• Asian-Australasian Journal of Animal Sciences
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• v.29 no.4
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• pp.464-470
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• 2016

The objective of this study was to investigate the accuracy of imputation from low density (LDC) to moderate density SNP chips (MDC) in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244) from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570), GGP26K (n = 540) and GGP80K (n = 134) chips. After checking for single nucleotide polymorphism (SNP) quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Animals were divided into two groups, a reference group (n = 912) and a test group (n = 332). The SNP markers chosen for the test group were those located in positions corresponding to GeneSeek GGP9K (n = 7,652). The LDC to MDC genotype imputation was carried out using three different software packages, namely Beagle 3.3 (population-based algorithm), FImpute 2.2 (combined family- and population-based algorithms) and Findhap 4 (combined family- and population-based algorithms). Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed SNP markers to overall imputed SNP markers. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94%) than Findhap (84.64%) and Beagle (76.79%). Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. Most chromosomes that showed either high (73%) or low (80%) imputation accuracies were the same chromosomes that had above and below average linkage disequilibrium (LD; defined here as the correlation between pairs of adjacent SNP within chromosomes less than or equal to 1 Mb apart). Results indicated that FImpute was more suitable than Findhap and Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by increasing the completeness of pedigree information.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.508-518
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• 2019

Objective: This research aimed to determine biological pathways and protein-protein interaction (PPI) networks for 305-d milk yield (MY), 305-d fat yield (FY), and age at first calving (AFC) in the Thai multibreed dairy population. Methods: Genotypic information contained 75,776 imputed and actual single nucleotide polymorphisms (SNP) from 2,661 animals. Single-step genomic best linear unbiased predictions were utilized to estimate SNP genetic variances for MY, FY, and AFC. Fixed effects included herd-year-season, breed regression and heterosis regression effects. Random effects were animal additive genetic and residual. Individual SNP explaining at least 0.001% of the genetic variance for each trait were used to identify nearby genes in the National Center for Biotechnology Information database. Pathway enrichment analysis was performed. The PPI of genes were identified and visualized of the PPI network. Results: Identified genes were involved in 16 enriched pathways related to MY, FY, and AFC. Most genes had two or more connections with other genes in the PPI network. Genes associated with MY, FY, and AFC based on the biological pathways and PPI were primarily involved in cellular processes. The percent of the genetic variance explained by genes in enriched pathways (303) was 2.63% for MY, 2.59% for FY, and 2.49% for AFC. Genes in the PPI network (265) explained 2.28% of the genetic variance for MY, 2.26% for FY, and 2.12% for AFC. Conclusion: These sets of SNP associated with genes in the set enriched pathways and the PPI network could be used as genomic selection targets in the Thai multibreed dairy population. This study should be continued both in this and other populations subject to a variety of environmental conditions because predicted SNP values will likely differ across populations subject to different environmental conditions and changes over time.

• Animal Bioscience
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• v.37 no.3
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• pp.428-436
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• 2024

Objective: This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population. Methods: The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows. Results: Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population. Conclusion: This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.9
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• pp.1237-1246
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• 2013

The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade $B{\times}F$ cows (3/16B 13/16F) had the highest least squares means (LSM) for LY ($2,490{\pm}178.9kg$), IY ($10.5{\pm}0.8kg$), PY ($12.7{\pm}0.9kg$), YD ($7.6{\pm}0.55kg$) and LL ($361.4{\pm}31.2d$), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single-trait analyses yielded low heritability ($0.03{\pm}0.03$ and $0.08{\pm}0.02$) and repeatability ($0.14{\pm}0.01$ to $0.24{\pm}0.02$) estimates for LL, DP and parameter c. Medium heritability ($0.21{\pm}0.03$ to $0.33{\pm}0.04$) and repeatability ($0.27{\pm}0.02$ to $0.53{\pm}0.01$) estimates were obtained for LY, IY, PY, YD and ln(a). Genetic correlations between LY, IY, PY, YD, ln(a), and LL ranged from 0.59 to 0.99. Spearman's rank correlations between sire estimated breeding values for LY, LL, IY, PY, YD, ln(a) and c were positive (0.67 to 0.99, p<0.001). These results suggested that selection for IY, PY, YD, or LY would genetically improve lactation milk yield in this Ethiopian dairy cattle population.

• Animal Bioscience
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• v.37 no.4
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• pp.576-590
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• 2024

Objective: The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. Methods: A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-year-season, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. Results: A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. Conclusion: Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.9
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• pp.1340-1348
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• 2019

Objective: The objectives were to compare variance components, genetic parameters, prediction accuracies, and genomic-polygenic estimated breeding value (EBV) rankings for milk yield (MY) and fat yield (FY) in the Thai multibreed dairy population using five single nucleotide polymorphism (SNP) sets from GeneSeek GGP80K chip. Methods: The dataset contained monthly MY and FY of 8,361 first-lactation cows from 810 farms. Variance components, genetic parameters, and EBV for five SNP sets from the GeneSeek GGP80K chip were obtained using a 2-trait single-step average-information restricted maximum likelihood procedure. The SNP sets were the complete SNP set (all available SNP; SNP100), top 75% set (SNP75), top 50% set (SNP50), top 25% set (SNP25), and top 5% set (SNP5). The 2-trait models included herd-year-season, heterozygosity and age at first calving as fixed effects, and animal additive genetic and residual as random effects. Results: The estimates of additive genetic variances for MY and FY from SNP subsets were mostly higher than those of the complete set. The SNP25 MY and FY heritability estimates (0.276 and 0.183) were higher than those from SNP75 (0.265 and 0.168), SNP50 (0.275 and 0.179), SNP5 (0.231 and 0.169), and SNP100 (0.251and 0.159). The SNP25 EBV accuracies for MY and FY (39.76% and 33.82%) were higher than for SNP75 (35.01% and 32.60%), SNP50 (39.64% and 33.38%), SNP5 (38.61% and 29.70%), and SNP100 (34.43% and 31.61%). All rank correlations between SNP100 and SNP subsets were above 0.98 for both traits, except for SNP100 and SNP5 (0.93 for MY; 0.92 for FY). Conclusion: The high SNP25 estimates of genetic variances, heritabilities, EBV accuracies, and rank correlations between SNP100 and SNP25 for MY and FY indicated that genotyping animals with SNP25 dedicated chip would be a suitable to maintain genotyping costs low while speeding up genetic progress for MY and FY in the Thai dairy population.