• Journal of Animal Science and Technology
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• v.65 no.6
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• pp.1194-1204
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• 2023

Meat quality comprises a set of key traits such as pH, meat color, water-holding capacity, tenderness and marbling. These traits are complex because they are affected by multiple genetic and environmental factors. The aim of this study was to investigate the molecular genetic basis underlying nine meat quality-related traits in a Yorkshire pig population using a genome-wide association study (GWAS) and subsequent biological pathway analysis. In total, 45,926 single nucleotide polymorphism (SNP) markers from 543 pigs were selected for the GWAS after quality control. Data were analyzed using a genome-wide efficient mixed model association (GEMMA) method. This linear mixed model-based approach identified two quantitative trait loci (QTLs) for meat color (b^*) on chromosome 2 (SSC2) and one QTL for shear force on chromosome 8 (SSC8). These QTLs acted additively on the two phenotypes and explained 3.92%-4.57% of the phenotypic variance of the traits of interest. The genes encoding HAUS8 on SSC2 and an lncRNA on SSC8 were identified as positional candidate genes for these QTLs. The results of the biological pathway analysis revealed that positional candidate genes for meat color (b^*) were enriched in pathways related to muscle development, muscle growth, intramuscular adipocyte differentiation, and lipid accumulation in muscle, whereas positional candidate genes for shear force were overrepresented in pathways related to cell growth, cell differentiation, and fatty acids synthesis. Further verification of these identified SNPs and genes in other independent populations could provide valuable information for understanding the variations in pork quality-related traits.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.628-634
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• 2014

Data on age and body weight at breeding, parity, previous litter size, days open and some descriptive body linear traits from 389 meat-type, prolific Black Bengal goats in Tripura State of India, were collected for 3 and 1/2 years (2007 to 2010) and analyzed using logistic regression model. The objectives of the study were i) to evaluate the effect of age and body weight at breeding, parity, previous litter size and days open on litter size of does; and ii) to investigate if body linear type traits influenced litter size in meat-type, prolific goats. The incidence of 68.39% multiple births with a prolificacy rate of 175.07% was recorded. Higher age (>2.69 year), higher parity order (>2.31), more body weight at breeding (>20.5 kg) and larger previous litter size (>1.65) showed an increase likelihood of multiple litter size when compared to single litter size. There was a strong, positive relationship between litter size and various body linear type traits like neck length (>22.78 cm), body length (>54.86 cm), withers height (>48.85 cm), croup height (>50.67 cm), distance between tuber coxae bones (>11.38 cm) and distance between tuber ischii bones (>4.56 cm) for discriminating the goats bearing multiple fetuses from those bearing a single fetus.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.1
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• pp.7-12
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• 2006

The objective of this study was to estimate genetic parameters between first and later parities as different traits in reproductive traits of pigs using multiple trait animal model procedures. Data related to reproductive traits from a total of 2,371 individuals maintained at a farm were taken from the pedigree file. Sires and dams were consisted of Duroc, Landrace, and Yorkshire breeds, respectively. The first and later parity records were considered as different traits. Traits included in analyses were total pigs born (TB1), number of pigs born alive (NBA1), number of pigs weaned (NW1), and litter weaning weight (LWT1) in the first parity, and total pigs born (TB2), number of pigs born alive (NBA2), number of pigs weaned (NW2), litter weaning weight (LWT2) and interval between farrowing events (FTF) in later parities. Heritability estimates of TB1, NBA1, NW1 and LWT1 in the first parity were 0.27, 0.25, 0.16 and 0.20, respectively. For TB2, NBA2, NW2, LWT2 and FTF in later parities, heritabilities were estimated as 0.15, 0.15, 0.08, 0.11 and 0.07, respectively. Genetic correlations between sow reproductive traits in the first parity and in the second and later parity were estimated to be 0.89, 0.77, 0.58 and 0.66, respectively, between TB1 and TB2, NBA1 and NBA2, NW1 and NW2, and LWT1 and LWT2. While phenotypic correlations between TB1 and TB2, NBA1 and NBA2, NW1 and NW2, and LWT1 and LWT2 were estimated as 0.18, 0.15, 0.06 and 0.10, respectively. Genetic correlations between reproductive traits of first and later parities were not high indicating that reproductive traits for sows should be analyzed while considering the parities as different traits.

