Massey Research Online - Browsing by Author "Lopez-Villalobos N"

Browsing by Author "Lopez-Villalobos N"

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A Capra hircus chromosome 19 locus linked to milk production influences mammary conformation
(BioMed Central Ltd, 2022-02-11) Jiang A; Ankersmit-Udy A; Turner S-A; Scholtens M; Littlejohn MD; Lopez-Villalobos N; Proser CG; Snell RG; Lehnert K
Background Economically important milk production traits including milk volume, milk fat and protein yield vary considerably across dairy goats in New Zealand. A significant portion of the variation is attributable to genetic variation. Discovery of genetic markers linked to milk production traits can be utilised to drive selection of high-performance animals. A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait locus (QTL) located on chromosome 19. The most significantly associated single nucleotide polymorphism (SNP) marker for this locus is located at position 26,610,610 (SNP marker rs268292132). This locus is associated with multiple milk production traits including fat, protein and volume. The predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2 kg fat, 1.9 kg protein and 73.6 kg milk yield. An outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic effects. An adverse relationship between milk production and udder health traits has been reported at this locus. Therefore, a genome wide association study was undertaken looking for loci associated with udder traits. Results The QTL and production associated marker rs268292132 was identified in this study to also be associated with several goat udder traits including udder depth (UD), fore udder attachment (FUA) and rear udder attachment (RUA). Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610 (SNP marker rs268292132) associated with an adverse change in UD, FUA and RUA. Conclusions Our study has confirmed the negative relationship between udder traits and production traits in the NZ goat population. We have found that the frequency of the high production allele is relatively high in the NZ goat population, indicating that its effect on udder conformation is not significantly detrimental on animal health. It will however be important to monitor udder conformation as the chromosome 19 locus is progressively implemented for marker assisted selection. It will also be of interest to determine if the gene underlying the production QTL has a direct effect on mammary gland morphology or whether the changes observed are a consequence of the increased milk volume.
Advantage of including Genomic Information to Predict Breeding Values for Lactation Yields of Milk, Fat, and Protein or Somatic Cell Score in a New Zealand Dairy Goat Herd
(MDPI (Basel, Switzerland), 2021-01) Scholtens M; Lopez-Villalobos N; Lehnert K; Snell R; Garrick D; Blair HT
Selection on genomic breeding values (GBVs) is now readily available for ranking candidates in improvement schemes. Our objective was to quantify benefits in terms of accuracy of prediction from including genomic information in the single-trait estimation of breeding values (BVs) for a New Zealand mixed breed dairy goat herd. The dataset comprised phenotypic and pedigree records of 839 does. The phenotypes comprised estimates of 305-day lactation yields of milk, fat, and protein and average somatic cell score from the 2016 production season. Only 388 of the goats were genotyped with a Caprine 50K SNP chip and 41,981 of the single nucleotide polymorphisms (SNPs) passed quality control. Pedigree-based best linear unbiased prediction (PBLUP) was used to obtain across-breed breeding values (EBVs), whereas a single-step BayesC model (ssBC) was used to estimate across-breed GBVs. The average prediction accuracies ranged from 0.20 to 0.22 for EBVs and 0.34 to 0.43 for GBVs. Accuracies of GBVs were up to 103% greater than EBVs. Breed effects were more reliably estimated in the ssBC model compared with the PBLUP model. The greatest benefit of genomic prediction was for individuals with no pedigree or phenotypic records. Including genomic information improved the prediction accuracy of BVs compared with the current pedigree-based BLUP method currently implemented in the New Zealand dairy goat population.
Animal factors affecting the cheese-making properties and the heat coagulation time of milk from dairy sheep in a New Zealand flock
(Taylor and Francis Group on behalf of the Royal Society of New Zealand, 2024-03-27) Marshall AC; Lopez-Villalobos N; Loveday SM; Weeks M; McNabb W
The objective of this study was to evaluate the effect of animal factors on the cheese-making properties and on the heat coagulation time of milk from individual dairy sheep in a New Zealand flock. A total of 521 individual records were obtained from a seasonal pasture-based flock of 169 ewes milked once-a-day, from 50 to 182 days in milk. A statistical model was used to quantify the effects of animal factors (coat colour variety, age, litter size and stage of lactation) on the studied traits. Stage of lactation, confounded with seasonality, strongly influenced all properties of milk investigated. With the advancement of lactation, the milk took longer to coagulate after rennet addition, and the curd was softer. Higher relative cheese yield was achieved towards the end of lactation. The milk was also less stable to high-temperature treatment in late lactation. Coefficient of variation for processability traits was high and ranged from 20.2% to 58%, which can be largely attributed to stage of lactation but could also indicate room for genetic improvement of traits. Further genetic studies are underway to define animal genetic variance, heritability, and the phenotypic and genetic correlations between these processability and milk composition traits.
