single nucleotide polymorphism (SNP) markers. Substantial variation in RFI and 250-d body weight (BW250) was demonstrated. Heritabilities of RFI and BW250 estimated using genomic relationships among the heifers were 0.22 and 0.28 in AU heifers and 0.38 and 0.44 in NZ heifers, respectively. Genomic breeding values for RFI and BW250 were derived using genomic BLUP and 2 bayesian methods (BayesA, BayesMulti). The accuracies of genomic breeding values for RFI were evaluated using cross-validation. When 624,930 SNP were used to derive the prediction equation, the accuracies averaged 0.37 and 0.31 for RFI in AU and NZ validation data sets, respectively, and 0.40 and 0.25 for BW250 in AU and NZ, respectively. The greatest advantage of using the full 624,930 SNP over a reduced panel of 36,673 SNP (the widely used BovineSNP50 array) was when the reference population included only animals from either the AU or the NZ experiment. Finally, the bayesian methods were also used for quantitative trait loci detection. On chromosome 14 at around 25 Mb, several SNP closest to PLAG1 (a gene believed to affect stature in humans and cattle) had an effect on BW250 in both AU and NZ populations. In addition, 8 SNP with large effects on RFI were located on chromosome 14 at around 35.7 Mb. These SNP may be associated with the gene NCOA2, which has a role in controlling energy metabolism.

Genetic variation in PLAG1 associates with early life body weight and peripubertal weight and growth in Bos taurus

Variation at the pleiomorphic adenoma gene 1 (PLAG1) locus has recently been implicated in the regulation of stature and weight in Bos taurus. Using a population of 942 outbred Holstein-Friesian dairy calves, we report confirmation of this effect, demonstrating strong association of early life body weight with PLAG1 genotype. Peripubertal body weight and growth rate were also significantly associated with PLAG1 genotype. Growth rate per kilogram of body weight, daily feed intake, gross feed efficiency and residual feed intake were not significantly associated with PLAG1 genotype. This study supports the status of PLAG1 as a key regulator of mammalian growth. Further, the data indicate the utility of PLAG1 polymorphisms for the selection of animals to achieve enhanced weight gain or conversely to aid the selection of animals with lower mature body weight and thus lower maintenance energy requirements.

Effects of reduced frequency of milk removal on gene expression in the bovine mammary gland

Regulation of milk synthesis and secretion is controlled mostly through local (intramammary) mechanisms. To gain insight into the molecular pathways comprising this response, an analysis of mammary gene expression was conducted in 12 lactating cows shifted from twice daily to once daily milking. Tissues were sampled by biopsy from adjacent mammary quarters of these animals during the two milking frequencies, allowing changes in gene expression to be assessed within each animal. Using bovine-specific, oligonucleotide arrays representing 21,495 unique transcripts, a range of differentially expressed genes were found as a result of less frequent milk removal, constituting transcripts and pathways related to apoptotic signaling (NF-kappaB, JUN, ATF3, IGFBP5, TNFSF12A) mechanical stress and epithelial tight junction synthesis (CYR61, CTGF, THBS1, CLDN4, CLDN8), and downregulated milk synthesis (LALBA, B4GALT1, UGP2, CSN2, GPAM, LPL). Quantitative real-time PCR was used to assess the expression of 13 genes in the study, and all 13 of these were correlated (P < 0.05) with values derived from array analysis. It can be concluded that the physiological changes that occur in the bovine mammary gland as a result of reduced milk removal frequency likely comprise the earliest stages of the involution response and that mechano-signal transduction cascades associated with udder distension may play a role in triggering these events.

Holstein-Friesian calves selected for divergence in residual feed intake during growth exhibited significant but reduced residual feed intake divergence in their first lactation

Residual feed intake (RFI), as a measure of feed conversion during growth, was estimated for around 2,000 growing Holstein-Friesian heifer calves aged 6 to 9 mo in New Zealand and Australia, and individuals from the most and least efficient deciles (low and high RFI phenotypes) were retained. These animals (78 New Zealand cows, 105 Australian cows) were reevaluated during their first lactation to determine if divergence for RFI observed during growth was maintained during lactation. Mean daily body weight (BW) gain during assessment as calves had been 0.86 and 1.15 kg for the respective countries, and the divergence in RFI between most and least efficient deciles for growth was 21% (1.39 and 1.42 kg of dry matter, for New Zealand and Australia, respectively). At the commencement of evaluation during lactation, the cows were aged 26 to 29 mo. All were fed alfalfa and grass cubes; it was the sole diet in New Zealand, whereas 6 kg of crushed wheat/d was also fed in Australia. Measurements of RFI during lactation occurred for 34 to 37 d with measurements of milk production (daily), milk composition (2 to 3 times per week), BW and BW change (1 to 3 times per week), as well as body condition score (BCS). Daily milk production averaged 13.8 kg for New Zealand cows and 20.0 kg in Australia. No statistically significant differences were observed between calf RFI decile groups for dry matter intake, milk production, BW change, or BCS; however a significant difference was noted between groups for lactating RFI. Residual feed intake was about 3% lower for lactating cows identified as most efficient as growing calves, and no negative effects on production were observed. These results support the hypothesis that calves divergent for RFI during growth are also divergent for RFI when lactating. The causes for this reduced divergence need to be investigated to ensure that genetic selection programs based on low RFI (better efficiency) are robust.

