• Asian-Australasian Journal of Animal Sciences
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• 제14권11호
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• pp.1505-1510
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• 2001

A method for mapping quantitative trait loci (QTL) was introduced incorporating the information of mixed progeny from complex pedigrees. The method consisted of two steps based on single marker analysis. The first step was to examine the marker-trait association with a mixed model considering common environmental effect and reversed QTL-marker linkage phase. The second step was to estimate QTL effects by a weighted least square analysis. A simulation study indicated that the method incorporating mixed progeny from multiple generations improved the accuracy of QTL detection. The influence of within-genotype variance and recombination rate on QTL analysis was further examined. Detecting a QTL with a large within-genotype variance was more difficult than with a small within-genotype variance. Most of the significant marker-QTL association was detectable when the recombination rate was less than 15%.

• Asian-Australasian Journal of Animal Sciences
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• 제12권6호
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• pp.850-853
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• 1999

Angus postweaning daily gain (PWDG) was analyzed to investigate effects of the heterogeneous variance and the genotypes by sex interaction on prediction of EBVs with data sets of various environmental levels. A whole data (16,239 records) was divided into six data sets according to averages of the best linear unbiased estimator (BLUE) of herd environment. The results comparing prediction models showed that single-trait model is adequate for most of the data sets except for the data set of poor environment for both of the bulls and the heifers where the heterogeneity of variance and the genotypes by sex interaction exists. In the prediction with the data set of the low environment level, the bull's EBVs by single-trait models had high product moment correlations with male EBVs of the bulls by the multitrait model. Whereas the heifer's EBVs had moderate correlations with female EBVs by the multitrait model. This moderate correlation seems to be resulted by the heterogeneity of variance and low heritability of the heifer's PWDG. The prediction models with heterogeneity of variance had little effect on the prediction of EBVs for the data sets with moderate to high genetic correlations.

• Asian-Australasian Journal of Animal Sciences
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• 제24권11호
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• pp.1525-1528
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• 2011

The purpose of this study was to detect SNPs that were responsible for a carcass trait in Hanwoo populations. A non-parametric model applying a restricted partition method (RPM) was used, which exploited a partitioning algorithm considering statistical criteria for multiple comparison testing. Phenotypic and genotypic data were obtained from the Hanwoo Improvement Center, National Agricultural Cooperation Federation, Korea, in which the pedigree structure comprised 229 steers from 16 paternal half-sib proven sires that were born in Namwon or Daegwanryong livestock testing station between spring of 2002 and fall of 2003. A carcass trait, longissimus dorsi muscle area for each steer was measured after slaughter at approximately 722 days. Three SNPs (19_1, 18_4 and 28_2) near the microsatellite marker ILSTS035 on BTA6, around which the quantitative trait loci (QTL) for meat quality were previously detected, were used in this study. The RPM analyses resulted in two significant interaction effects between SNPs (19_1 and 18_4) and (19_1 and 28_2) at ${\alpha}$ = 0.05 level. However, under a general linear (parametric) model no interaction effect between any pair of the three SNPs was detected, while only one main effect for SNP19_1 was found for the trait. Also, under another non-parametric model using a multifactor dimensionality reduction (MDR) method, only one interaction effect of the two SNPs (19_1 and 28_2) explained the trait significantly better than the parametric model with the main effect of SNP19_1. Our results suggest that RPM is a good alternative to model choices that can find associations of the interaction effects of multiple SNPs for quantitative traits in livestock species.