Association of Single Nucleotide Polymorphism in the DGAT1 Gene with the Fatty Acid Composition of Cows Milked Once and Twice a Day
(MDPI (Basel, Switzerland), 2023-03-21) Sanjayaranj I; MacGibbon AKH; Holroyd SE; Janssen PWM; Blair HT; Lopez-Villalobos N
A single nucleotide polymorphism (SNP) rs109421300 of the diacylglycerol acyltransferase 1 (DGAT1) on bovine chromosome 14 is associated with fat yield, fat percentage, and protein percentage. This study aimed to investigate the effect of SNP rs109421300 on production traits and the fatty acid composition of milk from cows milked once a day (OAD) and twice a day (TAD) under New Zealand grazing conditions. Between September 2020 and March 2021, 232 cows from a OAD herd and 182 cows from a TAD herd were genotyped. The CC genotype of SNP rs109421300 was associated with significantly (p < 0.05) higher fat yield, fat percentage, and protein percentage, and lower milk and protein yields in both milking frequencies. The CC genotype was also associated with significantly (p < 0.05) higher proportions of C16:0 and C18:0, higher predicted solid fat content at 10 °C (SFC10), and lower proportions of C4:0 and C18:1 cis-9 in both milking frequencies. The association of SNP with fatty acids was similar in both milking frequencies, with differences in magnitudes. The SFC10 of cows milked OAD was lower than cows milked TAD for all three SNP genotypes suggesting the suitability of OAD milk for producing easily spreadable butter. These results demonstrate that selecting cows with the CC genotype is beneficial for New Zealand dairy farmers with the current payment system, however, this would likely result in less spreadable butter.
Bivariate analysis to improve genetic evaluations with incomplete databases in Charolais cattle
(Universidad de Cordoba, 2021-03-17) Herrera-Ojeda J; Parra-Bracamonte GM; Lopez-Villalobos N; Herrera-Camacho J; Orozco-Durán KE
Objective: Estimate (co)variance components and genetic parameters of live weight traits and examine the effect of selection culling when using bivariate analysis in registered Charolais beef cattle. Materials and methods: The effect of incomplete data over accuracies was compared, expected progeny differences (EPD) and standard errors of prediction (SEP) were obtained and evaluated by comparing univariate and bivariate models for birth (BW), weaning (WW) and yearling (YW) weights. Results: Bivariate models for WW and YW, improved accuracies of EPDs and reduced the SEPs. Joint analysis for BW and WW increased in a 38% the accuracies and reduced SEP estimators for YW (p̌0.001). Accuracies of EPD for BW obtained from univariate models were improved when BW was included in bivariate models. Conclusions: The results support the use of bivariate genetic analysis in limited or incomplete live weight indicators databases that were registered after birth, such as weaning and yearling weight.
Can Nitrogen Excretion of Dairy Cows Be Reduced by Genetic Selection for Low Milk Urea Nitrogen Concentration?
