• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1836-1843
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• 2019

Objective: Social genetic effects (SGE) are an important genetic component for growth, group productivity, and welfare in pigs. The present study was conducted to evaluate i) the feasibility of the single-step genomic best linear unbiased prediction (ssGBLUP) approach with the inclusion of SGE in the model in pigs, and ii) the changes in the contribution of heritable SGE to the phenotypic variance with different scaling ${\omega}$ constants for genomic relationships. Methods: The dataset included performance tested growth rate records (average daily gain) from 13,166 and 21,762 pigs Landrace (LR) and Yorkshire (YS), respectively. A total of 1,041 (LR) and 964 (YS) pigs were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel. With the BLUPF90 software package, genetic parameters were estimated using a modified animal model for competitive traits. Giving a fixed weight to pedigree relationships (${\tau}:1$), several weights (${\omega}_{xx}$, 0.1 to 1.0; with a 0.1 interval) were scaled with the genomic relationship for best model fit with Akaike information criterion (AIC). Results: The genetic variances and total heritability estimates ($T^2$) were mostly higher with ssGBLUP than in the pedigree-based analysis. The model AIC value increased with any level of ${\omega}$ other than 0.6 and 0.5 in LR and YS, respectively, indicating the worse fit of those models. The theoretical accuracies of direct and social breeding value were increased by decreasing ${\omega}$ in both breeds, indicating the better accuracy of ${\omega}_{0.1}$ models. Therefore, the optimal values of ${\omega}$ to minimize AIC and to increase theoretical accuracy were 0.6 in LR and 0.5 in YS. Conclusion: In conclusion, single-step ssGBLUP model fitting SGE showed significant improvement in accuracy compared with the pedigree-based analysis method; therefore, it could be implemented in a pig population for genomic selection based on SGE, especially in South Korean populations, with appropriate further adjustment of tuning parameters for relationship matrices.

• 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.

• Animal Bioscience
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• v.37 no.5
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• pp.795-806
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• 2024

Objective: Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (N_e) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of N_e and LD for the long-term sustainability of these breeds. Methods: The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes. Results: The average LD between single nucleotide polymorphisms (SNPs) was r² = 0.13 in the present study. LD decay (r² = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based N_e of KF was determined to be 78, while the N_e estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for N_e estimation), respectively. Conclusion: KF cattle have an N_e exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for long-term sustainable development.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1244-1251
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• 2015

A herd of Berkshire pigs was established in 2003 and subjected to selection without introduction of any genetic resources until 2007. The complete pedigree, including 410 boars and 916 sows, as well as the records from 5,845 pigs and 822 litters were used to investigate the results obtained from the selections. The index of selection for breeding values included days to 90 kg (D90kg), backfat thickness (BF) and number of piglets born alive (NBA). The average inbreeding coefficients of pigs were found to be 0.023, 0.008, 0.013, 0.025, 0.026, and 0.005 from 2003 to 2007, respectively. The genetic gains per year were 12.1 g, -0.04 mm, -3.13 days, and 0.181 head for average daily gain (ADG), BF, D90kg, and NBA, respectively. Breeding values of ADG, BF and D90kg were not significantly correlated with inbreeding coefficients of individuals, except for NBA (-0.21). The response per additional 1% of inbreeding was 0.0278 head reduction in NBA. The annual increase of inbreeding was 0.23% and the annual decrease in NBA due to inbreeding was 0.0064 head. This magnitude could be disregarded when compared with the annual gain in NBA (0.181 head). These results suggest that inbreeding and inbreeding depression on ordinary farms can be controlled with a proper breeding scheme and that breeding programs are economical and safe relative to the risks associated with importation of pigs.

• Genomics & Informatics
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• v.13 no.4
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• pp.146-151
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• 2015

Previous studies in Holstein have shown 35% to 51.8% heritability in milk production traits, such as milk yield, fat, and protein, using pedigree data. Other studies in complex human traits could be captured by common single-nucleotide polymorphisms (SNPs), and their genetic variations, attributed to chromosomes, are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analyzed three quantitative Holstein traits relevant to milk production in Korean Holstein data harvested from 462 individuals genotyped for 54,609 SNPs. For all three traits (milk yield, fat, and protein), we estimated a nominally significant (p = 0.1) proportion of variance explained by all SNPs on the Illumina BovineSNP50 Beadchip ($h^2_G$). These common SNPs explained approximately most of the narrow-sense heritability. Longer genomic regions tended to provide more phenotypic variation information, with a correlation of 0.46~0.53 between the estimate of variance explained by individual chromosomes and their physical length. These results suggested that polygenicity was ubiquitous for Holstein milk production traits. These results will expand our knowledge on recent animal breeding, such as genomic selection in Holstein.

• Animal Bioscience
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• v.34 no.8
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• pp.1283-1289
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• 2021

Objective: The progestogen-associated endometrial protein (PAEP) gene encodes the main whey protein in milk, β-lactoglobulin. The aim of the study was to investigate polymorphism in the PAEP gene and its association with milk yield, composition, and quality. Methods: Test-day records for 782 dairy cows were analysed. A total of 10 single nucleotide polymorphisms (SNP) within the PAEP gene were investigated. The following parameters were recorded: milk yield (MY, kg/d), percent milk fat (%), protein (PP, %), dry matter (DMP, %) and lactose (LP, %), urea content (UC, mg/L) as well as natural logarithm for somatic cell count (LnSCC, ln). Effect on genomic estimated breeding values accuracy was evaluated with pedigree and single step model. Results: Results show that only three SNPs were polymorphic, creating 5 composite genotypes: P1 to P5. Differences in MY between composite genotypes were noted in the two tested herds. Cows with P5 composite genotypes were characterised by the highest PP and LnSCC and the lowest LP and UC (p<0.05). P4 was linked to an increased DMP and UC, while P3 to an increase in LP and decrease in PP and LnSCC. Both factors are important markers in herd management and have high influences on the herds economics. For 5 out of 7 traits the accuracy of prediction was improved by including the haplotype as a fixed effect. Conclusion: Presented results may suggest a new way to optimise breeding programmes and demonstrate the impact of using genomic data during that process.