• Journal of Animal Science and Technology
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• v.44 no.6
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• pp.685-692
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• 2002

This study was carried out to estimate the genetic correlations for the carcass and growth traits of Hanwoo bulls measured at 12 and 18 months of age on the basis of the data form 1,823 heads of Hanwoo bulls raised at the Livestock Improvement Main Center from 1991 to 1998. Genetic correlations were estimated with multiple trait animal model using MTDFREML. The genetic correlations of the body weight at 12 months with average daily gain during 6${\sim}$12 months and with the body length were 0.76 and 0.79, respectively. The genetic correlations of the body weight at 18 months with average daily gain during 6${\sim}$18 months and with the body length were 0.86 and 0.82, respectively. The genetic correlations of the carcass weight with dressing percent, eye muscle area, backfat thickness and carcass length were 0.39, 0.37, 0.44 and 0.63, respectively. And estimate of 0.36 was obtained for the genetic correlation between backfat thickness and marbling score. The high and positive genetic correlations of 0.71 and 0.96 were estimated for the carcass weight with the body weights at 12 and 18 months. The genetic correlations of the carcass weight with body lengths at 12 and 18 months were 0.63 and 0.75, respectively. Positive genetic correlations were estimated for the dressing percentage with the body weight, average daily gain, body length, thurls width and chest girth. Low genetic correlations were estimated between eye muscle area and the growth traits ranging from -0.07 to 0.32. Dressing percentage was low correlated genetically with the growth traits except for the chest girth at 18 months. The genetic correlation between marbling score and chest girth at 18 months estimated was 0.25.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.3
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• pp.303-310
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• 2015

The study was conducted to analyze the genetic parameters of somatic cell score (SCS) of Holstein cows, which is an important indicator to udder health. Test-day records of somatic cell counts (SCC) of 305-day lactation design from first to fifth lactations were collected on Holsteins in Korea during 2000 to 2012. Records of animals within 18 to 42 months, 30 to 54 months, 42 to 66 months, 54 to 78 months, and 66 to 90 months of age at the first, second, third, fourth and fifth parities were analyzed, respectively. Somatic cell scores were calculated, and adjusted for lactation production stages by Wilmink's function. Lactation averages of SCS ($LSCS_1$ through $LSCS_5$) were derived by further adjustments of each test-day SCS for five age groups in particular lactations. Two datasets were prepared through restrictions on number of sires/herd and dams/herd, progenies/sire, and number of parities/cow to reduce data size and attain better relationships among animals. All LSCS traits were treated as individual trait and, analyzed through multiple-trait sire models and single trait animal models via VCE 6.0 software package. Herd-year was fitted as a random effect. Age at calving was regressed as a fixed covariate. The mean LSCS of five lactations were between 3.507 and 4.322 that corresponded to a SCC range between 71,000 and 125,000 cells/mL; with coefficient of variation from 28.2% to 29.9%. Heritability estimates from sire models were within the range of 0.10 to 0.16 for all LSCS. Heritability was the highest at lactation 2 from both datasets (0.14/0.16) and lowest at lactation 5 (0.11/0.10) using sire model. Heritabilities from single trait animal model analyses were slightly higher than sire models. Genetic correlations between LSCS traits were strong (0.62 to 0.99). Very strong associations (0.96 to 0.99) were present between successive records of later lactations. Phenotypic correlations were relatively weaker (<0.55). All correlations became weaker at distant lactations. The estimated breeding values (EBVs) of LSCS traits were somewhat similar over the years for a particular lactation, but increased with lactation number increment. The lowest EBV in first lactation indicated that selection for SCS (mastitis resistance) might be better with later lactation records. It is expected that results obtained from these multi-trait lactation model analyses, being the first large scale SCS data analysis in Korea, would create a good starting step for application of advanced statistical tools for future genomic studies focusing on selection for mastitis resistance in Holsteins of Korea.

• Animal Bioscience
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• v.34 no.1
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• pp.20-25
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• 2021

Objective: The objective of the study was to investigate the possibility of utilizing an early litter size trait as an indirect selection trait for longevity and to estimate genetic parameters between sow stayability and litter size at different parities using a linear-threshold model for longevity in Thai Large White (LW) and Landrace (LR) populations. Methods: The data included litter size at first, second, and third parities (NBA1, NBA2, and NBA3) and sow stayability from first to fourth farrowings (STAY14). The data was obtained from 10,794 LR and 9,475 LW sows. Genetic parameters were estimated using the multiple-trait animal model. A linear-threshold model was used in which NBA1, NBA2, and NBA3 were continuous traits, while STAY14 was considered a binary trait. Results: Heritabilities for litter size were low and ranged from 0.01 to 0.06 for both LR and LW breeds. Similarly, heritabilities for stayability were low for both breeds. Genetic associations between litter size and stayability ranged from 0.43 to 0.65 for LR populations and 0.12 to 0.55 for LW populations. The genetic correlation between NBA1 and STAY14 was moderate and in a favorable direction for both LR and LW breeds (0.65 and 0.55, respectively). Conclusion: A linear-threshold model could be utilized to analyze litter size and sow stayability traits. Furthermore, selection for litter size at first parity, which was the genetic trait correlated with longevity, is possible when one attempts to improve lifetime productivity in Thai swine populations.