(MDPI (Basel, Switzerland), 2021-03-08) Ariyarathne HBPC; Correa-Luna M; Blair H; Garrick D; Lopez-Villalobos N
The objectives of this study were two-fold. Firstly, to estimate the likely correlated responses in milk urea nitrogen (MUN) concentration, lactation yields of milk (MY), fat (FY) and crude protein (CPY) and mature cow liveweight (LWT) under three selection scenarios which varied in relative emphasis for MUN; 0% relative emphasis (MUN0%: equivalent to current New Zealand breeding worth index), and sign of the economic value; 20% relative emphasis positive selection (MUN+20%), and 20% relative emphasis negative selection (MUN−20%). Secondly, to estimate for these three scenarios the likely change in urinary nitrogen (UN) excretion under pasture based grazing conditions. The predicted genetic responses per cow per year for the current index were 16.4 kg MY, 2.0 kg FY, 1.4 kg CPY, −0.4 kg LWT and −0.05 mg/dL MUN. Positive selection on MUN in the index resulted in annual responses of 23.7 kg MY, 2.0 kg FY, 1.4 kg CPY, 0.6 kg LWT and 0.10 mg/dL MUN, while negative selection on MUN in the index resulted in annual responses of 5.4 kg MY, 1.6 kg FY, 1.0 kg CPY, −1.1 kg LWT and −0.17 mg/dL MUN. The MUN−20% reduced both MUN and cow productivity, whereas the MUN+20% increased MUN, milk production and LWT per cow. Per cow dry matter intake (DMI) was increased in all three scenarios as milk production increased compared to base year, therefore stocking rate (SR) was adjusted to control pasture cover. Paradoxically, ten years of selection with SR adjusted to maintain annual feed demand under the MUN+20% actually reduced per ha UN excretion by 3.54 kg, along with increases of 63 kg MY, 26 kg FY and 16 kg CPY compared to the base year. Ten years of selection on the MUN0% index generated a greater reductions of 10.45 kg UN and 30 kg MY, and increases of 32 kg FY and 21 kg CPY per ha, whereas the MUN−20% index reduced 14.06 kg UN and 136 kg MY with increases of 32 kg FY and 18 kg CPY compared to base year. All three scenarios increased partitioning of nitrogen excreted as feces. The selection index that excluded MUN was economically beneficial in the current economic circumstances over selection indices including MUN regardless of whether selection was either for or against MUN. There was no substantial benefit from an environmental point of view from including MUN in the Breeding Worth index, because N leaching is more a function of SR rather than of individual cow UN excretion. This study demonstrates that attention needs to be paid to the whole system consequences of selection for environmental outcomes in pastoral grazing circumstances.
Carcass characteristics and meat quality of Hereford sired steers born to beef-cross-dairy and Angus breeding cows.
(2016-11) Coleman LW; Hickson RE; Schreurs NM; Martin NP; Kenyon PR; Lopez-Villalobos N; Morris ST
Steers from Angus, Angus×Holstein Friesian, Angus×Holstein Friesian-Jersey and Angus×Jersey cows and a Hereford sire were measured for their carcass and meat quality characteristics. Steers from the Angus×Holstein Friesian cows had a greater final body weight and carcass weight (P<0.05). Steers from Angus×Jersey cows had the lowest carcass weight and dressing-out percentage (P<0.05). There was a greater fat depth over the rump at 12 and 18months of age for the steers from Angus cows (P<0.05) but, not at 24months of age. The steers had similar meat quality characteristics across the breed groups. Steers from Angus×Holstein Friesian and Angus×Jersey cows had a higher ratio of n6 to n3 fatty acids. Using beef-cross-dairy cows to produce steers for meat production does not impact on meat quality. Using Jersey in the breed cross reduced the carcass tissues in the live weight and the potential meat yield.
Cumulative dairy cow genetic change from selection and crossbreeding over the last 2 decades in New Zealand closely aligns to model-based predictions published in 2000
(Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2021-03) Lopez-Villalobos N; Blair HT; Garrick DJ
A deterministic model was developed in 1998 to evaluate the concurrent effects of selection and crossbreeding on the rate of genetic gain and increases in productivity of New Zealand dairy cattle over the ensuing 25-yr period. The predictions of today's breed composition of the national dairy herd and genetic trends for body weight and lactation yields of milk, fat, and protein are compared with today's actual values. Selection was assumed to use an index that included live weight and lactation yields of milk, fat, and protein. Mating strategies involving the Holstein-Friesian (F), Jersey (J), and Ayrshire (A) breeds were evaluated. Effects of heterosis and age were included to calculate phenotypic live weight and yields of milk, fat, and protein per cow. At the time the model was developed, New Zealand had an across-breed evaluation system, but only straightbred bulls were used after progeny testing based on records of straightbred and crossbred daughters. The model predicted that if crossbred cows and bulls could be considered as bull parents, faster rates of genetic gain may result because of increased selection intensities in the cow to breed bull selection pathway. This scenario transpired, and the best bulls and cows for farm profit were used regardless of breed. Under that mating strategy for the 2018 birthyear, the model predicted the national breed composition would be 11% F, 34% J, 52% F×J, and 2% A; the actual breed composition was 36% F, 9% J, 53% F×J, and 1% A. The model-predicted annual genetic gains would be 16.7 L of milk, 1.2 kg of fat, 1.5 kg of protein, and −0.7 kg of body weight; the realized annual improvements were 13.6 L of milk, 1.31 kg of fat, 1.17 kg of protein, and −0.36 kg of body weight. Predicted long-term responses to selection can closely mirror realized improvements, confirming the value of modeling to inform animal breeding decision making.
