• Animal Bioscience
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• 제37권3호
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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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• 제19권6호
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• pp.769-774
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• 2006

Fractions of herd-year-season, sire by herd interaction, additive genetic and dominance genetic variances were estimated for milk production traits in Holsteins of Japan using Method R. Inbreeding depressions for milk production traits were also estimated. Estimated fractions of herd-year-season variances ranged from 0.056 to 0.074 for yield traits and from 0.033 to 0.035 for content traits. Estimated fractions of additive genetic variances to phenotypic variances (heritabilities across a herd in the narrow sense) were 0.306, 0.287, 0.273, 0.255, 0.723, 0.697 and 0.663 for milk, fat, SNF and protein yields, and fat, SNF and protein contents, respectively. Estimated fractions of dominance genetic variances ranged from 0.019 to 0.022 for yield traits and from 0.014 to 0.018 for content traits. Fractions of variances for sire by herd interaction were estimated to range from 0.020 to 0.025 for yield traits and 0.011 to 0.012 for content traits. Estimates of inbreeding depression for milk, fat, SNF and protein yields were -36.16 kg, -1.42 kg, -3.24 kg and -1.15 kg per 1% inbreeding for milk, fat, SNF and protein yields, respectively. Estimates of depression per 1% inbreeding for content traits were positive at $0.39{\times}10^{-3}%$, $0.31{\times}10^{-3}%$ and $0.82{\times}10^{-3}%$ for fat, SNF and protein contents, respectively.

• Asian-Australasian Journal of Animal Sciences
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• 제32권3호
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• pp.334-340
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• 2019

Objective: The objective of this study was to investigate the genetic components of daily milk yield and to re-rank bulls in South Korea by estimated breeding value (EBV) under heat stress using the temperature-humidity index (THI). Methods: This study was conducted using 125,312 monthly test-day records, collected from January 2000 to February 2017 for 19,889 Holstein cows from 647 farms in South Korea. Milk production data were collected from two agencies, the Dairy Cattle Genetic Improvement Center and the Korea Animal Improvement Association, and meteorological data were obtained from 41 regional weather stations using the Automated Surface Observing System (ASOS) installed throughout South Korea. A random regression model using the THI was applied to estimate genetic parameters of heat tolerance based on the test-day records. The model included herd-year-season, calving age, and days-in-milk as fixed effects, as well as heat tolerance as an additive genetic effect, permanent environmental effect, and direct additive and permanent environmental effect. Results: Below the THI threshold (${\leq}72$; no heat stress), the variance in heat tolerance was zero. However, the heat tolerance variance began to increase as THI exceeded the threshold. The covariance between the genetic additive effect and the heat tolerance effect was -0.33. Heritability estimates of milk yield ranged from 0.111 to 0.176 (average: 0.128). Heritability decreased slightly as THI increased, and began to increase at a THI of 79. The predicted bull EBV ranking varied with THI. Conclusion: We conclude that genetic evaluation using the THI function could be useful for selecting bulls for heat tolerance in South Korea.

• Asian-Australasian Journal of Animal Sciences
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• 제29권6호
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• pp.775-781
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• 2016

A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM) considering different order of Legendre polynomial for the additive genetic effect (4th order) and the permanent environmental effect (5th order). Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11) to 0.99 (TD-4 and TD-5). The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields.

• Asian-Australasian Journal of Animal Sciences
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• 제5권3호
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• pp.567-570
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• 1992

Variance components were estimated for calf daily gain from birth to 45 days of age in small (S), medium (M) and large (L) lines of beef cattle. Analyses involved records collected on 682 (S), 510 (M) and 228 (L) calves in Iowa, USA from 1978 to 1986. Cytoplasmic lines were determined based on the foundation female in the maternal lineage of each animal. Data were analyzed separately by size line using a derivative-free restricted maximum likelihood procedure under an animal model including additive direct (a), additive maternal (m), cytoplasmic lineage effects and covariance (a, m). The heritabilities for direct and maternal, and the cytoplasmic effects, were 0.13, 0.35 and 0.00 for S, 0.14, 0.32 and 0.00 for M, and 0.05, 0.33 and 0.03 for L. Genetic correlations (a, m) for S, M and L were -0.33, -0.57 and -1.00, respectively. The maternal genetic effect was the most important for calf growth between birth and 45 dyas of age and cytoplasmic variances were not important in any line.

• Asian-Australasian Journal of Animal Sciences
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• 제17권2호
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• pp.153-158
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• 2004

Data containing 14,188 lactation and reproductive records of Korean Holstein cows at first parity distributed across 3,734 herd-year-season groups were analyzed to get genetic (co)variance estimates for milk yield, fat yield, calving ease, and days open. Milk and Fat yields were adjusted to 305 d. Heritabilities and genetic correlations were estimated in two different animal models on which were included direct genetic effects (Model 1) and direct+maternal genetic effects (Model 2) using REML algorithms. Milk and fat yields were affected by age at first calving as linear and quadratic. Heritability estimates of direct effects were 0.25 for milk yield, 0.17 for fat yield, 0.03 for calving ease and 0.03 for days open in Model 2. These estimates for maternal effects were 0.05, 0.08, 0.04 and less than 0.01 for each corresponding trait. Milk productions at first lactation were to show genetically favorable correlation with calving ease and days open for direct genetic effects (-0.24 - -0.11). Moreover, calving ease was correlated with days open of 0.30 for direct genetic effects. Correlations between direct and maternal effects for each trait were negatively correlated (-0.63 - -0.32). This study suggested that maternal additive genetic variance would be not ignorable for genetic evaluation of milk production as well as reproductive traits such as calving ease and days open at first parity. Furthermore, difficult calving would genetically influence the next conception.

