Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
Browse
20 results
Search Results
Item Comparison of genomic prediction accuracies in dairy cattle lactation traits using five classes of functional variants versus generic SNP(BioMed Central Ltd, 2025-12) Alemu SW; Lopdell TJ; Trevarton AJ; Snell RG; Littlejohn MD; Garrick DJBackground: Genomic selection, typically employing genetic markers from SNP chips, is routine in modern dairy cattle breeding. This study assessed the impact of functional sequence variants on genomic prediction accuracy relative to 50 k SNP chip markers for fat percent, protein percent, milk volume, fat yield, and protein yield in lactating dairy cattle. The functional variants were identified through GWAS, RNA-seq, Histone modification ChIP-seq, ATAC-seq, or were coding variants. The genomic prediction accuracy obtained using each class of functional variants was compared with matched numbers of SNPs randomly selected from the Illumina 50 k SNP chip. Results: The investigation revealed that variants identified by GWAS or RNA-seq, significantly improved the prediction accuracy across all five traits. Contributions from ChIP-seq, ATAC-seq, and coding variants varied. Some variants identified using ChIP-seq showed marked improvements, while others reduced accuracy in protein yield predictions. Relative to a matched number of 32,595 SNPs from the SNP chip, pooling all the functional variants demonstrated prediction accuracy increases of 1.76% for fat percent, 2.97% for protein percent, 0.51% for milk volume, and 0.26% for fat yield, but with a slight decrease of 0.43% in protein yield. Conclusion: The study demonstrates that functional variants can improve prediction accuracy relative to equivalent numbers of variants from a generic SNP panel, with percent traits showing more significant gains than yield traits. The main advantage of using functional variants for genomic prediction was achievement of comparable accuracy using a smaller, more selective set of loci. This is particularly evident in trait-specific scenarios. Our findings indicate that specific combinations of functional variants comprising 16 k variants can achieve genomic prediction accuracy comparable to employing a standard panel of twice the size (32.6 k), especially for percent traits. This highlights the potential for the development of more efficient, trait-focused SNP panels utilizing functional variants.Item Genetic Trends for Production and Reproduction Traits in Ultrafine Merino Sheep of Uruguay(John Wiley and Sons Ltd, 2025-03-21) Ramos Z; Garrick DJ; Blair HT; De Barbieri I; Ciappesoni G; Montossi F; Kenyon PRGenetic trends were estimated for production and reproduction traits in an Uruguayan Merino genetic nucleus. Two consecutive periods with different selection objectives were studied. During the first period (1999–2010), the selection objective of this flock focused on reducing fibre diameter (FD), while allowing for a slight loss in clean fleece weight (CFW). From 2011 to 2018, the breeding objective was shifted and then focused on maintaining FD, while increasing both CFW and live weight (LW). Data from approximately 5380 yearling lambs and 2000 ewes born between 1999 and 2018 were analysed. Genetic trends were estimated for yearling and adult FD (Y_FD and A_FD, respectively), yearling and adult CFW (Y_CFW and A_CFW, respectively), yearling LW (Y_LW), 2-year-old ewe mating live weight and mating body condition score (2-yo_LWM and 2-yo_BCSM, respectively) and the number of lambs weaned per ewe joined (NLWEJ). Estimated breeding values were predicted to calculate genetic trends for the two periods of selection. From 1999 to 2010, yearling lambs showed significant reductions in FD (−0.210 μm/year, corresponding to −1.28% of the mean of the trait for that period). Before 2010, yearling lambs showed reductions of −0.013 kg/year (−0.62%) in CFW, whereas from 2011 to 2018, this trait increased by 0.052 kg/year (1.88%). The annual genetic gain for Y_LW was greater in the second period than in the first period (0.286 vs. 0.091 kg/year). The genetic trends for FD, CFW and LW were affected by period (p < 0.001), indicating that the change in the selection index applied in the genetic nucleus was effective. Over the entire study period (1999–2018), the total genetic responses for 2-yo_BCSM and NLWEJ were near zero. These results indicate that the breeding programme utilised in the genetic nucleus improved the traits under selection (FD, CFW and LW) and had a marginal impact on 2-yo_BCSM and NLWEJ. To also achieve relevant genetic gains in ewe reproductive performance, in the future, reproduction traits should be incorporated into the selection programme for Uruguayan fine-wool sheep. The results obtained in this study will be used to refine the breeding programmes for Merino sheep in Uruguay.Item Estimating Heritabilities and Breeding Values From Censored Phenotypes Using a Data Augmentation Approach.