Effect of Breed on the Fatty Acid Composition of Milk from Dairy Cows Milked Once and Twice a Day in Different Stages of Lactation
(MDPI (Basel, Switzerland), 2022-09) Sanjayaranj I; Lopez-Villalobos N; Blair HT; Janssen PWM; Holroyd SE; MacGibbon AKH; Ametaj B
The objective of this study was to evaluate the effect of breed on the overall composition and fatty acid composition of milk from cows milked once a day (OAD) and twice a day (TAD) in different stages of lactation. Milk samples were taken from 39 Holstein-Friesian (F), 27 Jersey (J), and 34 Holstein-Friesian × Jersey (F × J) crossbred cows from a OAD milking herd and 104 F and 83 F × J cows from a TAD milking herd in early (49 ± 15 days in milk), mid (129 ± 12 days in milk), and late (229 ± 13 days in milk) lactation. Calibration equations to predict the concentrations of individual fatty acids were developed using mid-infrared (MIR) spectroscopy. There was a significant interaction between breed within the milking frequency and stage of lactation for the production traits and composition traits. Holstein-Friesian cows milked OAD produced milk with lower concentrations of C18:0 in early and mid lactations compared to F × J and J cows. Holstein-Friesian cows milked TAD produced lower concentrations of C18:0 in early lactation and lower concentrations of C16:0 and C18:0 in late lactation compared to F × J. Lower concentrations of these fatty acids would reduce the hardness of the butter when the milk is processed. In the OAD milking herd, F cows were superior for daily milk yield compared to J cows, but Jersey cows produced significantly (p < 0.05) higher percentages of fat and a higher concentration of C18:0 fatty acid. The relative concentrations of C18:0 and C18 cis-9 in F and J cows milked OAD imply there is no breed effect on the activity of delta-9-desaturase, whereas stages of lactation likely have an effect. These results can be used to assist with selecting breeds and cows that are suitable for either OAD or TAD milking, allowing closer alignment with milk processing needs.
Effect of genetic merit for milk urea on milk production and efficiency of crude protein utilization of grazing cows with contrasting supplement inclusion
(NZSAP, 2019-06-17) Correa-Luna M; Donaghy DJ; Kemp PD; Schutz MM; Lopez-Villalobos N
Milk urea (MU) has been proposed as a predictor of nitrogen excreted through urine into the environment. The objective of this study was to evaluate milk production performance and efficiency of crude protein utilization (ECPU) of cows with low and high MU breeding values (MUBV) in grazing conditions with two levels of dietary supplementation inclusion. From July 2016 to May 2017, 257 cows were milked once daily with low supplementation (LS; 366 kg/cow/lactation) and 210 cows were milked twice daily with high supplementation (HS; 2,091 kg/cow/lactation). Cows within each herd were ranked as low, intermediate, or high for MUBV. The dataset consisted of 2,318 records of milk production collected from monthly herd-tests of both herds; and 853 additional milk samples obtained at early, mid and late lactation to measure MU. The ECPU was calculated as the proportion of protein yield (PY) with respect to crude protein intake (CPI); with CPI derived from feed intake estimates based on energy requirements. Cows with HS had superior milk yield (MY) and milk solids yield (MSY) [MSY= PY + fat yield (FY)] (P<0.001). Feed intake was less in LS (P<0.001) but CPI was superior compared to HS. The ECPU was better in HS (P<0.001) because of higher PY (P<0.001) along with lower CPI (P<0.001). Levels of MU were superior for LS because of higher CPI. Cows with low-MUBV had significantly lower MU along with less total daily excretion of MU during the lactation (P<0.001). Irrespective of supplementary feed level, cows with low-MUBV had less MY (P<0.001). Low-MUBV did not result in improved ECPU for either supplementary feed level: under LS, ECPU was inferior in cows of low-MUBV (P<0.001), and this was explained by reduced PY (P<0.001).