• Korean Journal of Breeding Science
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• v.41 no.3
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• pp.319-323
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• 2009

Strawberry is an out-crossed crop that is relatively sensitive to inbreeding, and as a result, most of breeding programmes in strawberry have been based on selection breeding where elite parents are selected from intercrossing. Also, pedigree breeding has been successfully employed in a number of instances to concentrate genes of interest. Therefore, in order to obtain inbred line having the genotype of excellent combining ability by selfing and incrossing to improve breeding efficiency of strawberry, elite varieties were self-pollinated. From the selfing line of "Benihoppe" cultivar, we selected "Wongyo 3111" having excellent horticultural traits such as plant vigor, sugar content and fruit hardness among these progenies. "Wongyo 3111" shows erect plant type, vigorous growth habit, early flower bud differentiation with 16~17 flowers per cluster. Fruits of "Wongyo 3111" are conical type having a bright red skin color, and 17.2 g in an average weight. Also that have a relatively more high sugar/acid ratio and firmness than check cultivars as sugar content of 11.3oBx, acidity of 0.50% and firmness of 21.7 g/$mm^2$. But although yield of "Wongyo 3111" is not significantly different from check cultivars, its marketable yield is remarkably lower than that of check cultivars because of poor fruit-setting under low temperature. Disease and pest reactions of "Wongyo 3111" are more sensitive to powery mildew, anthracnose and spotted spider mites than check cultivars. Therefore, "Wongyo 3111" is suitable for intermediate parent line better than as a cultivation cultivar.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.4
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• pp.470-475
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• 2013

The objective of this study was to estimate genetic parameters that are to be used for across-herd genetic evaluations of seed stock pigs at GGP level. Performance data with pedigree information collected from swine breeder farms in Korea were provided by Korea Animal Improvement Association (AIAK). Performance data were composed of final body weights at test days and ultrasound measures of back fat thickness (BF), rib eye area (EMA) and retail cut percentage (RCP). Breeds of swine tested were Landrace, Yorkshire and Duroc. Days to 90 kg body weight (DAYS90) were estimated with linear function of age and ADG calculated from body weights at test days. Ultrasound measures were taken with A-mode ultrasound scanners by trained technicians. Number of performance records after censoring outliers and keeping records pigs only born from year 2000 were of 78,068 Duroc pigs, 101,821 Landrace pigs and 281,421 Yorkshire pigs. Models included contemporary groups defined by the same herd and the same seasons of births of the same year, which was regarded as fixed along with the effect of sex for all traits and body weight at test day as a linear covariate for ultrasound measures. REML estimation was processed with REMLF90 program. Heritability estimates were 0.40, 0.32, 0.21 0.39 for DAYS90, ADG, BF, EMA, RCP, respectively for Duroc population. Respective heritability estimates for Landrace population were 0.43, 0.41, 0.22, and 0.43 and for Yorkshire population were 0.36, 0.38, 0.22, and 0.42. Genetic correlation coefficients of DAYS90 with BF, EMA, or RCP were estimated to be 0.00 to 0.09, -0.15 to -0.25, 0.22 to 0.28, respectively for three breeds populations. Genetic correlation coefficients estimated between BF and EMA was -0.33 to -0.39. Genetic correlation coefficient estimated between BF and RCP was high and negative (-0.78 to -0.85) but the environmental correlation coefficients between these two traits was medium and negative (near -0.35), which describes a highly correlated genetic response to selection on one or the other of these traits. Genetic Trends of all three breeds tend to be towards bigger EMA or greater RCP and shorter DAYS90 especially from generations born after year 2000.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.10
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• pp.1395-1397
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• 2002

The tyrosinase gene was selected as a candidate for uncovering genetic mechanism causing 'black ear' coat color in rabbits. A PCR-SSCP detection method was established for the $881^A{\rightarrow}881^G$ mutation located in the central region of the tyrosinase gene between the CuA and CuB binding region signatures, and this was confirmed by sequencing and alignment. Fully consistent associations between the SNP and 'black ear' coat color were observed by analysis in a "black ear" pedigree and on 61 unrelated individuals. This SNP can serve as a molecular marker for use in "back ear" wool rabbit breeding.

• Horticultural Science & Technology
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• v.16 no.1
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• pp.18-20
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• 1998

The present research was conducted to study genetic relationship and cultivar identification in sweet potato (lpomoea batatas) using RAPD method. Thirteen cultivars of sweet potato in Korea were classified by UPGMA clustering method into three groups as follows; group I was corresponded to 'Choongsung100'; group II, 'Eunmi', 'Saengmi', 'Suwon147' and 'Yulmi'; group III, 'Hongmi', 'Jinmi', 'Kwandong95', 'Seonmi', 'Wonmi', 'Shinyulmi', 'Jeungmi', and 'Poongmi'. Identification using RAPD was generally consistent with breeding pedigree of those parents. However, inconsistent results may be caused by clonal variation. The results presented in this study suggest that RAPDs in sweetpotato are likely to be useful for cultivar identification and various procedures in breeding. The use of various DNA marker system assists selection programs for economically important trait, and may facilitate selection in earlier growing stage. This systems may enhance the prospects for improving sweet potato cultivar by accurate marking desirable traits at DNA level.