(Frontiers Media S.A., 2022-07-25) Stephen MA; Cheng H; Pryce JE; Burke CR; Steele NM; Phyn CVC; Garrick DJ; Cánovas ATime-dependent traits are often subject to censorship, where instead of precise phenotypes, only a lower and/or upper bound can be established for some of the individuals. Censorship reduces the precision of phenotypes but can represent compromise between measurement cost and animal ethics considerations. This compromise is particularly relevant for genetic evaluation because phenotyping initiatives often involve thousands of individuals. This research aimed to: 1) demonstrate a data augmentation approach for analysing censored phenotypes, and 2) quantify the implications of phenotype censorship on estimation of heritabilities and predictions of breeding values. First, we simulated uncensored phenotypes, representing fine-scale "age at puberty" for each individual in a population of some 5,000 animals across 50 herds. Analysis of these uncensored phenotypes provided a gold-standard control. We then produced seven "test" phenotypes by superimposing varying degrees of left, interval, and/or right censorship, as if herds were measured on only one, two or three occasions, with a binary measure categorized for animals at each visit (either pre or post pubertal). We demonstrated that our estimates of heritabilities and predictions of breeding values obtained using a data augmentation approach were remarkably robust to phenotype censorship. Our results have important practical implications for measuring time-dependent traits for genetic evaluation. More specifically, we suggest that data collection can be designed with relatively infrequent repeated measures, thereby reducing costs and increasing feasibility across large numbers of animals.Item Wool shedding and lamb fleece weights: first-cross and backcross Wiltshire–Romney sheep scored at lamb, hogget and two-tooth ages(Taylor and Francis Group, 2024-05-03) Sneddon NW; Handcock RC; Corner-Thomas RA; Kenyon PR; Burnham DL; Garrick DJ; Littlejohn MD; Blair HT; Morris STWith decreasing wool values, interest is increasing regarding shedding sheep. To investigate this, two long-term studies introducing Wiltshire genes into Romney flocks were initiated. Data from these two studies provide phenotypic relationships between a range of shedding scores at different ages. The data included shedding scores (on a 0–5 scale) repeated on lambs (∼5 months), hoggets (∼14–18 months) and two-tooths (∼27 months), and lamb fleece weights. Positive relationships between shedding scores on the same animals were observed. Lamb fleece weight was negatively correlated with all shedding scores. Lamb shedding score in February had a correlation of 0.54 (P < 0.001) with the February score as a hogget at Riverside farm. Scoring wool shedding is a laborious activity requiring individual animals to be scored in the shearing position. Therefore, lamb fleece weight was investigated for its relationship with shedding scores, as a potentially easier alternative. Lamb fleece weight had a greater correlation with February hogget shedding score than with the lamb shedding score (−0.76 vs −0.52, P < 0.001). This study indicated that February scores are an accurate predictor of future shedding phenotypes, and when used in conjunction with fleece weight, are a good predictor of phenotypes expressed at later ages.Item Genetic and phenotypic relationships between ewe reproductive performance and wool and growth traits in Uruguayan Ultrafine Merino sheep.(Oxford University Press on behalf of the American Society of Animal Science, 2023-03-07) Ramos Z; Garrick DJ; Blair HT; De Barbieri I; Ciappesoni G; Montossi F; Kenyon PRThis study reports genetic parameters for yearling and adult wool and growth traits, and ewe reproductive performance. Data were sourced from an Uruguayan Merino flock involved in a long-term selection program focused on reduced fiber diameter (FD), and increased clean fleece weight (CFW) and live weight (LW). Pedigree and performance data from approximately 5,700 mixed-sex yearling lambs and 2,000 mixed-age ewes born between 1999 and 2019 were analyzed. The number of records ranged from 1,267 to 5,738 for yearling traits, and from 1,931 to 7,079 for ewe productive and reproductive performance. Data on yearling and adult wool traits, LW and body condition score (BCS), yearling eye muscle area (Y_EMA), and fat thickness (Y_FAT), and several reproduction traits were analyzed. The genetic relationships between FD and reproduction traits were not different from zero. Moderate unfavorable genetic correlations were found between adult CFW and ewe lifetime reproduction traits (-0.34 ± 0.08 and -0.33 ± 0.09 for the total number of lambs weaned and total lamb LW at weaning, respectively). There were moderate to strong positive