Effect of protein polymorphisms on milk composition, coagulation properties, and protein profile in dairy sheep
(Elsevier Ltd, 2025-01-01) Marshall AC; Vigolo V; De Marchi M; Lopez-Villalobos N; Loveday SM; Weeks M; McNabb W
The objective of this study was to quantify the effect of protein polymorphisms on milk composition, coagulation properties, and protein profile in dairy sheep from a New Zealand flock. A total of 470 test-day records, from 147 lactating ewes, were used in the statistical analyses. Protein polymorphisms observed in the RP-HPLC were self-named for purposes of the present study. Data were analyzed using a mixed linear model, including the fixed effects of ewe age, litter size, coat-colour, and stage of lactation, and, as a covariate, deviation from the median lambing date of the flock. The effects of protein polymorphisms were added to the model, one at a time. Protein polymorphisms were significantly (p < 0.05) associated with milk composition and protein profile. Polymorphisms of β-lactoglobulin were significantly associated with milk heat stability, being AB type more heat stable than AA. The other processability traits were not significantly affected by protein polymorphisms. Further studies are required to confirm the protein variants and the properties of individual protein polymorphisms.
Estimated Breeding Values of Beef Sires Can Predict Performance of Beef-Cross-Dairy Progeny
(Frontiers Media S.A., 2021-09-30) Martín N; Coleman L; Lopez-Villalobos N; Schreurs N; Morris S; Blair H; McDade J; Back P; Hickson R
On average, half of the animal’s estimated breeding value (EBV) is passed on to their progeny. However, it is not known how the performance of beef-cross-dairy cattle relates to the EBV of their beef sire. Such information is required to determine the genetic potential of beef sires selected based on existing EBV to be used on dairy cows in New Zealand. This study evaluated the relationship between the EBV of 30 Angus and 34 Hereford sires and the performance of their progeny for birth, growth, and carcass traits, via progeny testing of 975 beef-cross-dairy offspring born to dairy cows and grown on hill country pasture. Overall, BREEDPLAN EBV did predict progeny performance of the beef-cross-dairy cattle from this study. Gestation length and birthweight increased with increasing sire EBV (mean 0.37–0.62days and 0.52–0.64kg, respectively, p<0.05). Age at weaning decreased with increasing sire EBV for liveweight at 200days (0.17–0.21days per extra kilo of sire EBV, p<0.05) but sire EBV for liveweight at 200days had no effect on the liveweight of the progeny at 200days for either breed (p>0.05). Liveweight increased with sire EBV for liveweight at 400, 600, and 800days, by a similar amount for both breeds (between 0.23 and 0.42kg increase in progeny liveweight per extra kilo of sire EBV, p<0.05). The relationships were more inconsistent for carcass traits. For Hereford, carcass weight and eye muscle area increased with increasing sire EBV (0.27kg and 0.70cm2, respectively, p<0.05). For Angus, marble score increased by 0.10 with 1% extra in sire EBV for intramuscular fat (p<0.05). Rib fat depth tended to increase with sire EBV for both breeds (p<0.1). EBV derived from beef-breed data work in dairy-beef systems but maybe slightly less than the expected 0.5units of performance per unit of EBV. New Zealand farmers should consider BREEDPLAN EBV when selecting sires to mate dairy cows or when buying beef-cross-dairy calves for beef production, to ensure the resulting calves are born safely and on time and then grow well to produce carcasses of suitable meat and fat composition.
Estimates of Genetic Parameters for Milk, the Occurrence of and Susceptibility to Clinical Lameness and Claw Disorders in Dairy Goats
(MDPI (Basel, Switzerland), 2023-04-17) Jaques N; Turner S-A; Vallée E; Heuer C; Lopez-Villalobos N; Davis ME; Bagnicka E
The New Zealand goat industry accesses niche markets for high-value products, mainly formula for infants and young children. This study aimed to estimate the genetic parameters of occurrence and susceptibility of clinical lameness and selected claw disorders and establish their genetic associations with milk production traits. Information on pedigree, lameness, claw disorders, and milk production was collected on three farms between June 2019 and July 2020. The dataset contained 1637 does from 174 sires and 1231 dams. Estimates of genetic and residual (co)variances, heritabilities, and genetic and phenotypic correlations were obtained with uni- and bi-variate animal models. The models included the fixed effects of farm and parity, deviation from the median kidding date as a covariate, and the random effects of animal and residual error. The heritability (h2) estimates for lameness occurrence and susceptibility were 0.07 and 0.13, respectively. The h2 estimates for claw disorder susceptibilities ranged from 0.02 to 0.23. The genotypic correlations ranged from weak to very strong between lameness and milk production traits (-0.94 to 0.84) and weak to moderate (0.23 to 0.84) between claw disorder and milk production traits.