• 한국수정란이식학회지
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• 제29권3호
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• pp.289-296
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• 2014

제주마 경주 능력 개량을 위한 기초 자료 확보를 위하여 혈통 정보량과 오류량이 유전 모수 추정에 미치는 영향을 분석하였다. 혈통 자료는 램덤으로 혈통 정보의 삭제(0~25%) 또는 오류 유발(0~25%)과 각 수준별 20회 반복으로 모의자료를 형성하였다. 분석에 이용된 형질은 제주마 1,000m 경주의 주파 시간을 이용하였고, 상가적 유전 분산의 추정은 DF-REMLAI 알고리즘을 이용하였다. 개체의 양부모에 대한 정보 유실량과 오류량의 증가는 선형적인 회귀관계로 상가적 유전 분산 성분(유실 b = -0.079, 오류 b= -0.114)과 유전력 추정치(유실, b= -0.006; 오류, b = 0.008)의 감소를 초래했다(p<0.01). 특히 개체의 양부모에 대한 정보유실보다는 정보 오류가 상가적 유전분산량과 유전력 추정치를 보다 크게 왜곡하는 것으로 나타났다. 부 또는 모에 대한 정보의 유실과 오류의 증가도 대부분 오차 분산 성분과 영구 환경 분산 성분의 증가를 유발시키고, 상가적 유전 분산성분의 감소를 가져왔다. 원자료에서 얻은 모수를 기준으로 했을 때 양부모에 대한 정보의 유실량과 오류량이 1% 증가함에 따라 유전력은 각각 0.92% 및 1.39%씩 낮아지는 관계를 보였다 (p<0.01). 제주마의 1,000m 주파 속도에 대한 유전력은 0.60으로 추정되었지만, 초기 집단에 존재하는 혈통 정보의 누락 및 오류를 고려한다면 실제보다도 10% 정도는 낮게 추정되고 있다고 사료되었다. 이와 같은 결과는 상가적 유전 분산량의 감소는 물론, 선발에 따른 제주마의 경주 능력에 대한 유전적 개량량에도 영향을 줄 것으로 판단된다.

• Asian-Australasian Journal of Animal Sciences
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• 제30권10호
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• pp.1382-1387
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• 2017

Objective: During the last decade, genetic evaluation of dairy cows using longitudinal data (test day milk yield or 305-day milk yield) using random regression method has been officially adopted in several countries. The objectives of this study were to estimate covariance functions for genetic and permanent environmental effects and to obtain genetic parameters of 305-day milk yield over seven parities. Methods: Data including 60,279 total 305-day milk yield of 17,309 Iranian Holstein dairy cows in 7 parities calved between 20 to 140 months between 2004 and 2011. Residual variances were modeled by homogeneous and step functions with 7 and 10 classes. Results: The results showed that a third order polynomial for additive genetic and permanent environmental effects plus a step function with 10 classes for the residual variance was the most adequate and parsimonious model to describe the covariance structure of the data. Heritability estimates obtained by this model varied from 0.17 to 0.28. The performance of this model was better than repeatability model. Moreover, 10 classes of residual variance produce the more accurate result than 7 classes or homogeneous residual effect. Conclusion: A quadratic Legendre polynomial for additive genetic and permanent environmental effects with 10 step function residual classes are sufficient to produce a parsimonious model that explained the change in 305-day milk yield over consecutive parities of Iranian Holstein cows.

• Asian-Australasian Journal of Animal Sciences
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• 제28권8호
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• pp.1090-1094
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• 2015

The aim of the study was to select traits that may constitute a prospective criterion for breeding value prediction of young horses. The results of 1,232 starts of 894 four-, five-, six-, and seven-year-old horses, obtained during jumping championships for young horses which had not been evaluated in, alternative to championships, training centres were analyed. Nine traits were chosen of those recorded: ranking in the championship, elimination (y/n), conformation, rating of style on day one, two, and three, and penalty points on day one, two, and three of a championship. (Co)variance components were estimated via the Gibbs sampling procedure and adequate (co)variance component ratios were calculated. Statistical classifications were trait dependent but all fitted random additive genetic and permanent environment effects. It was found that such characteristics as penalty points and jumping style are potential indicators of jumping ability, and the genetic variability of the traits was within the range of 14% to 27%. Given the low genetic correlations between the conformation and other results achieved on the parkour, the relevance of assessment of conformation in four-years-old horses has been questioned.

• Asian-Australasian Journal of Animal Sciences
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• 제15권7호
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• pp.925-931
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• 2002

Gibbs sampling algorithms were implemented to the multi-trait threshold animal models with any combinations of multiple binary, ordered categorical, and linear traits and investigate the amount of bias on these models with two kinds of parameterization and algorithms for generating underlying liabilities. Statistical models which included additive genetic and residual effects as random and contemporary group effects as fixed were considered on the models using simulated data. The fully conditional posterior means of heritabilities and genetic (residual) correlations were calculated from 1,000 samples retained every 10th samples after 15,000 samples discarded as "burn-in" period. Under the models considered, several combinations of three traits with binary, multiple ordered categories, and continuous were analyzed. Five replicates were carried out. Estimates for heritabilities and genetic (residual) correlations as the posterior means were unbiased when underlying liabilities for a categorical trait were generated given by underlying liabilities of the other traits and threshold estimates were rescaled. Otherwise, when parameterizing threshold of zero and residual variance of one for binary traits, heritability estimates were inflated 7-10% upward. Genetic correlation estimates were biased upward if positively correlated and downward if negatively correlated when underling liabilities were generated without accounting for correlated traits on prior information. Residual correlation estimates were, consequently, much biased downward if positively correlated and upward if negatively correlated in that case. The more categorical trait had categories, the better mixing rate was shown.