• Asian-Australasian Journal of Animal Sciences
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• v.10 no.4
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• pp.422-427
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• 1997

Breeding efficiency was investigated to reveal crucial factors for constructing effective breeding system with subdivided populations under equal genetic level. Simulation study of selection experiment was performed for 20 generations with 20 replications each, comparing average breeding values and inbreeding coefficients between the two breeding systems; single population scheme and two population scheme, each of which had the same genetic parameters. Genetic correlations (-0.5 to 0.5) were assumed to be caused only by pleiotropic effect of a gene. Phenotypes of the two traits generated by polygenic effect with additive 36 loci and residuals distributed normally were selected by two traits selection index procedure. Comparing between the single population scheme and the two population scheme, the single population scheme showed higher genetic gain with lower inbreeding coefficient. This result was confirmed particularly for the situation of high selection intensity, high heritability and high degree of unevenness for economic weight. Genetic correlations in the single population scheme were significantly lower than the two population scheme when initial genetic correlation was negative. When terminal crossbreeding for the two population scheme is taken into account, superiority of the two population scheme was suggested. The terminal crossbreeding was effective under the situation of long term selection, existence of moderate inbreeding depression and use of less extreme economic weight.

• Journal of Life Science
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• v.17 no.11
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• pp.1477-1481
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• 2007

The mating systems of natural populations of Vicia tetrasperm in Korea were determined using allozyme analysis. The result suggests that V. tetrasperm is low rates of outcrossing or mix-mating outcrossing (self-fertilization, s < 0.5). At the population levels, the values of inbreeding coefficient of ten populations in Korea varied from 0.131 to 0.176, giving an average 0.154. For ten natural populations, multi-locus estimates of outcrossing (tm) was 0.333 across fifteen polymorphic loci, with individual population values ranging from 0.269 to 0.423. The differences between the tm and ts values were not close to zero (tm - ts > 0.154), indicating that biparental inbreeding was significant in the loci. The reason for relatively low outcrossing rates of some populations could be attributed to extensive consanguineous mating and isolation of flowering mature plants. Although heterozygote excess was observed in one natural population, most populations exhibited varying degrees of inbreeding and heterozygotes deficit. Thus, selection against homozygotes operated in the progeny populations throughout the life cycle.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.7
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• pp.938-942
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• 2006

Genetic diversity of Magra - a lustrous carpet wool breed of India, was investigated by means of 25 ovine microsatellite markers proposed by the Food and Agriculture Organization and the International Society for Animal Genetics (FAO-ISAG). All used microsatellites amplified well and exhibited polymorphisms. A wide range of genetic variability was observed as allele number from 3 (BM6506, OarCP20) to 10 (CSSM31), observed heterozygosity from 0.200 (BM6506) to 0.947 (OarHH35), expected heterozygosity from 0.368 (CSSM47) to 0.864 (BM1314) and Polymorphism Information Content (PIC) from 0.347 (CSSM47) to 0.849 (BM1314). This supported the utility of these microsatellite loci in the measurement of genetic diversity indices in Indian sheep too. Various average genetic variability measures viz., allele diversity (5.7), observed heterozygosity (0.597), expected heterozygosity (0.694) and mean PIC (0.648) values showed high genetic variability despite accumulated inbreeding as reflected by the high average inbreeding coefficient ($F_{IS}=0.159$) due to the unequal sex ratio of the breeding animals.

• Journal of Ecology and Environment
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• v.30 no.3
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• pp.225-229
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• 2007

The mating systems of natural populations of Potentilla freyniana in Korea were determined using allozyme analysis. The result suggests that P. freyniana is outcrossing as well as employing vegetative reproduction by stolon (self-fertilization rate, s < 0.5). The values of the inbreeding coefficient of eight populations in Korea varied from 0.244 to 0.331, with an average value of 0.274. For eight natural populations, multi-locus estimates of outcrossing (tm) was 0.603 across 13 polymorphic loci, with individual population values ranging from 0.530 to 0.652. The relatively low outcrossing rates of some populations could be attributed to extensive vegetative reproduction by stolon and the isolation of flowering mature plants. Although P. freyniana usually propagated by asexually-produced ramets, I could not rule out the possibility that sexual reproduction occurred at a low rate because each ramet may produce terminal flowers. Although heterozygote excess was observed in some natural populations, most populations exhibited varying degrees of inbreeding and a heterozygote deficit.

• Journal of Animal Science and Technology
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• v.55 no.5
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• pp.367-371
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• 2013

This study was carried out to estimate the average inbreeding coefficients and effective population size (EPS) and to seek alternatives on the problems of Holstein cattle in Korea. The data used in this study was obtained from the Korean Animal Improvement Association (KAIA) and 635,268 heads of Holstein records out of 1,872,195 Holstein registration data were used for the analysis. The average inbreeding coefficients were estimated at a range of 0.11 to 1.07%. The average inbreeding coefficients at the $14^{th}$, $19^{th}$ and $22^{nd}$ generation were estimated at 0.43%, 0.92% and 1.07%, respectively. The estimated inbreeding coefficients within the range of 0%, 0 to 6.25%, 6.25 to 12.5%, 12.5 to 25%, and >25% were observed in 50.5%, 48.3%, 0.8%, 0.1%, and 0.3% of the animals, respectively. The estimated effective population size (EPS) was 619 heads from the $8^{th}$ to $22^{nd}$ generation, and 922 heads from the $19^{th}$ to $22^{nd}$ generation.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.212-218
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• 2020

