• Asian-Australasian Journal of Animal Sciences
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• v.19 no.3
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• pp.324-328
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• 2006

Carbonic anhydrase III (CA3) is a member of a multigene family that encode carbonic anhydrase isozymes. In this study, a complete coding sequence of the pig CA3 gene which encodes a 260 amino-acid protein was determined. The amino acid comparison showed high sequence similarities with previously identified human (86.5%) CA3 gene and mouse (91.5%) Car3 gene. The partial genomic DNA sequences were also investigated. The length of intron 1 was 727 bp. Comparative sequencing of three pig breeds revealed that there was a T${\rightarrow}$C substitution at position 363 within intron 1. The substitution was situated within a NcoI recognition site and was developed as a PCR-restriction fragment length polymorphism (RFLP) marker for further use in population variation investigations and association analysis. Two alleles (A and B) were identified, and 617 bp fragments were observed for the AA genotype and 236 bp and 381 bp fragments for the BB genotype. The polymorphism of CA3 was detected in 8 pig breeds. Allele B was predominant in the Western pig breeds. In addition, association studies of the CA3 polymorphism with carcass traits in 140 $Yorkshire{\times}Meishan$ $F_2$ offspring showed that the NcoI PCR- RFLP genotype may be associated with variation in several carcass traits of interest for pig breeding. Allele B was associated with increases in lean meat percentage, loin eye height and loin eye area. Statistically significant association with backfat thickness was also found; pigs with the AB genotype had much less backfat thickness than AA or BB genotypes.

• Journal of Animal Science and Technology
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• v.53 no.1
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• pp.1-6
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• 2011

This simulation study was performed to investigate the accuracy of the estimated breeding value by using genomic information (GEBV) by way of Bayesian framework. Genomic information by way of single nucleotide polymorphism (SNP) from a chromosome with length of 100cM were simulated with different marker distance (0.1cM, 0.5cM), heritabilities (0.1, 0.5) and half sibs families (20 heads, 4 heads). For generating the simulated population in which animals were inferred to genomic polymorphism, we assumed that the number of quantitative trait loci (QTL) were equal with the number of no effect markers. The positions of markers and QTLs were located with even and scatter distances, respectively. The accuracies of estimated breeding values by way of indicating correlations between true and estimated breeding values were compared on several cases of marker distances, heritabilities and family sizes. The accuracies of breeding values on animals only having genomic information were 0.87 and 0.81 in marker distances of 0.1cM and 0.5cM, respectively. These accuracies were shown to be influenced by heritabilities (0.87 at $h^2$ =0.10, 0.94 at $h^2$ =0.50). According to half sibs' family size, these accuracies were 0.87 and 0.84 in family size of 20 and 4, respectively. As half sibs family size is high, accuracy of breeding appeared high. Based on the results of this study it is concluded that the amount of marker information, heritability and family size would influence the accuracy of the estimated breeding values in genomic selection methodology for animal breeding.

• Journal of Forest and Environmental Science
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• v.34 no.1
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• pp.71-76
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• 2018

The long-tailed goral (Naemorhedus caudatus) has slowly recolonized habitats in South Korea. Because it is necessary to know the status of groups in recolonized areas, we determined detection frequencies and group sizes using camera trapping, a non-invasive monitoring method. In Uljin, a far southern goral habitat in South Korea, we used a Moultrie 5.0 camera and mineral block as bait during the breeding season in BaekAm Mountain (148 days, 18 May to 11 October) and Geumjong Mountain (63 days, 18 May to 18 July) in 2010. Totally, 155 images were captured in BaekAm Mountain, whereas four images were captured in Geumjong Mountain. The species was most frequently detected at sunrise (05:00-08:00) and sunset (18:00-20:00). Through population structure evaluation, we identified at least 11 individuals, including one solitary mature male, four females, four kids, and two solitary subadults in BaekAm Mountain. However, in Geumjong Mountain, we identified only two individuals (female with kid). Monitoring efficiency in the recolonized area differed depending on population density and habitat conditions. Because we could evaluate the population structure, and behavioral patterns in the study sites, monitoring using camera traps could be applied for the recolonized habitats in South Korea.

• Fisheries and Aquatic Sciences
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• v.10 no.4
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• pp.186-190
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• 2007

We examined the genetic variability of Asian chum salmon (Oncorhynchus keta) populations using nuclear microsatellite (ms) DNA analysis with four polymorphic loci (OKM4, OKM5, OKM7, and OKM8) in 397 individuals from nine populations, including one in Korea, seven in Japan, and one in Russia. The msDNA gene diversity was highest in the Japanese populations, suggesting greater genetic variation in the populations in Japan than in populations in Korea and Russia. The pairwise $F_{ST}$ estimates based on our msDNA data showed that the Korean population was genetically different from the Japanese and Russian populations, and there were higher $F_{ST}$ estimates between Hokkaido and Honshu populations than between other population pairs. A neighbor-joining tree showed that the Korean population was distinct from two other clusters, representing the populations in Honshu and the populations in Hokkaido and Russia. These results suggest that the observed population genetic patterns of Asian chum salmon might be influenced by low or restricted gene flow.

