• Asian-Australasian Journal of Animal Sciences
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• 제20권3호
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• pp.453-460
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• 2007

An overview of developments important in the future of animal breeding is discussed. Examples from the application of quantitative genetic principles to selection in chickens and mice are given. Lessons to be learned from these species are that selection for production traits in livestock must also consider selection for reproduction and other fitness-related traits and inbreeding should be minimized. Short-term selection benefits of best linear unbiased predictor methodology must be weighed against long-term risks of increased rate of inbreeding. Different options have been developed to minimize inbreeding rates while maximizing selection response. Development of molecular genetic methods to search for quantitative trait loci provides the opportunity for incorporating marker-assisted selection and introgression as new tools for increasing efficiency of genetic improvement. Theoretical and computer simulation studies indicate that these methods hold great promise once genotyping costs are reduced to make the technology economically feasible. Cloning and transgenesis are not likely to contribute significantly to genetic improvement of livestock production in the near future.

• Asian-Australasian Journal of Animal Sciences
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• 제28권1호
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• pp.25-36
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• 2015

The complex analysis of the pedigree records of Czech Landrace (CLA), Czech Large White-dam line (CLWd), Czech Large White-sire line (CLWs), Duroc (DC), and Pietrain (PN) was performed to determine trends of genetic diversity (GD), and to find the main sources of the GD loss. The total size of the pedigree was 132,365, 391,151, 32,913, 13,299, and 7,160 animals in CLA, CLWd, CLWs, DC, and PN, respectively. Animals born in the years 2011 through 2013 were assumed as the reference population. The average pedigree completeness index for one generation back was 95.9%, 97.4%, 91.2%, 89.8%, and 94.2% for appropriate breeds. Number of ancestors explaining 100% of gene pool was 186, 373, 125, 157, and 37 in CLA, CLWd, CLWs, DC, and PN, respectively. The relative proportion of inbred animals (58%, 58%, 54%, 47%, and 25%), the average inbreeding (2.7%, 1.4%, 2.5%, 3.6%, and 1.3%) and the average co-ancestry (3.1%, 1.6%, 3.3%, 4.2%, and 3.3%) were found over the past decade in analysed breeds. The expected inbreeding under random mating increased during the last 10 years in CLWs and PN and varied from 1.27% to 3.2%. The effective population size computed on the basis of inbreeding was 76, 74, 50, 35, and 83 in 2012 in CLA, CLWd, CLWs, DC, and PN, respectively. The shortest generation interval (1.45) was observed for CLWd in sire to son selection pathway. The longest generation interval obtained PN (1.95) in sire to daughter pathway. The average relative GD loss within last generation interval was 7.05%, 4.70%, 9.81%, 7.47%, and 10.46%, respectively. The relative proportion of GD loss due to genetic drift on total GD loss was 85.04%, 84.51%, 89.46%, 86.19%, and 83.68% in CLA, CLWd, CLWs, DC, and PN, respectively. All breeds were characterized by a high proportion of inbred animals, but the average inbreeding was low. The most vulnerable breeds to loss of GD are DC and PN. Therefore, a breeding program should be more oriented to prevent the increase of GD loss in these breeds.

• Journal of Animal Science and Technology
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• 제52권6호
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• pp.451-457
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• 2010

The porcine MHC (Major Histocompatibility Complex), encoding the SLA (Swine Leukocyte Antigen) genes, is one of the most significant regions associated with immune rejection in relation to transplantation. In this study, three SLA class I (SLA-1, SLA-3, SLA-2) loci and three SLA class II (DRB1, DQB1, DQA) loci were investigated in the previously unidentified Korean native pig (KNP) population that was closely inbred in the Livestock Technology Research Station in Cheongyang, Korea. Total thirteen KNPs from four generations were genotyped for the SLA alleles and haplotypes were investigated using PCR-SSP (Sequence-Specific Primer) method. The results showed that all of these KNPs had Lr-56.30/56.30 homozygous haplotype, indicating high level of inbreeding in the SLA genes. The inbreeding status of these animals was also investigated using microsatellite (MS) markers. From the 50 MS markers investigated, 17 MS markers were fixed in all generations and the fixed alleles are increased as 26 loci for the fourth generation. Two MS markers, S0069 and SW173, were heterozygous for all the animals tested. Observed and expected heterozygosities were calculated and the average inbreeding coefficients for each generation were also calculated. In the fourth generation, the average inbreeding coefficients was 0.732 and this may increase with further inbreeding process. Analysis of the SLA haplotypes and MS alleles can give important information for breeding the pigs for xenotransplantation studies.