genetic correlations between yearling LW and all reproduction traits other than ewe-rearing ability (-0.08 ± 0.11) and pregnancy rate (0.18 ± 0.08). The genetic correlations between Y_EMA and reproduction traits were positive and ranged from 0.15 to 0.49. Moderate unfavorable genetic correlations were observed between yearling FD and Y_FAT and between adult FD and BCS at mating (0.31 ± 0.12 and 0.23 ± 0.07, respectively). The genetic correlations between adult fleece weight and ewe BCS at different stages of the cycle were negative, but generally not different from zero. This study shows that selection for reduced FD is unlikely to have any effect on reproduction traits. Selection for increased yearling LW and Y_EMA will improve ewe reproductive performance. On the other hand, selection for increased adult CFW will reduce ewe reproductive performance, whereas selection for reduced FD will negatively impact body fat levels. Although unfavorable genetic relationships between wool traits and both FAT and ewe reproductive performance existed, simultaneous improvements in the traits would occur using appropriately designed indexes.Item Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci(BioMed Central Ltd, 2022-12) Reynolds EGM; Lopdell T; Wang Y; Tiplady KM; Harland CS; Johnson TJJ; Neeley C; Carnie K; Sherlock RG; Couldrey C; Davis SR; Harris BL; Spelman RJ; Garrick DJ; Littlejohn MDBACKGROUND: Deleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious recessive mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) of quantitative growth and developmental traits in cattle, which showed that quantitative traits can be used as proxies of genetic disorders when such traits are indicative of whole-animal health status. We reasoned that lactation traits in cattle might also reflect genetic disorders, given the increased energy demands of lactation and the substantial stresses imposed on the animal. In this study, we screened more than 124,000 cows for recessive effects based on lactation traits. RESULTS: We discovered five novel quantitative trait loci (QTL) that are associated with large recessive impacts on three milk yield traits, with these loci presenting missense variants in the DOCK8, IL4R, KIAA0556, and SLC25A4 genes or premature stop variants in the ITGAL, LRCH4, and RBM34 genes, as candidate causal mutations. For two milk composition traits, we identified several previously reported additive QTL that display small dominance effects. By contrasting results from milk yield and milk composition phenotypes, we note differing genetic architectures. Compared to milk composition phenotypes, milk yield phenotypes had lower heritabilities and were associated with fewer additive QTL but had a higher non-additive genetic variance and were associated with a higher proportion of loci exhibiting dominance. CONCLUSIONS: We identified large-effect recessive QTL which are segregating at surprisingly high frequencies in cattle. We speculate that the differences in genetic architecture between milk yield and milk composition phenotypes derive from underlying dissimilarities in the cellular and molecular representation of these traits, with yield phenotypes acting as a better proxy of underlying biological disorders through presentation of a larger number of major recessive impacts.Item Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs(MDPI (Basel, Switzerland), 2022-06-25) Fanalli SL; da Silva BPM; Gomes JD; de Almeida VV; Freitas FAO; Moreira GCM; Silva-Vignato B; Afonso J; Reecy J; Koltes J; Koltes D; de Almeida Regitano LC; Garrick DJ; de Carvalho Balieiro JC; Meira AN; Freitas L; Coutinho LL; Fukumasu H; Mourão GB; de Alencar SM; Luchiari Filho A; Cesar ASM; Hernandez PThe aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.Item Genetic Parameters for Maternal Performance Traits in Commercially Farmed New Zealand Beef Cattle(MDPI (Basel, Switzerland), 2021-08-26) Weik F; Hickson RE; Morris ST; Garrick DJ; Archer JA; Michael E DMaternal performance is a major driver of profitability in cow-calf beef cattle enterprises. The aim of this research was to evaluate the inheritance of maternal performance traits and examine the intercorrelation among reproduction, live weight, hip height, body condition and maternal contribution to calf weaning weight in 15-month-old heifers, 2-year-old cows and mature cows in New Zealand beef herds. Data were collected on a total of 14,241 cows and their progeny on five commercial New Zealand hill country farms. Heritabilities were low for reproductive traits in heifers and mature cows (0-0.06) but were greater in 2-year-old cows (0.12-0.21). Body condition scores were lowly (0.15-0.26) and live weights (0.42-0.48) and hip heights (0.47-0.65) highly heritable in heifers, 2-year-old cows and mature cows. Results indicate that 2-year-old cows with higher genetic potential for rebreeding ability may