Measuring residual feed intake in dairy heifers fed an alfalfa (Medicago sativa) cube diet

Selection for divergence between individuals for efficiency of feed utilization (residual feed intake, RFI) has widespread application in the beef industry and is usually undertaken when animals are fed diets based on silages with grain. The objective of this research was to develop a feeding system (using Gallagher, Hamilton, New Zealand, electronics) to measure RFI for growth in Holstein-Friesian heifers (aged 5-9 mo), and identify divergent individuals to be tested for RFI during lactation. A dry forage diet (alfalfa cubes) was fed because intakes could be measured accurately, and the New Zealand dairy industry (4.4 million milking cows in lactation) relies heavily on forage feeding. The evaluation was undertaken over 3 yr with 1,052 animals fed in a facility for 7 wk, and weighed 3 times weekly. The mean age at the start of measurements was 215 d, body weight (BW) 189 kg, and mean daily dry matter intakes averaged 6.7 kg. Body weight gain (all animals) averaged 0.88 kg/d. The RFI was determined as the residuals from the regression of mean intake on mean BW(0.75) and daily BW gain of individuals. Actual and fitted intakes were strongly related (R(2) = 0.82). In terms of gross efficiency (feed intake/BW gain), RFI+year explained 43% of the variation, BW gain+year explained 66%, and RFI+BW gain+year explained 79% of the variation (all P<0.001). Daily BW gains (kg) of the most and least efficient 10% averaged (± standard deviation) 0.88 ± 0.15 and 0.88 ± 0.12 (P = 0.568), respectively, and the divergence between mean intakes was 1.46 kg of dry matter/d. The most and least efficient animals will be tested for RFI during lactation and genetic markers will be identified for the trait.

Genetic parameters for milk components including lactose from test day records in the New Zealand dairy herd

There are currently few published estimates of genetic parameters for lactose yield or lactose percentage for dairy cows. Recent trends in milk standardisation for whole milk powder have resulted in whole milk being standardised with the ratio of protein to protein-plus-lactose of at least 0.39. Currently whole milk powder produced from New Zealand milk has a protein to protein-plus-lactose ratio of 0.43, thus requiring additional lactose to be imported to maximise the return from the current product portfolio. Estimates of genetic parameters were obtained using 15,366 test day records from 4378 first-lactation cows in the Livestock Improvement Corporation sire proving scheme in the 2011–12 dairy season, distributed across 70 herds. These data included milk, fat, protein and lactose yields; fat, protein and lactose percentages; somatic cell count; days in milk; and the protein to fat ratio and protein to protein-plus-lactose ratio. Mean milk yield was 13.8 L/day, containing 5.16% fat, 3.93% protein and 5.12% lactose. Heritability estimates were 0.22, 0.35, 0.32 and 0.25 for milk yield, fat, protein and lactose percentages, respectively, which were lower than those reported in the literature but enough to allow for selection of lactose percentage.

Non‐replication of genome‐wide‐based associations of efficient food conversion in dairy cows

Animal growth relative to food energy input is of key importance to agricultural production. Several recent studies highlighted genetic markers associated with food conversion efficiency in beef cattle, and there is now a requirement to validate these associations in additional populations and to assess their potential utility for selecting animals with enhanced food-use efficiency. The current analysis tested a population of dairy cattle using 138 DNA markers previously associated with food intake and growth in a whole-genome association analysis of beef animals. Although seven markers showed point-wise significance at P < 0.05, none of the single-nucleotide polymorphisms tested were significantly associated with food conversion efficiency after correction for multiple testing. These data do not support the involvement of this subset of previously implicated markers in the food conversion efficiency of the physiologically distinct New Zealand Holstein-Friesian dairy breed.

