• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1710-1720
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• 2008

A comprehensive genome profiling study was undertaken based on automated genotyping and analysis of 20 microsatellite markers that involved 155 birds representing eight different populations. The distribution of microsatellite markers in each of these breeds helped us to decipher genetic heterogeneity, population genetic structure and evolutionary relationships of the present day chicken populations in India. All the microsatellite loci utilized for the analysis were polymorphic and reasonably informative. A total of 285 alleles were documented at 20 loci with a mean of 14.25 alleles/locus. A total of 103 alleles were found to be population/strain specific of which, only 30 per cent had a frequency of more than 10. The mean PIC values ranged from 0.39 for the locus ADL158 to 0.71 for loci MCW005 or ADL267 across the genomes and 0.55 in Dahlem Red to 0.71 in Desi (non-descript), among the populations. The overall mean expected and observed heterozygosity estimates for our populations were 0.68 and 0.64, respectively. The overall mean inbreeding coefficients (FIS) varied between -0.05 (Babcock) and 0.16 (Rhode Island Red). The pairwise FST estimates ranged from 0.06 between Aseel and Desi (non-descript) to 0.14 between Dahlem Red and Babcock. The Nei's genetic distance varied from 0.30 (WLH-IWD and WLH-IWF) to 0.80 (Dahlem Red and Babcock. Phylogenetic analysis grouped all the populations into two main clusters, representing i) the pure breeds, Dahlem Red and Rhode Island Red, and ii) the remaining six populations/strains. All the chicken populations studied were in the state of mild to moderate inbreeding except for commercial birds. A planned breeding is advised for purebreds to revive their genetic potential. High genetic diversity exists in Desi (non-descript), local birds, which can be exploited to genetically improve the birds suitable for backyard poultry.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.10
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• pp.1355-1359
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• 2004

Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree nformation. Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree information.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.8
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• pp.1217-1223
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• 2020

Objective: Eggshells with a uniform color and intensity are important for egg production because many consumers assess the quality of an egg according to the shell color. In the present study, we evaluated the influence of dominant effects on the variations in eggshell color after 32 weeks in a crossbred population. Methods: This study was conducted using 7,878 eggshell records from 2,626 hens. Heritability was estimated using a univariate animal model, which included inbreeding coefficients as a fixed effect and animal additive genetic, dominant genetic, and residuals as random effects. Genetic correlations were obtained using a bivariate animal model. The optimal diagnostic criteria identified in this study were: L^🟉 value (lightness) using a dominance model, and a^🟉 (redness), and b^🟉 (yellowness) value using an additive model. Results: The estimated heritabilities were 0.65 for shell lightness, 0.42 for redness, and 0.60 for yellowness. The dominance heritability was 0.23 for lightness. The estimated genetic correlations were 0.61 between lightness and redness, -0.84 between lightness and yellowness, and -0.39 between redness and yellowness. Conclusion: These results indicate that dominant genetic effects could help to explain the phenotypic variance in eggshell color, especially based on data from blue-shelled chickens. Considering the dominant genetic variation identified for shell color, this variation should be employed to produce blue eggs for commercial purposes using a planned mating system.

• Animal Bioscience
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• v.34 no.9
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• pp.1460-1465
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• 2021

Objective: The study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea. Methods: A total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys. Results: The observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were H_E = 0.6721 and H_O = 0.6600 in Thoroughbreds, H_E = 0.7898 and H_O = 0.7100 in Jeju Halla horses, and H_E = 0.5635 and H_O = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (-0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys. Conclusion: Genetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.

• Animal Bioscience
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• v.35 no.12
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• pp.1839-1849
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• 2022

Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (F_PED) was significantly different from those estimated from runs of homozygosity (F_ROH) and single nucleotide polymorphism (F_SNP) based on genome. The Pearson correlation coefficient between F_ROH and F_SNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40

• Journal of Life Science
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• v.23 no.9
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• pp.1088-1095
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• 2013

The swimming crab, Portunus trituberculatus, inhabits seafloor habitats containing sand or pebbles and is widely distributed throughout the world. The present study investigated genetic polymorphisms of 10 microsatellites in 281 samples of P. trituberculatus collected from four locations along the coastal water of the Korean side of the Yellow Sea (Yeonggwang, Taean, Sorea, and Yeonpyeong-do Island). The number of alleles per locus ranged from 50 to 129, with a mean of 69.5. The observed and expected hetrozygosity varied from 0.111 to 1.000 and from 0.609 to 0.979, respectively. The inbreeding coefficients (Fis) varied among the loci from -0.0207 to 0.8175. The genetic differentiation (Fst) was less than 0.05 (range 0.0020-0.0124). Therefore, the four groups of P. trituberculatus appeared to exhibit little genetic differentiation. The lack of differentiation was confirmed in a phylogenetic tree constructed by the unweighted pair group method with the arithmetic average (UPGMA). The hypervariation between the populations and the lack of genetic differentiation may reflect active gene flow among the Yellow Sea populations and the absence of geographical boundaries. The highly polymorphic microsatellite loci will be useful for molecular and phylogenetic studies, as well as stock management, of swimming crab, which is an important fishery resource.

• Journal of Aquaculture
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• v.19 no.3
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• pp.205-209
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• 2006

Genetic change from broodstock to hatchery stock of the olive flounder Paralichthys olivaceus and effective number of breeders (Ne) were investigated by the different fertilized-egg collecting methods; E1 (eggs collected one day after spawning) and E2 (eggs collected two days after spawning) using seven microsatellite loci (Kop2, Kop22, Kop18, Kop3, Kop21, Kop9 and Kop26) for the better understanding of stock enhancement. Observed heterozygosity in three stocks ranged from 0.651 at Kop3 to 0.928 at Kop22, with offspring being slightly higher heterozygous over their parents. However, the genetic reduction of offspring was significant. The offspring allele number per locus was reduced to 23.5% for E1 and 17.6% for E2 of their maternal number. Ne to the hatchery stock was estimated to be 21.9 for E1 and 34.3 for E2. The inbreeding coefficients of populations El and E2 were 0.023 and 0.015, respectively. The present study suggests the extension of the egg collection period for a recovery of the genetic diversity in artificially produced offspring.

• Journal of Animal Science and Technology
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• v.53 no.5
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• pp.397-408
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• 2011

The study was carried to identify the impact on nation-wide genetic evaluation and to obtain basic materials for the development of strategies in Swine Improvement Network Project (SINP). Data consisted of pedigree records of 235,511 and performance records of 70,747 for Duroc from 1987 to 2010 were collected by Korea Animal Improvement Association. Performance traits included three point back fat thickness (Shoulder, Belly, Waist), loin area, days to 90 kg and average daily gain. Exchange of genetic resources cross the breeding farms was not high, and furthermore the sizable farms which can accommodate genetic evaluation within the farm were scarce. Three data sets (individual farm evaluation: I, two sub-group evaluation: S, and whole eight farm evaluation: P) were used for genetic analysis. Genetic variances were larger in subordinate farms than in joiners farms for connectedness, and consequently the heritabilities were generally higher in subordinate farms than in joiner farms with I. The standard errors of heritability were small in the order of I, S and P. Estimated average inbreeding coefficients were 1.12%, 0.95% and 1.53% for joiner and subordinate group with S and population with P, respectively. The estimated correlations of breeding values with I and P were lowest. The correlations of breeding values with I and P for traits ranged 0.22 to 0.45 for moved parent animals and 0.24 to 0.72 for all animals. The results in the study suggest that nation-wide evaluation uses more pedigree information and improves accuracy. Furthermore SINP for connectedness could help to improve the accuracy of evaluation.