• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Journal of Animal Science and Technology
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• v.62 no.6
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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.

• Animal Bioscience
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• v.35 no.9
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• pp.1340-1350
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• 2022

Objective: Luxi Black Head sheep (LBH) is the first crossbreed specialized for meat production and was developed by crossbreeding Black Head Dorper sheep (DP) and Small Tailed Han sheep (STH) in the farming areas of northern China. Research on the genomic variations and selection signatures of LBH caused by continuous artificial selection is of great significance for identifying the genetic mechanisms of important traits of sheep and for the continuous breeding of LBH. Methods: We explored the genetic relationships of LBH, DP, and several Mongolian sheep breeds by constructing phylogenetic tree, principal component analysis and linkage disequilibrium analysis. In addition, we analysed 29 whole genomes of sheep. The genome-wide selection signatures have been scanned with four methods: heterozygosity (H_P), fixation index (F_ST), cross-population extended haplotype homozygosity (XP-EHH) and the nucleotide diversity (𝜃_π) ratio. Results: The genetic relationships analysis showed that LBH appeared to be an independent cluster closer to DP. The candidate signatures of positive selection in sheep genome revealed candidate genes for developmental process (HoxA gene cluster, BCL2L11, TSHR), immunity (CXCL6, CXCL1, SKAP2, PTK6, MST1R), growth (PDGFD, FGF18, SRF, SOCS2), and reproduction (BCAS3, TRIM24, ASTL, FNDC3A). Moreover, two signalling pathways closely related to reproduction, the thyroid hormone signalling pathway and the oxytocin signalling pathway, were detected. Conclusion: The selective sweep analysis of LBH genome revealed candidate genes and signalling pathways associated with developmental process, immunity, growth, and reproduction. Our findings provide a valuable resource for sheep breeding and insight into the mechanisms of artificial selection.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.3
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• pp.439-445
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• 2017

Objective: Production of alpha-1,3-galactosyltransferase (${\alpha}GT$)-deficient pigs is essential to overcome xenograft rejection in pig-to-human xenotransplantation. However, the production of such pigs requires a great deal of cost, time, and labor. Heterozygous ${\alpha}GT$ knockout pigs should be bred at least for two generations to ultimately obtain homozygote progenies. The present study was conducted to produce ${\alpha}GT$-deficient miniature pigs in much reduced time using mitotic recombination in neonatal ear skin fibroblasts. Methods: Miniature pig fibroblasts were transfected with ${\alpha}GT$ gene-targeting vector. Resulting gene-targeted fibroblasts were used for nuclear transfer (NT) to produce heterozygous ${\alpha}GT$ gene-targeted piglets. Fibroblasts isolated from ear skin biopsies of these piglets were cultured for 6 to 8 passages to induce loss of heterozygosity (LOH) and treated with biotin-conjugated IB4 that binds to galactose-${\alpha}$-1,3-galactose, an epitope produced by ${\alpha}GT$. Using magnetic activated cell sorting, cells with monoallelic disruption of ${\alpha}GT$ were removed. Remaining cells with LOH carrying biallelic disruption of ${\alpha}GT$ were used for the second round NT to produce homozygous ${\alpha}GT$ gene-targeted piglets. Results: Monoallelic mutation of ${\alpha}GT$ gene was confirmed by polymerase chain reaction in fibroblasts. Using these cells as nuclear donors, three heterozygous ${\alpha}GT$ gene-targeted piglets were produced by NT. Fibroblasts were collected from ear skin biopsies of these piglets, and homozygosity was induced by LOH. The second round NT using these fibroblasts resulted in production of three homozygous ${\alpha}GT$ knockout piglets. Conclusion: The present study demonstrates that the time required for the production of ${\alpha}GT$-deficient miniature pigs could be reduced significantly by postnatal skin biopsies and subsequent selection of mitotic recombinants. Such procedure may be beneficial for the production of homozygote knockout animals, especially in species, such as pigs, that require a substantial length of time for breeding.