have greater genetic merit for live weight, hip height and body condition as heifers (rg = 0.19-0.54) but are unlikely to be larger cows at maturity (rg = -0.27--0.10). The maternal genetic effect on weaning weight had a heritability of 0.20 and was negatively genetically correlated with body condition score in lactating cows (rg = -0.55--0.40) but positively genetically correlated with rebreeding performance (rg = 0.48).Item Agent-Based Modelling to Improve Beef Production from Dairy Cattle: Young Beef Production(MDPI (Basel, Switzerland), 2023-04-19) Addis AH; Blair HT; Kenyon PR; Morris ST; Schreurs NM; Garrick DJ; Zaborowicz M; Frankowski JApproximately 42% of the total calves born in New Zealand’s dairy industry are either euthanized on farms or commercially slaughtered as so-called bobby calves within 2 weeks of age. These practices have perceived ethical issues and are considered a waste of resources because these calves could be grown on and processed for beef. Young beef cattle harvested between 8 and 12 months of age would represent a new class of beef production for New Zealand and would allow for a greater number of calves to be utilized for beef production, reducing bobby calf numbers in New Zealand. However, the acceptance of such a system in competition with existing sheep and beef cattle production systems is unknown. Therefore, the current study employed an agent-based model (ABM) developed for dairy-origin beef cattle production systems to understand price levers that might influence the acceptance of young beef production systems on sheep and beef cattle farms in New Zealand. The agents of the model were the rearer, finisher, and processor. Rearers bought in 4-days old dairy-origin calves and weaned them at approximately 100 kg live weight before selling them to finishers. Finishers managed the young beef cattle until they were between 8 and 12 months of age in contrast to 20 to 30 months for traditional beef cattle. Processing young beef cattle in existing beef production systems without any price premium only led to an additional 5% of cattle being utilized compared to the traditional beef cattle production system in New Zealand. This increased another 2% when both weaner cattle and young beef were sold at a price premium of 10%. In this scenario, Holstein Friesian young bull contributed more than 65% of total young beef cattle. Further premium prices for young beef cattle production systems increased the proportion of young beef cattle (mainly as young bull beef), however, there was a decrease in the total number of dairy-origin cattle processed, for the given feed supply, compared to the 10% premium price. Further studies are required to identify price levers and other alternative young beef production systems to increase the number of young beef cattle as well the total number of dairy-origin beef cattle for beef on sheep and beef cattle farms. Some potential options for investigation are meat quality, retailer and consumer perspectives, and whether dairy farmers may have to pay calf rearers to utilize calves with lower growth potentialItem Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle(BioMed Central Ltd, 2021-07-20) Tiplady KM; Lopdell TJ; Reynolds E; Sherlock RG; Keehan M; Johnson TJJ; Pryce JE; Davis SR; Spelman RJ; Harris BL; Garrick DJ; Littlejohn MDBACKGROUND: Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. While there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Using imputed whole-genome sequence for 38,085 mixed-breed New Zealand dairy cattle, we conducted GWAS on 895 individual FT-MIR wavenumber phenotypes, and assessed the value of these direct phenotypes for identifying candidate causal genes and variants, and improving our understanding of the physico-chemical properties of milk. RESULTS: Separate GWAS conducted for each of 895 individual FT-MIR wavenumber phenotypes, identified 450 1-Mbp genomic regions with significant FT-MIR wavenumber QTL, compared to 246 1-Mbp genomic regions with QTL identified for FT-MIR predicted milk composition traits. Use of mammary RNA-seq data and gene annotation information identified 38 co-localized and co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in the ABO gene that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, we examined the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum. This revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk. CONCLUSIONS: This study demonstrates the utility of FT-MIR wavenumber phenotypes for improving our understanding of milk composition, presenting a larger number of QTL and putative causative genes and variants than found from FT-MIR predicted composition traits. Examining patterns of significance across the mid-infrared spectrum for loci of interest further highlighted commonalities of association, which likely reflects the physico-chemical properties of milk constituents.