• Journal of agriculture & life science
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• v.44 no.2
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• pp.29-38
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• 2010

This study looked into estimation of variance component over swine's economic traits by multiple animal model and maternal effect model using on-farm test data of total 31,455 swine of Duroc, Landrace and Yorkshire species that were born between 2000 and 2008. Heritability by estimated additive genetic effect showed higher than one by maternal genetic effect using multivariate maternal animal model in each trait examined by each breed and most heritability when considering only additive genetic effect in multiple traits animal model was estimated to be higher than one by estimated additive genetic effect in multivariate maternal animal model. In correlation between breeding value by estimated maternal genetic effect and phenotypic value using multivariate maternal animal model, rank correlation and simple correlation of breeding value and phenotypic value by maternal genetic effect also showed low positive correlation or strong negative correlation, which can be considered that if correlation with phenotype were increased properly considering maternal genetic effect in each trait by each breed, even better improvement could be promoted.

• Animal Bioscience
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• v.35 no.11
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• pp.1649-1655
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• 2022

Objective: The primary objective of this study was to determine the genetic parameters for reproductive traits among Large White pigs, including the following traits: total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), gestation length (GL), age at first service (AFS) and age at first farrowing (AFF). Methods: The dataset consisted of 19,036 reproductive records from 4,986 sows, and a multi-trait animal model was used to estimate genetic variance components of seven reproductive traits. Results: The heritability estimates for these reproductive traits ranged from 0.09 to 0.26, with the highest heritability for GL and AFF, and the lowest heritability for NBA. The repeatabilities for TNB, NBA, LWB, ABW, and GL were ranged from 0.16 to 0.34. Genetic and phenotypic correlations ranged from -0.41 to 0.99, and -0.34 to 0.98, respectively. In particular, the correlations between TNB, NBA and LBW, between AFS and AFF, exhibited a strong positive correlation. Furthermore, for TNB, NBA, LBW, ABW, and GL, genetic correlations of the same trait between different parities were moderately to strongly correlated (0.32 to 0.97), and the correlations of adjacent parities were higher than those of nonadjacent parities. Conclusion: All the results in the present study can be used as a basis for the genetic assessment of the target population. In the formulation of dam line selection index, AFS or AFF can be considered to combine with TNB in a multiple trait swine breeding value estimation system. Moreover, breeders are encouraged to increase the proportion of sows at parity 3-5 and reinforce the management of sows at parity 1 and parity ≥8.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.8
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• pp.1088-1096
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• 2008

Data from milk performance testing were used to analyze genetic and environmental trends for purebred Tsigai, Improved Valachian and Lacaune sheep. 103,715 (Tsigai), 212,962 (Improved Valachian) and 2,196 (Lacaune) test-day records gathered by the State Breeding Institute of the Slovak Republic entered the analyses. The respective pedigree data comprised 23,724 (Tsigai), 51,401 (Improved Valachian) and 438 (Lacaune) records. The multiple-trait, mixed model methodology was used to predict the breeding values for daily milk yield, fat and protein content and to estimate the fixed and remaining random effects assumed to affect the above mentioned traits, separately for each breed. The breeding values for daily milk yield were adjusted for 150-day standardized lactation length by multiplying with the constant 150, as the breeding goal of the selection scheme in Slovakian sheep is to increase 150-day milk production and constant heritability throughout the whole lactation is assumed. The genetic trends were expressed as changes in averages of breeding values across birth years of animals. For Tsigai and Lacaune breeds, cumulative genetic changes over the analyzed period were 3.8 and 5.1 kg for 150-day milk, 0 and -0.16% for fat content and 0 and -0.12% for protein content. For Improved Valachian breed, either a low (1.6 kg for 150-day milk yield) or zero (fat and protein content) cumulative genetic change was found. The environmental trends were calculated as averages of solutions for flock-test day effect across years and months in which measurements were taken. A distinctive cyclical pattern which reflected short-time variation in milk production traits was found. Possible explanations for this phenomenon are given and discussed.

• Asian-Australasian Journal of Animal Sciences
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• v.13 no.2
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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.