• Journal of Korean Society of Forest Science
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• v.78 no.4
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• pp.345-359
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• 1989

This study was conducted to estimate genetic variation of Pinus densiflora in Kyungpook province which shows morphological variation between northern and southern types. Six isozymes sueh as IDH, ME, PGI, ADH, GOT and LAP was analyzed using megagametophyte tissue of seeds by electrophoresis and 16 populations of Pinus densiflora and 5 of Pinus thunbergii were tested. The results obtained were as follows ; 1. In P. densiflora, 13 Loci were found in 6 isozymes and 8 loci of them were polymorphic, having 24 alleles, while in Pinus thunbergii, there were 18 alleles detected from 6 loci among the same number of loci as in Pinus densiflora. 2. The genotypic frequency in Pinus densiflora vary slightly among populations for some isozymes, but most of them satisfied the law of Hardy-Weinherg equilibrium, while some populations such as Youngil for ADH and LAY, Youngyang for ADH and Bonghwa for LAY did not follow the law and showed high fixation index values and homozygosities higher than expected. 3. The variation among populations based on the genetic distance was small except populations of Youngju, Baegam, Gyungju and Sangju, however they could be clustered by three groups : northern Kyungpook group including Mt. Taebak, inland Kyungpook group represented by Sungju, Eusung and Kumleung population and coastal Kyungpook group represented by Baegam and Gyungju population. 4. No significant difference was found in 6 isozymes between northern and southern types of Pinus densiflora which was morphologically different. 5. The frequency of heterozygous loci per tree was higher in Pinus densiflora especially for ME-A and A DH-B, while that of homozygous loci was higher in Pinus thunbergii except for ADH-B, LAY-B and PGI-B locus.

• Korean Journal of Agricultural Science
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• v.9 no.1
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• pp.396-450
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• 1982

To obtain basic information on the Korean local corn lines a total of 57 lines were selected from 1,000 Korean local collection at Chungnam National University, classified by principal component analysis, and genetic nature was investigated. The results are summarized as follows. 1. There were a great variation in mean values of plant characters of the lines. The mean values of plant characters except for density of kernels varied with types of crossing. All characters except. for tasselling dates were reduced in magnitude when selfed, while those characters were increased when topcrossed. 2. The correlation coefficients among characters studied ranged front 0.99 to -0.59. The correlation coefficients among characters were not greatly changed depending upon types of crosses. 3. In order to classify the lines more effectively, selected 12 plant characters were used to classify 57 local lines by principal component analysis. The first four component could explain 86.4%, 83.4% and 81.1% of the total variations in sibbed lines, selfed lines and topcrossed lines, respectively. 4. Contribution of characters to principal component was high at upper principal components and low at lower principal components. 5. Biological meaning of the principal component and plant types corresponding to the each principal component were explained clearly by the correlation coefficient between principal components and characters. The first principal component appeared to correspond to the size of plant and ear. The second principal component appeared to correspond to the degree of differentiation in organs and the duration of vegetative growing period. But biological meaning of the third and fourth principal components was not clear. 6. The lines were classified into 4 lineal groups by the taxonomic distance. Group I included 52 lines which was 91.2% of total lines, group II 3 lines, group III 1 lines and group IV I lines, respectively. Four groups could be characterized as follows : Group I : early maturity, short-culmed, medium height plant, small ears, medium kernels and medium yielding. Group II : late maturity, medium height plant, small ears, small kernels, prolific ears and higher yielding. Group III : medium maturity, tall-culmed, small ears, small kernels and low yielding. Group IV : medium maturity, tall-calmed, large ears, one ear plant and me yielding. 7. The inbreeding depression varied with plant characters and lines. The characters such as yield, kernel weight per ear, ear weight and plant height showed great degree of inbreeding depression. Group I showed high inbreeding depression in such characters as 100 kernel weight, leaf number, plant height and days to tasselling, while group II showed high inbreeding depression in other plant characters. 8. Heterosis of plant characters varied also with lines. The ear weight, kernel weight per ear, yield, 100 kernel weight, and plant height were some of the plant characters showing high heterosis. Group II showed high values of heterosis in such characters as ear length, ear diameter, ear weight, kernel weight per ear, 100 kernel weight, and leaf length, while group I was high in heterosis in other plant characters. 9. The degree of homozgosity was highest in ear weight (79.1%) and lowest in ear number per plant (-21%). Group II showed higher degree of homozygosity than group I. 10. Correlation coefficients between characters of ribbed and topcrossed lines were positive for all characters. Highly significant. correlation coefficients between ribbed and topcrossed lines were obtained especially for characters such as ear number per plant, plant height, leaf length and yield per plot.