Milk production of Holstein-Friesian, Jersey and crossbred cows milked once-a-day or twice-a-day in New Zealand

ABSTRACT The objective of this study was to compare Holstein-Friesian (F), Jersey (J) and crossbred (F × J) cows milked once-a-day (OAD) or twice-a-day (TAD) in New Zealand for milk, fat and protein yield, lactation persistency and average somatic cell score (SCS). Data consisted of 223,149 herd-test records (89,297 and 133,852 OAD and TAD, respectively) from 11,848 F; 11,677 J and 27,720 F × J spring-calving cows between 2008 and 2012. Compared to TAD systems, cows milked OAD yielded 722, 28.0 and 22.2 kg less milk, fat and protein, respectively. Crossbred and J cows were less affected than F cows by OAD milking with a reduction in milk yield traits of ≤ 19.0%, while in F cows the reduction ranged between 19%–25%. Cows milked OAD had higher SCS than cows milked TAD (6.20 vs. 6.08). The greatest SCS difference in OAD and TAD systems was in first-lactation cows (6.40 vs. 6.02). Persistency of production traits was greater in F and F × J cows milked OAD than in F and F × J cows milked TAD, but J cows had similar milk and protein persistency in both systems. Overall, cows milked OAD had greater persistency than cows milked TAD (79%–90% vs. 76%–85%). These results show that, in commercial herds, the relative difference in production traits between OAD and TAD systems was smaller than those reported in experimental trials.

Detection and assessment of copy number variation using PacBio long read and Illumina sequencing in New Zealand dairy cattle

Single nucleotide polymorphisms have been the DNA variant of choice for genomic prediction, largely because of the ease of single nucleotide polymorphism genotype collection. In contrast, structural variants (SV), which include copy number variants (CNV), translocations, insertions, and inversions, have eluded easy detection and characterization, particularly in nonhuman species. However, evidence increasingly shows that SV not only contribute a substantial proportion of genetic variation but also have significant influence on phenotypes. Here we present the discovery of CNV in a prominent New Zealand dairy bull using long-read PacBio (Pacific Biosciences, Menlo Park, CA) sequencing technology and the Sniffles SV discovery tool (version 0.0.1; https://github.com/fritzsedlazeck/Sniffles). The CNV identified from long reads were compared with CNV discovered in the same bull from Illumina sequencing using CNVnator (read depth-based tool; Illumina Inc., San Diego, CA) as a means of validation. Subsequently, further validation was undertaken using whole-genome Illumina sequencing of 556 cattle representing the wider New Zealand dairy cattle population. Very limited overlap was observed in CNV discovered from the 2 sequencing platforms, in part because of the differences in size of CNV detected. Only a few CNV were therefore able to be validated using this approach. However, the ability to use CNVnator to genotype the 557 cattle for copy number across all regions identified as putative CNV allowed a genome-wide assessment of transmission level of copy number based on pedigree. The more highly transmissible a putative CNV region was observed to be, the more likely the distribution of copy number was multimodal across the 557 sequenced animals. Furthermore, visual assessment of highly transmissible CNV regions provided evidence supporting the presence of CNV across the sequenced animals. This transmission-based approach was able to confirm a subset of CNV that segregates in the New Zealand dairy cattle population. Genome-wide identification and validation of CNV is an important step toward their inclusion in genomic selection strategies.

Comparative performance in Holstein-Friesian, Jersey and crossbred cows milked once daily under a pasture-based system in New Zealand

ABSTRACT Production and efficiency of Holstein-Friesian (F), Jersey (J) and crossbred F × J milked once-a-day (OAD) were studied at Massey University dairy farm No. 1. Herd test records of milk yields, somatic cell score (SCS), live weight (LW) and body condition score (BCS) were used to model the lactation curves using a third-order orthogonal polynomial. Total lactation yields of milk (MY), fat (FY), protein (PY) and milk solids (MS = FY + PY) were calculated based on predicted daily yields. Predicted efficiencies were feed conversion efficiency (FCE; total lactation MS per kg of predicted total lactation dry matter intake [DMI]); biological efficiency (BE; total lactation MS per 100 kg of LW) and DMI capacity (DMIC; total lactation DMI per 100 kg of LW). Holstein-Friesian cows yielded 376 kg milk more than F × J cows and 1101 kg milk more than J cows per lactation. Holstein-Friesian and F × J produced similar total lactation MSY (366 and 369 kg, respectively). Jersey cows were more efficient than cows of the other breeds: FCE was 78.2, 82.3 and 86.3; BE was 69.7, 74.1 and 77.8; and DMIC was 887.9, 896.8 and 897.7 for F, F × J and J cows, respectively. There were significant differences in production and efficiency among the breeds, with J cows being more efficient per 100 kg of LW than F or F × J cows. Further research is required to compare breed profit per ha in order to conclude the best breed for OAD systems.