Estimation of genetic parameters and individual and maternal breed, heterosis, and recombination loss effects for production and fertility traits of spring-calved cows milked once daily or twice daily in New Zealand
(Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2023-01) Jayawardana JMDR; Lopez-Villalobos N; Hickson RE; McNaughton LR
The objectives of this study were to estimate genetic parameters and individual and maternal breed, heterosis, and recombination loss effects for milk production and fertility traits of Holstein Friesian (F), Jersey (J), and crossbred Holstein Friesian and Jersey (F × J) cows milked once daily (OAD) or twice daily (TAD) in New Zealand. Data on 278,776 lactations from 30,217 OAD and 170,680 TAD milking cows across 644 spring-calving herds were available. Genetic parameters and individual and maternal breed, heterosis, and recombination loss estimates were obtained from univariate animal models. Heritability and repeatability estimates for milk production, milk composition, and fertility traits were consistent across the milking frequencies. Heritability estimates for yields of milk, fat, protein, and lactose varied between 0.21 and 0.29 in OAD and TAD. Heritability estimates for fertility traits ranged from 0.01 to 0.08 in both populations, and estimates were slightly greater in TAD than OAD milking cows. In both milking populations, individual breed effects for yields were in favor of F cows; however, maternal breed effects for yields were in favor of J dams. Jersey cows were more fertile than the F cows in both milking populations, but maternal breed effects for fertility traits were in favor of F dams. Individual heterosis effects were favorable for all traits and were consistent across milking regimens. Crossbred F × J cows had significantly shorter intervals from start of mating to first service and from start of mating to conception, and a higher proportion of 3-wk submission, 3-wk in calf, and 3-wk calving relative to the average of purebred F and J cows. Recombination loss effects were not always unfavorable for production and fertility traits, but most estimates were small with larger standard errors. Favorable maternal heterosis effects were associated with production traits in both milking systems, but maternal heterosis effects were less likely to influence reproductive performance.
Estimation of genetic parameters for production, composition and processability of milk from dairy sheep in a New Zealand flock
(Taylor and Francis Group, 2024-06-27) Marshall AC; Lopez-Villalobos N; Loveday SM; Weeks M; McNabb W
This paper aimed to estimate the heritability and genetic correlations for processability (milk coagulation properties, cheese yield, and heat stability), milk production, and milk composition of dairy sheep in a New Zealand flock. Test-day records from 169 ewes were obtained during the 2021–2022 season. Heritability estimates for yield traits (milk, fat, protein, and lactose yield) were moderate and ranged from 0.33 to 0.38. Whereas heritability estimates for processability traits were lower and ranged from 0.17 to 0.27. The genetic correlations indicated that poorer milk coagulation properties were associated with lower mammary health indicated by higher SCS, higher pH, and lower lactose content. Additionally, a higher ratio of casein to calcium i.e. lower availability of soluble calcium was associated with poorer milk coagulation properties. Higher yields of milk, fat, protein, and lactose were associated, but to a smaller degree, with better MCP. It is proposed that genetic improvement of dairy sheep for higher yields of fat and protein, and for lower SCS, could indirectly improve milk processability for cheese-making. However, it is recommended that larger studies involving more dairy sheep flocks are conducted to validate the present results before developing a selection index for this industry.