• Korean Journal of Poultry Science
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• v.16 no.2
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• pp.61-71
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• 1989

The purposes of this study were to investigate the genetic variations by backcrossing in commercial chickens. Backcrossing was carried out successively back to parent stock (P.S). Heritabilities and genetic correlation coefficients were estimated to verify the genetic variations. The data obtained from a breeding programme with commercial chickens (I strain) were collected from 1955 to 1987 at Poultry Breeding Farm, Seoul National University. Data came from a total of 1230 female offspring. The results obtained are summarized as follows： 1. The general performance ($Mean\pmStandard deviation$) of each trait was $663.94\pm87.11$g for 8 weeks body weight, $1579.1\pm155.43$g for 20 weeks body weight, $2124.1\pm215.3$g for 40 weeks body weight, $2269.1\pm242.94$g for 60 weeks body weight, $168.43\pm12.94$ day for a9e at sexual maturity (SM), $214.52\pm29.82$ eggs , for total egg number to 60 weeks of age (TEN), $61.45\pm3.48$ g for average weight (AEW), $13180.7\pm1823.22$ g for total egg mass to 60 weeks of age(TEM). All traits, except 10 weeks body weight and AEW, were significant for the degrees of backcross (p＜0.01). 2. The pooled estimates of heritabilities derived from the sire, dam and combined variance components were 0.47~0.52 for age at sexual maturity (SM), 0.07~0.37 for total egg number (TEN), 0.40~0.54 for average egg weight (AEW), 0.18~0.27 for total egg mass (TEM). High heritability estimates were found for SM and AEW. TEN and TEM were estimated to be a lowly heritable traits. Heritability estimates from dam components were higher than those from sire components. These differences might be due to non-additive genetic effect and maternal effect. 3. The estimates of heritabilities and standard errors derived from combined variance components for different degrees of backcross were $0.47\pm0.11$ (BCO), $0.42\pm0.16$ (BC1), $0.51\pm0.29$ (BC2) for TEN, $0.59\pm0.20$ (BCO), $0.43\pm0.17$ (BC1), $0.35\pm0.18$ (BC2) for AEW, $0.28\pm0.12$(BC0), $0.20\pm0.11$(BC1), $0.18\pm0.14$ (BC2) for TEM. Heritability estimates for AEW and TEM were decreased by backcrossing while those for SM and TEN remained constant. Since backcrossing contributes to increased homozygosity, the genetic variation of the traits (AEW and TEM) decreased . 4. The pooled estimates of genetic correlation coefficients were -0.55 between SM and TEN, 0.20 between SM and AEW, -0.29 between TEN and AEW, 0.82 between TEM and TEN, 0.31 between TEM and AEW, -0.42 between TEM and SM. The genetic correlation between TEM and TEN was higher than that between TEM and AEW, and it was suggested that egg mass was strongly affected by egg number. Also, age at sexual maturity(SM) contributes to egg mass(TEM). 5. When backcrossing was carried out successively, the genetic correlation between TEM and TEN increased (BC0：0.79, BC1：0.82, BC2：0.91) but those between TEM and SM decreased (BC0：-0.54, BC1：-0.36, BC2：-0.09) with successive backcrosses.