• BMB Reports
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• v.46 no.6
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• pp.305-309
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• 2013

The determination of relatedness between individuals in a family is crucial in analysis of common complex diseases. We present a method to infer close inter-familial relationships based on SNP genotyping data and provide the relationship coefficient of kinship in Korean families. We obtained blood samples from 43 Korean individuals in two families. SNP data was obtained using the Affymetrix Genome-wide Human SNP array 6.0 and the Illumina Human 1M-Duo chip. To measure the kinship coefficient with the SNP genotyping data, we considered all possible pairs of individuals in each family. The genetic distance between two individuals in a pair was determined using the allele sharing distance method. The results show that genetic distance is proportional to the kinship coefficient and that a close degree of kinship can be confirmed with SNP genotyping data. This study represents the first attempt to identify the genetic distance between very closely related individuals.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.2
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• pp.212-220
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• 2023

Over the past 50 years, red sea bream Pagrus major has been selectively bred for more than 10 generations to improve its growth rate. However, the effect of genetic factors on growth under low- or non-fish meal diet is still unclear. Here, we analyzed 251 individuals randomly mating 21 females (dam) and 16 males (sire) to determine the difference in growth between non-fish meal (i.e., treatment group) and fish meal-based diet (i.e., control group), if any. The kinship coefficient between each group of individuals and their parents was estimated by the KING (Kinship-based Inference for GWASs) software package. The presumed parents of 74 individuals in the treatment group and 57 individuals in the control group could be effectively identified. Notably, one specific female was consistently related to high- rather than low-growth individuals in both groups. In addition, more than one parent in each group was related to either high- or low-growth individuals. Parents of both high-growth individuals in the treatment group and low-growth individuals in the control group were also identified. Although further study is required on various growth factors, this study suggests the possibility of selective breeding under non-fish meal diet.

• Animal Bioscience
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• v.36 no.9
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• pp.1327-1335
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• 2023

Objective: When evaluating individuals with the same parent and no phenotype by pedigree best linear unbiased prediction (BLUP), it is difficult to explain carcass grade difference and select individuals because they have the same value in pedigree BLUP (PBLUP). However, single step GBLUP (ssGBLUP), which can estimate the breeding value suitable for the individual by adding genotype, is more accurate than the existing method. Methods: The breeding value and accuracy were estimated with pedigree BLUP and ssGBLUP using pedigree and genotype of 408 Hanwoo cattle from 16 families with the same parent among siblings produced by fertilized egg transplantation. A total of 14,225 Hanwoo cattle with pedigree, genotype and phenotype were used as the reference population. PBLUP obtained estimated breeding value (EBV) using the pedigree of the test and reference populations, and ssGBLUP obtained genomic EBV (GEBV) after constructing and H-matrix by integrating the pedigree and genotype of the test and reference populations. Results: For all traits, the accuracy of GEBV using ssGBLUP is 0.18 to 0.20 higher than the accuracy of EBV obtained with PBLUP. Comparison of EBV and GEBV of individuals without phenotype, since the value of EBV is estimated based on expected values of alleles passed down from common ancestors. It does not take Mendelian sampling into consideration, so the EBV of all individuals within the same family is estimated to be the same value. However, GEBV makes estimating true kinship coefficient based on different genotypes of individuals possible, so GEBV that corresponds to each individual is estimated rather than a uniform GEBV for each individual. Conclusion: Since Hanwoo cows bred through embryo transfer have a high possibility of having the same parent, if ssGBLUP after adding genotype is used, estimating true kinship coefficient corresponding to each individual becomes possible, allowing for more accurate estimation of breeding value.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.10
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• pp.1501-1510
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• 2019

Objective: An experiment was conducted to evaluate genetic diversity of 26 Chinese indigenous goats by 30 microsatellite markers, and then to define conservation priorities to set up the protection programs according to the weight given to within- and between-breed genetic diversity. Methods: Twenty-six representative populations of Chinese indigenous goats, 1,351 total, were sampled from different geographic regions of China. Within-breed genetic diversity and marker polymorphism were estimated calculating the mean number of alleles, observed heterozygosities, expected heterozygosities, fixation index, effective number of alleles and allelic richness. Conservation priorities were analyzed by statistical methods. Results: A relatively high level of genetic diversity was found in twenty-four population; the exceptions were in the Daiyun and Fuqing goat populations. Within-breed kinship coefficient matrices identified seven highly inbred breeds which should be of concern. Of these, six breeds receive a negative contribution to heterozygosity when the method was based on proportional contribution to heterozygosity. Based on Weitzman or Piyasatian and Kinghorn methods, the breeds distant from others i.e. Inner Mongolia Cashmere goat, Chengdu Brown goat and Leizhou goat obtain a high ranking. Evidence from Caballero and Toro and Fabuel et al method prioritized Jining Gray goat, Liaoning Cashmere goat, and Inner Mongolia Cashmere goat, which agree with results from Kinship-based methods. Conclusion: Conservation priorities were determined according to multiple methods. Our results suggest Inner Mongolia Cashmere goat (most methods), Jining Gray goat and Liaoning Cashmere goat (high contribution to heterozygosity and total diversity) should be prioritized based on most methods. Furthermore, Daiyun goat and Shannan White goat also should be prioritized based on consideration of effective population size. However, if one breed can continually survive under changing conditions, the straightforward approach would be to increase its utilization and attraction for production via mining breed germplasm characteristics.

• Journal of the Korean Data and Information Science Society
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• v.25 no.5
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• pp.1025-1038
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• 2014

Linear mixed model has often been utilized for genetic association analysis with family-based samples. The correlation matrix for family-based samples is constructed with kinship coefficient and assumes that parental phenotypes are independent and the amount of correlations between parent and offspring is same as that of correlations between siblings. However, for instance, there are positive correlations between parental heights, which indicates that the assumption for correlation matrix is often violated. The statistical validity and power are affected by the appropriateness of assumed variance covariance matrix, and in this thesis, we provide the linear mixed model with flexible variance covariance matrix. Our results show that the proposed method is usually more efficient than existing approaches, and its application to genome-wide association study of body mass index illustrates the practical value in real data analysis.

• Animal Bioscience
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• v.34 no.11
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• pp.1757-1765
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• 2021

Objective: The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited. Methods: Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds. Results: In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively. Conclusion: This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.