• Animal Bioscience
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• 제34권12호
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• pp.1895-1902
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• 2021

Objective: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods: In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results: In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (F_ROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion: This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

• Animal Bioscience
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• 제34권6호
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• pp.975-984
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• 2021

Objective: Inbreeding depression of reproduction is a major concern in the conservation of native chicken genetic resources. Here, based on the successful development of strongly inbred (Sinb) and weakly inbred (Winb) Langshan chickens, we aimed to evaluate inbreeding effects on reproductive traits and identify candidate genes involved in inbreeding depression of reproduction in Langshan chickens. Methods: A two-sample t-test was performed to estimate the differences in phenotypic values of reproductive traits between Sinb and Winb chicken groups. Three healthy chickens with reproductive trait values around the group mean values were selected from each of the groups. Differences in ovarian and hypothalamus transcriptomes between the two groups of chickens were analyzed by RNA sequencing (RNA-Seq). Results: The Sinb chicken group showed an obvious inbreeding depression in reproduction, especially for traits of age at the first egg and egg number at 300 days (p<0.01). Furthermore, 68 and 618 differentially expressed genes (DEGs) were obtained in the hypothalamus and ovary between the two chicken groups, respectively. In the hypothalamus, DEGs were mainly enriched in the pathways related to vitamin metabolism, signal transduction and development of the reproductive system, such as the riboflavin metabolism, Wnt signaling pathway, extracellular matrix-receptor interaction and focal adhesion pathways, including stimulated by retinoic acid 6, serpin family F member 1, secreted frizzled related protein 2, Wnt family member 6, and frizzled class receptor 4 genes. In the ovary, DEGs were significantly enriched in pathways associated with basic metabolism, including amino acid metabolism, oxidative phosphorylation, and glycosaminoglycan degradation. A series of key DEGs involved in folate biosynthesis (gamma-glutamyl hydrolase, guanosine triphosphate cyclohydrolase 1), oocyte meiosis and ovarian function (cytoplasmic polyadenylation element binding protein 1, structural maintenance of chromosomes 1B, and speedy/RINGO cell cycle regulator family member A), spermatogenesis and male fertility (prostaglandin D2 synthase 21 kDa), Mov10 RISC complex RNA helicase like 1, and deuterosome assembly protein 1) were identified, and these may play important roles in inbreeding depression in reproduction. Conclusion: The results improve our understanding of the regulatory mechanisms underlying inbreeding depression in chicken reproduction and provide a theoretical basis for the conservation of species resources.

• 한국가금학회지
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• 제44권2호
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• pp.83-92
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• 2017

본 연구에서는 가금연구소에서 집단의 혈통 구조 및 근친 수준을 평가하기 위하여 근교계수와 유효집단크기를 추정하였으며, 추정한 근교계수의 신뢰 정도를 제시하기 위하여 혈통의 품질로써 1) 아비 어미를 모두 아는 개체의 비율과 2) 근교계수가 0이 아닌 개체의 비율을 태어난 부화 년도와 계통에 따라 제시하였다. 아비 어미를 모두 아는 개체의 비율에서 대부분 계통이 1~2년 사이에 거의 100%에 도달하였으며, 근교계수가 0이 아닌 개체의 비율에서 기초집단인 0세대부터 5~6년 사이에 비율이 100%에 가깝게 도달하는 것을 보면 가금연구소 혈통기록 시스템이 잘 이루어졌으며, 이 논문에서 추정한 근교계수가 신뢰할 수 있음을 나타낸다. 각 계통의 평균 근교계수에서는 20세대 동안 7.6~10.9%의 근교계수 상승도를 보였다. 세대당 가장 높은 근교계수 상승도를 보인 계통은 S계통으로 10세대 동안 8.2%의 근교계수 상승도를 보였으며, 평균 번식에 참여한 아비 어미의 수가 다른 계통에 비해 낮은 것이 원인인 것으로 사료된다. 평균 근교계수 변화량(${\Delta}F$)으로 추정한 유효집단크기를 보면 모든 계통에서 평균 근교계수 변화량이 0.39~0.85%로 1% 이하로 관리되는 것을 보이며, 따라서 유효집단크기도 모든 계통에서 50 이상의 값을 보였으며, 현 교배 관리에서 토종 닭 집단이 단시간에 근친퇴화나 집단의 멸종으로부터의 위험으로부터 안전하다고 사료된다. 그리고 유효집단크기를 유지하기 위하여, 즉 유전적 다양성을 유지하기 위하여, 적정 수의 아비 어미가 번식에 참여해야 된다고 사료된다.