Objective: Agu pigs are indigenous to the Okinawa prefecture, which is the southernmost region of Japan. Agu pigs were exposed to a genetic bottleneck during the 20th century, due to the introduction of European pig breeds. The objective of this study was to elucidate the genetic structure of Agu pigs and to determine their relationships with those of five European breeds, two Chinese breeds and Ryukyu wild boar using microsatellite markers. Methods: A total of 203 DNA samples from 8 pig breeds were used in this study. Genotyping was performed using 21 microsatellite markers distributed across 17 chromosomes. Results: Numbers of effective alleles in Agu pigs were fewer than in European breeds and Ryukyu wild boar. Among domestic pigs, Agu pigs had the lowest heterozygosity (0.423) and highest inbreeding coefficient (F_IS = 0.202), indicating a severe loss of heterozygosity in Agu pigs possibly due to inbreeding. Neighbor-joining tree analysis was performed based on Reynolds' genetic distances, which clustered Agu pigs with Duroc pigs. However, principal component analysis revealed a unique genetic position of the Agu pig, and the second principal component separated Agu pigs from all other breeds. Structure analysis with the optimal assumption of seven groups (K = 7) indicated that Agu pigs form an independent cluster from the other breeds. In addition, high and significant F_ST values (0.235 to 0.413) were identified between Agu pigs and the other breeds. Conclusion: This study revealed a substantial loss of genetic diversity among Agu pigs due to inbreeding. Our data also suggest that Agu pigs have a distinctive genetic structure, although gene flows from European breeds were observed.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.75-81
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• 2017

A total of 340 individuals from seven duck populations were studied using 24 polymorphic microsatellite (MS) markers to identify plumage colors with genetic diversity. The estimated average number of alleles (Na), polymorphic information content (PIC) value, and expected heterozygosity (He) per locus of all populations were 11.5, 0.602, and 0.635, respectively. The calculated population genetic distance (Fst), inbreeding coefficient of individuals within duck populations (Fis), and total inbreeding among populations (Fit) were 0.135, 0.105, and 0.229, respectively. Statistical analyses for each population using 24 marker combinations, revealed that the estimated average number of effective alleles (Ne), observed heterozygosity (Ho), and fixation index of inbreeding within populations (F) were 3.129, 0.505, and 0.104, respectively. The results of genetic distance and phylogenetic analysis revealed that Korean native duck populations were clearly separated from all Bangladeshi duck populations. Moreover, all populations clustered well according to their genetic distance, but could not be clearly separated according to black and white plumage colors or plumage color pattern. The combination of these 24 MS markers can be used for discrimination and determination of the genetic diversity of native duck breeds in further investigations for conservation and special development purposes.

• Journal of agriculture & life science
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• v.50 no.2
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• pp.107-116
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• 2016

The study was aimed to analyze pedigree structure and inbreeding coefficients for performance tested Holstein cows in Korea. A total of 400,029 Holstein cows data which born between 2002 and 2012 were obtained from Dairy Cattle Improvement Center of National Agricultural Cooperative Federation(NACF). Their related pedigrees, as obtained from Korean Animal Improvement Association(KAIA), consisted of 509,740 animals. Pedigree depth of the cows were traced back to 3 generations earlier. The percentage of cows with fully identified ancestors in various provinces of Korea were 55.18%(Gyeonggi-do), 23.49%(Gangwon-do), 47.83%(Chungcheongnam-do), 53.62%(Chungcheongbuk-do), 56.38%(Gyeongsangbuk-do), 51.35% (Gyeongsangnam-do), 26.58%(Jeollanam-do), 49.41%(Jeollabuk-do), and 56.90%(Jeju-do), whereas, it was about 63.20% as a whole in Korea. The average inbreeding coefficients showed increment across the consecutive years of birth such as, 0.43(2002), 0.44(2003), 0.58(2004), 0.64(2005), 0.78(2006), 0.93(2007), 1.08(2008), 1.23(2009), 1.46(2010), 1.77(2011), and 2.03 (2012). However, this coefficient was 0.93 in overall Korean population. An average generation interval for sire to daughter genetic path was 8.15 years; which was about 4.20 years considering dam to daughter genetic path. The estimated effective population sizes (Ne) were 56.5, 51.3, and 32.2 animals born in 2004, 2009, and 2012, respectively. These results indicated that an increased rate of inbreeding has led to a significant reduction in the Ne over the decade.

• Fisheries and Aquatic Sciences
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• v.15 no.2
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• pp.151-155
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• 2012

We used nine microsatellite DNA markers to estimate genetic variation among wild and cultured populations of the sea squirt Halocynthia roretzi. The loci were polymorphic, with 6-32 alleles, and allelic richness ranged from 6.0 to 26.1 in each population. The wild and the cultured populations had similar mean heterozygosities ($H_O$ and $H_E$), allele numbers, and allelic richness. One cultured population with softness syndrome had a lower mean in the observed heterozygosity ($H_O$ = 0.57) and higher mean inbreeding coefficient ($F_{IS}$ = 0.261) than any other populations. This suggests that the loss of genetic variation in the diseased population might be due to increased inbreeding. A neighbor-joining tree and pairwise population estimates of $F_{ST}$ showed moderate genetic differentiation between the wild and the cultured populations. Additionally, the softness syndrome population was genetically divergent from wild populations, but it was genetically close to the cultured populations.