• Journal of Animal Science and Technology
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• 제63권6호
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• pp.1211-1222
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• 2021

Data of 651 lambs (68 Romanov, 49 Rahmani, 151 [♀1/2 Rahmani × ♂1/2 Romanov) and 383 (♀3/4 Rahmani and 1/4♂ Romanov]) were collected from Mehalet Mousa Farm, belonging to Animal Production Research Institute from the period of 2009 to 2016 to estimate phenotypic and genetic parameters. The traits studied were birth weight (BW), body weight at four week (BW4), body weight at eight weeks (BW8) and body weight at twelve weeks (BW12) or weaning weight. Least squares analysis of variance shows significance of the effects of breed groups, gender of lambs, birth type; month of birth and year of birth on all traits studied. Rahmani lambs had heavier BW, BW4, BW8 and BW12 while Romanov lambs had the lowest ones. The first generation (♀1/2 Rhamani × ♂1/2 Romanov) had heavier body weights than Romanov and the second generation (♀3/4 Rahmani × ♂1/4 Roamnov). Gender of lambs had highly significant effect on body weights. Males were significantly (p < 0.01) heavier than females for all traits studied. Least square means of BW, BW4, BW8 and BW12 for single lambs were 2.69, 10.43, 13.53 and 16.10 kg, respectively. Least square means of BW, BW4, BW8 and BW12 for twin lambs were 2.50, 9.37, 12.5 and 15.16 kg, respectively, while least square means of BW, BW4, BW8 and BW12 for triple lambs were 2.09, 7.86, 10.83 and 13.67 kg, respectively. Estimates of direct heritability measured by single trait animal model were 0.14, 0.23, 0.25 and 0.26 for BW, BW4, BW8 and BW12, respectively, and the corresponding measured by multi trait animal model were 0.17, 0.24, 0.32 and 0.36 for the same traits, respectively. All genetic and phenotypic correlations among different traits studied are positive and significant.

• Asian-Australasian Journal of Animal Sciences
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• 제12권7호
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• pp.1015-1018
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• 1999

Single trait mixed models have been dominantly utilized for genetic evaluation of the reproductive traits in swine. However employing multiple trait approach may lead to more accurate genetic evaluations. For 5 litter size and litter weight traits of Danish Landrace, genetic parameters were estimated with a multiple trait mixed model. The heritability estimates were 0.02, 0.03, 0.03, 0.05, and 0.07, respectively for litter size at birth, litter size born alive, litter weight at birth, litter size at weaning, and litter weight at weaning. Negative genetic correlations were all positive. The litter weight at birth showed genetic antagonism with litter size born alive (-0.65) and litter size at weaning (-0.31), but positive with litter size at birth (0.47) and litter weight at weaning (0.31). The estimates of environmental correlations were larger than their corresponding genetic correlation estimates except for those between litter weight at birth and the other four traits. This study recommends simultaneous selection for two or more traits with multivariate mixed models in order to improve overall economic response.

• Asian-Australasian Journal of Animal Sciences
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• 제10권1호
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• pp.75-78
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• 1997

Season is very important as it defines the contemporaries for sire and cow evaluation. An attempt is made for defining season for animal model evaluation of Sahiwal animals, using 1,227 records from 730 cows. Cows were required to have a lactation length of 305-days. Ten different combinations of months for two, four, five or other seasons were tried. The other fixed effect in the model was age defined within parity. The random effects were permanent environment and animal's breeeding value along with the residual effects. A single trait animal model was used where all known relationships of an animal were incorporated in a relationship matrix. The error variance from the fitted model decreased as the number of year-season combinations increased, indicating a month-year model to be more appropriate. This, on the other hand, decreased the number of contemporaries for certain subclasses to a minimum of one, making the bull comparisons invalid. Use of a two season scenario, with winter (November through February) and summer (March through October) was better than the other combinations in terms of error variance of the fitted model and the number of lactations represented in any year-season subclass.

• Asian-Australasian Journal of Animal Sciences
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• 제20권9호
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• pp.1327-1333
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• 2007

Lactose synthase catalyses the formation of lactose which is the major osmole of bovine milk and regulates the milk volume. Alpha-lactalbumin (${\alpha}$-LA) is involved in the synthesis of lactose synthase in the mammary gland. Therefore ${\alpha}$-LA is regarded as a plausible candidate gene for the milk yield trait. To determine whether ${\alpha}$-LA is associated with milk performance traits, 1,028 Chinese Holstein cows were used to detect polymorphisms in the ${\alpha}$-LA by means of single-strand conformation polymorphism (SSCP). Two nucleotide transitions were identified in the 5'flanking region and intron 3 of ${\alpha}$-LA. Associations of such polymorphisms with five milk performance traits were analyzed using a general linear model procedure. No significant associations were observed between these polymorphisms and the five milk performance traits (p>0.05). RH mapping placed ${\alpha}$-LA on BTA5q21, linked most closely to markers U63110, CC537786 and L10347 (LOD>8.3), which is far distant from the region of the quantitative trait locus (QTL) on bovine chromosome 5 for variation in the milk yield trait. In summary, based on our findings, we eliminated these SNPs from having an effect on milk performance traits.

• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1537-1544
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• 2015

Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l'Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.

• Asian-Australasian Journal of Animal Sciences
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• 제13권2호
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• pp.149-154
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• 2000

The objectives of this study of Hanwoo (Korean Cattle) were 1) to estimate genetic parameters for direct and maternal genetic effects for birth weight, weaning weight, and six months weight which can be used for genetic evaluations and 2) to compare models with and without grandmatemal effects. Data were obtained from the National Livestock Research Institute in Rural Development Administration (RDA) of Korea and were used to estimate genetic parameters for birth weight (BW, n=10,889), weaning weight at 120-d (WW, n=8,637), and six month weight (W6, n=8,478) in Hanwoo. Total number of animals in pedigrees was 14,949. A single-trait animal model was initially used to obtain starting values for multiple-trait animal models. Estimates of genetic parameters were obtained with MTDFREML using animal models and derivative-free REML (Boldman et al., 1995). Estimates of direct heritability for BW, WW, and W6 analyzed as single-traits were 0.09, 0.03, and 0.02 from Model 3 which included direct and maternal genetic, maternal permanental environmental effects, and effects due to sire ${\times}$ region ${\times}$ year-season interaction, respectively. Ignoring sire ${\times}$ region ${\times}$ year-season interaction effect in the model (Model 2) resulted in larger estimates for direct heritability than for Model 3. Estimates of maternal heritability for BW, WW and W6 were 0.04, 0.05, and 0.07 from Model 3, respectively. The estimates of direct-maternal genetic correlation were positive for BW, WW, and W6 with Model 3 but were negative with Model 2 for WW and W6. Estimates of direct genetic correlations between BW and WW, BW and W6, and WW and W6 were large: 0.52, 0.45, and 0.90, respectively. Genetic correlations were also large and positive for maternal effects for BW with maternal effects for WW and W6 (0.69 and 0.74), and even larger for WW with W6 (0.97). The log likelihood values were the same for models including grandmatemal effects as for models including maternal effects for all traits. These results indicate that grandmatemal effects are not important for these traits for Hanwoo or that the data structure was not adequate for estimating parameters for a grandmatemal model.

• Asian-Australasian Journal of Animal Sciences
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• 제31권9호
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• pp.1407-1414
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• 2018

Objective: The aim of this study was to estimate (co) variance components and genetic parameters for categorical carcass traits using Bayesian inference via mixed linear and threshold animal models in Anglonubian goats. Methods: Data were obtained from Anglonubian goats reared in the Brazilian Mid-North region. The traits in study were body condition score, marbling in the rib eye, ribeye area, fat thickness of the sternum, hip height, leg perimeter, and body weight. The numerator relationship matrix contained information from 793 animals. The single- and two-trait analyses were performed to estimate (co) variance components and genetic parameters via linear and threshold animal models. For estimation of genetic parameters, chains with 2 and 4 million cycles were tested. An 1,000,000-cycle initial burn-in was considered with values taken every 250 cycles, in a total of 4,000 samples. Convergence was monitored by Geweke criteria and Monte Carlo error chain. Results: Threshold model best fits categorical data since it is more efficient to detect genetic variability. In two-trait analysis the contribution of the increase in information and the correlations between traits contributed to increase the estimated values for (co) variance components and heritability, in comparison to single-trait analysis. Heritability estimates for the study traits were from low to moderate magnitude. Conclusion: Direct selection of the continuous distribution of traits such as thickness sternal fat and hip height allows obtaining the indirect selection for marbling of ribeye.