Evaluation of equations for predicting ileal nutrient digestibility and digestible nutrient content of broiler diets based on their gross chemical composition
(Elsevier B V, 2024-06) Thiruchchenthuran S; Lopez-Villalobos N; Zaefarian F; Abdollahi MR; Wester TJ; Pedersen NB; Storm AC; Cowieson AJ; Morel PCH
The coefficient of apparent ileal digestibility (CAID) and ileal digestible contents (IDC) of nutrients of 56 diets using 10 feed ingredients were measured in broilers (21–24 d post-hatch). Diets contained varying inclusion levels of traditional and non-traditional ingredients and differed widely in chemical composition. The chemical composition and in vivo digestibility values were used to establish prediction equations for CAID and IDC of nutrients using stepwise multiple regression. The strength and accuracy of the developed equations were evaluated by root mean square error (RMSE), coefficient of determination (R2), adjusted R2 (adj. R2), and Akaikie's Information Criteria (AIC). The bootstrap method was used to validate the choice of variables by stepwise selection method in the original equation based on their frequencies of selection. Selection of variables was validated if the variables that appear in the original stepwise model were selected in more than 30% of the 1000 bootstrap samples. A close agreement between the original equations and bootstrap resampling was observed for CAID of nitrogen (N) and energy and IDC of energy, starch, and calcium (Ca). Additionally, the original data was subjected to another run of stepwise regression analysis using the selected variables by bootstrapping. The initial regression showed that the CAID of N and energy was highly dependent on crude fibre (CF) and energy contents of the diets. The CAID of energy can be predicted (R2 = 0.89 and RMSE = 0.035) by CF, gross energy (GE), CF2, and starch-to-CF ratio (starch:CF). Calcium content had a positive influence, while phosphorus (P) content had a negative influence on the prediction of CAID of fat. The main variable to predict CAID and IDC of most nutrients was the dietary CF content. Based on the lowest RMSE and AIC, the best predictors for IDC of N were ash, N, fat, CF, CF2, and starch:CF, while the best predictors for IDC of energy were CF, GE, CF2, and starch:CF. The results of the original stepwise regression models and the stepwise regression with the selected variables from the bootstrap results for CAID of N, energy, fat, and DM, as well as IDC of energy, starch, and Ca, were the same with no differences in R2, Adj. R2, RMSE, and AIC. This method can be useful for developing stable and reproducible models using stepwise regression. However, an external validation is needed to confirm the use of these equations in commercial settings.
Fatty Acid Composition of Dairy Milk: A Case Study Comparing Once- and Twice-a-Day Milking of Pasture-Fed Cows at Different Stages of Lactation
(MDPI (Basel, Switzerland), 2022-03) Sanjayaranj I; Lopez-Villalobos N; Blair HT; Janssen PWM; Holroyd SE; MacGibbon AKH
In this case study, we compared the gross composition and fatty acid (FA) composition of milk from cows milked once a day (OAD) and twice a day (TAD) at different stages of lactation in real farm conditions with no control on feed. Seventy-two cows from a OAD milking herd and 181 cows from a TAD milking herd were sampled in early, mid and late lactation. Calibration equations were developed to enable the prediction of proportions of individual FAs using mid-infrared (MIR) spectroscopy. Cows milked OAD produced 25% lower daily milk yield (MY) compared to cows milked TAD. Percentages of fat and protein were 21% and 9% higher in cows milked OAD compared to cows milked TAD, respectively. The proportion of saturated fatty acids (SFA) (molecules with unbranched hydrocarbon chains and all single bonds) was significantly lower, while the proportions of de novo synthesised FAs from C8:0 to C14:0 were significantly higher, in cows milked OAD compared to cows milked TAD. OAD milking improved the energy balance of cows, which led to higher proportions of de novo synthesised FAs and lower proportions of long-chain fatty acids (16:0 and above). The proportion of SFA was significantly higher in mid lactation (ML) compared to early lactation (EL) and late lactation (LL) in cows milked OAD and TAD. In EL, the proportions of C4:0 to C12:0 FAs in cows milked OAD were significantly higher compared to the cows milked TAD due to the improved energy status of cows milked OAD. Understanding the proportions of individual FAs in cows milked OAD and TAD will enable further studies on milk fat characteristics and on butter hardness and coagulation properties of milk.
Fertility of dairy cows milked once daily or twice daily in New Zealand.