• Journal of Animal Science and Technology
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• 제53권4호
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• pp.297-302
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• 2011

본 연구는 지금까지 보증 및 후보씨수소로 선발된 씨수소에 대하여 연도별 평균 근교 및 혈연계수를 추정하고 씨수소의 유효집단크기를 추정하여 현재 한우개량 체계의 문제를 도출하여 발전된 대안을 제시하고자 실시하였다. 분석에 이용된 자료는 한우개량사업소로부터 1983년부터 2008년까지 1,128두의 당 후대검정 씨수소자료와 한국종축개량협회로부터 3,760두에 대한 혈통자료를 받아 이용하였다. 보증 및 후보씨수소의 평균 근교계수는 0.04에서 0.97%의 분포로 추정되었으며, 평균 혈연계수는 0.10에서 6.82%의 분포로 추정되었다. 유효집단 크기는 1983년부터 2008년까지 26년간 평균 근교비율을 이용하였을 때 220두로 추정되었다. 근교수준은 최근 2년간 급격히 증가하였고, 평균 혈연계수 역시 점차 증가하는 추세이다. 유효집단크기도 최근 5년의 근교비율로 추정하였을 때 47두로 작게 추정되었다. 보증씨수소 선발시 후대검정우의 도체성적에 의한 유전능력평가 자료의 활용뿐만 아니라, 근교 및 혈연계수를 고려하고 한우의 유전적 다양성의 보존과 근교를 피하기 위하여 현행의 보증씨수소 두수를 증가시켜 유효집단크기를 높여야 될 필요성이 있다고 사료된다.

• Journal of Animal Science and Technology
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• 제62권6호
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• pp.777-789
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• 2020

Intense artificial selection has been imposed to Luzhong mutton sheep population in the past years. Improvements on growth and reproductive performance are two breeding goals in the present herd. Although some progresses were phenotypically observed possibly due to inbreeding induced by strong selection in terms of these traits, the genomic evaluation was poorly understood. Therefore, a high-density SNP array was used to characterize the pattern of runs of homozygosity (ROH), estimate inbreeding and inbreeding depressions on early growth performance and litter size based upon ROH, and scan positive selection signatures of recent population. Consequently, a low inbreeding level was observed which had negative effects on litter size, but not on early growth performance. And 160 genes were under selection, of which some were reported to be linked to several traits of sheep including body weight, litter size, carcass and meat quality, milk yield and composition, fiber quality and health, and the top genes were associated with growth (growth hormone [GH]- growth hormone receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding measures was highlighted, but purging selection was proposed to alleviate the inbreeding depression on litter size, providing some genomic insights to breeding management of Luzhong mutton sheep.

• Asian-Australasian Journal of Animal Sciences
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• 제15권6호
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• pp.767-771
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• 2002

Breeding efficiencies were compared among three population schemes: a single population, a population with two subpopulations and a population with three sub-populations. A simulation experiment of selection was carried out for 10 generations with 20 replications each by comparing average breeding values and inbreeding coefficients among the three population schemes. Phenotypes of three traits were generated with a model comprising 36 loci, each with additive genetic effects and residuals distributed normally. Among the three population schemes, the single population scheme was definitely superior to the other two with regards to selection response and inbreeding. The multiple sub-population scheme was, however, considered to be an alternative population scheme when the difference in economic weights of the traits was small among the sub-populations, assuming moderate inbreeding depression for traits and crossbreeding. The scheme with two sub-populations had a higher genetic value than that with three subpopulations; however, the genetic values of the schemes were comparable when maternal heterosis was taken into account. The choice of population schemes may depend on the cost-sharing policy between the breeding population and the commercial population rather than just the breeding efficiency.

• 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.