(Elsevier, 2022-11) Jayawardana JMDR; Lopez-Villalobos N; McNaughton LR; Hickson RE
The objective of this study was to evaluate the reproductive performance of New Zealand dairy cows with different milking regimens. A total of 2,562 herds calving in 2017 met the criteria for inclusion in this study. The herds were classified into 5 different milking regimens: 260 herds with cows milked once daily (OAD) during the entire lactation, 1,206 herds with cows milked twice daily (TAD) during the entire lactation, 94 herds that were switched to OAD milking from TAD milking during the mating period (OAD-M), 700 herds that were switched to OAD milking from TAD milking after peak lactation (OAD-P), and 302 herds that switched to OAD milking from TAD milking at end of the lactation (OAD-E). Time from the start of mating to first service (SMFS), start of mating to conception (SMCO) and first service to conception (FSCO) were analyzed using survival analysis. Time from SMFS, SMCO and FSCO was significantly shorter in cows milked OAD compared with cows milked TAD. Also, cows milked OAD had fewer services per conception and higher mean 3-wk submission (SR21), in calf by 3 wk (PR21), in calf by 6 wk (PR42), conception to the first service (PRFS), 3-wk calving (CR21) and 6-wk calving (CR42), and lower not in calf (NIC) than herds with TAD, OAD-M, OAD-P, OAD-E milking cows. Fertility performance differed with parity; first-parity cows had lower SR21, 6-wk submission (SR42), PR21, PR42, PRFS, CR21, and CR42 values, and higher NIC values than second-parity cows. Third parity cows had the highest values for SR42, PR21, PR42, PRFS, CR21, and CR42, and lowest value for NIC compared with cows of other parities. Significant but minor interactions between milking regimen and parity existed for SMFS, SMCO, FSCO, SR21, SR42, PR21, PR42, PRFS, NIC, and CR21.
Genome-wide association studies for citric and lactic acids in dairy sheep milk in a New Zealand flock
(Taylor and Francis Group, 2024-08-05) Zongqi A; Marshall AC; Jayawardana JMDR; Weeks M; Loveday SM; McNabb W; Lopez-Villalobos N
The objectives of this study were to estimate genetic parameters for citric acid content (CA) and lactic acid content (LA) in sheep milk and to identify the associated candidate genes in a New Zealand dairy sheep flock. Records from 165 ewes were used. Heritability estimates based on pedigree records for CA and LA were 0.65 and 0.33, respectively. The genetic and phenotypic correlations between CA and LA were strong-moderate and negative. Estimates of genomic heritability for CA and LA were also high (0.85, 0.51) and the genomic correlation between CA and LA was strongly negative (-0.96 ± 0.11). No significant associations were found at the Bonferroni level. However, one intragenic SNP in C1QTNF1 (chromosome 11) was associated with CA, at the chromosomal significance threshold. Another SNP associated with CA was intergenic (chromosome 15). For LA, the most notable SNP was intragenic in CYTH1 (chromosome 11), the other two SNPs were intragenic in MGAT5B and TIMP2 (chromosome 11), and four SNPs were intergenic (chromosomes 1 and 24). The functions of candidate genes indicate that CA and LA could potentially be used as biomarkers for energy balance and clinical mastitis. Further research is recommended to validate the present results.
Genome-Wide Association Studies of Live Weight at First Breeding at Eight Months of Age and Pregnancy Status of Ewe Lambs
(MDPI (Basel, Switzerland), 2023-03-27) Haslin E; Pettigrew EJ; Hickson RE; Kenyon PR; Gedye KR; Lopez-Villalobos N; Jayawardana JMDR; Morris ST; Blair HT; Ahmad SM
This study estimated genetic parameters and identified candidate genes associated with live weight, and the occurrence of pregnancy in 1327 Romney ewe lambs using genome-wide association studies. Phenotypic traits considered were the occurrence of pregnancy in ewe lambs and live weight at eight months of age. Genetic parameters were estimated, and genomic variation was assessed using 13,500 single-nucleotide polymorphic markers (SNPs). Ewe lamb live weight had medium genomic heritability and was positively genetically correlated with occurrence of pregnancy. This suggests that selection for heavier ewe lambs is possible and would likely improve the occurrence of pregnancy in ewe lambs. No SNPs were associated with the occurrence of pregnancy; however, three candidate genes were associated with ewe lamb live weight. Tenascin C (TNC), TNF superfamily member 8 (TNFSF8) and Collagen type XXVIII alpha 1 chain (COL28A1) are involved in extracellular matrix organization and regulation of cell fate in the immune system. TNC may be involved in ewe lamb growth, and therefore, could be of interest for selection of ewe lamb replacements. The association between ewe lamb live weight and TNFSF8 and COL28A1 is unclear. Further research is needed using a larger population to determine whether the genes identified can be used for genomic selection of replacement ewe lambs.

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