• ALGAE
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• v.37 no.2
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• pp.85-103
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• 2022

Korea is one of the most advanced countries in kelp aquaculture. The brown algae, Undaria pinnatifida and Saccharina japonica are major aquaculture species and have been principally utilized for human food and abalone feed in Korea. This review discusses the diversity, population structure and genomics of kelps. In addition, we have introduced new cultivar development efforts considering climate change, and potential carbon sequestration of kelp aquaculture in Korea. U. pinnatifida showed high diversity within the natural populations but reduced genetic diversity in cultivars. However, very few studies of S. japonica have been conducted in terms of population structure. Since studies on cultivar development began in early 2000s, five U. pinnatifida and one S. japonica varieties have been registered to the International Union for the Protection of New Varieties of Plants (UPOV). To meet the demands for seaweed biomass in various industries, more cultivars should be developed with specific traits to meet application demands. Additionally, cultivation technologies should be diversified, such as integrated multi-trophic aquaculture (IMTA) and offshore aquaculture, to achieve environmental and economic sustainability. These kelps are anticipated to be important sources of blue carbon in Korea.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1544-1557
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• 2020

Objective: Genomic selection (GS) is becoming popular in animals' genetic development. We, therefore, investigated the single-step genomic best linear unbiased prediction (ssGBLUP) as tool for GS, and compared its efficacy with the traditional pedigree BLUP (pedBLUP) method. Methods: A total of 9,952 males born between 1997 and 2018 under Hanwoo proven-bull selection program was studied. We analyzed body weight at 12 months and carcass weight (kg), backfat thickness, eye muscle area, and marbling score traits. About 7,387 bulls were genotyped using Illumina 50K BeadChip Arrays. Multiple-trait animal model analyses were performed using BLUPF90 software programs. Breeding value accuracy was calculated using two methods: i) Pearson's correlation of genomic estimated breeding value (GEBV) with EBV of all animals (r_M1) and ii) correlation using inverse of coefficient matrix from the mixed-model equations (r_M2). Then, we compared these accuracies by overall population, info-type (PHEN, phenotyped-only; GEN, genotyped-only; and PH+GEN, phenotyped and genotyped), and bull-types (YBULL, young male calves; CBULL, young candidate bulls; and PBULL, proven bulls). Results: The r_M1 estimates in the study were between 0.90 and 0.96 among five traits. The r_M1 estimates varied slightly by population and info-type, but noticeably by bull-type for traits. Generally average r_M2 estimates were much smaller than r_M1 (pedBLUP, 0.40 to0.44; ssGBLUP, 0.41 to 0.45) at population level. However, r_M2 from both BLUP models varied noticeably across info-types and bull-types. The ssGBLUP estimates of r_M2 in PHEN, GEN, and PH+ GEN ranged between 0.51 and 0.63, 0.66 and 0.70, and 0.68 and 0.73, respectively. In YBULL, CBULL, and PBULL, the r_M2 estimates ranged between 0.54 and 0.57, 0.55 and 0.62, and 0.70 and 0.74, respectively. The pedBLUP based r_M2 estimates were also relatively lower than ssGBLUP estimates. At the population level, we found an increase in accuracy by 2.0% to 4.5% among traits. Traits in PHEN were least influenced by ssGBLUP (0% to 2.0%), whereas the highest positive changes were in GEN (8.1% to 10.7%). PH+GEN also showed 6.5% to 8.5% increase in accuracy by ssGBLUP. However, the highest improvements were found in bull-types (YBULL, 21% to 35.7%; CBULL, 3.3% to 9.3%; PBULL, 2.8% to 6.1%). Conclusion: A noticeable improvement by ssGBLUP was observed in this study. Findings of differential responses to ssGBLUP by various bulls could assist in better selection decision making as well. We, therefore, suggest that ssGBLUP could be used for GS in Hanwoo proven-bull evaluation program.

• Korean Journal of Plant Resources
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• v.25 no.1
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• pp.72-79
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• 2012

Vaccinium oldhami Miq. is a Korean native tree, which is deciduous and shrub tree with broad leaf. It grows 1~4m in height generally. Ecologically, this tree grows well in shady place even in barren soil. Also, the tree has resistance to cold and dry, which tend to form a little community. This research investigates quantitative morphological characteristics of leaf and fruit among the V. oldhami in South Korea and then considers its relationship on the basis of raw data among the 10 populations. This study will give us invaluable information about growing conditions, reasonable management and breeding by selection of V. oldhami in South Korea. The main results obtained from this study are summarized as follows; Leaf size of Mudeung population was larger than other populations. Naebyeon population was smaller in size of the leaf than other populations. Anmyeondo population was larger in fruit characteristics compared with other populations and Deogyu population was the smallest among populations. According to cluster analysis based on the leaf and fruit morphological characteristics, the natural V. oldhami populations were classified into four groups such as the first group of Kumo population, the second group of Mudeung population, the third group of Anmyundo, Daedun, Doolyun population and the fourth group of the other five populations.

• Animal Bioscience
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• v.34 no.5
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• pp.789-800
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• 2021

Objective: Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods: Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei's genetic distance and Weir and Cockerham's FST. Results: Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 to -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion: This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.31-37
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• 2019

Objective: At least eight local duck breeds have been recognized and documented as national germplasm of Indonesia so far. It is necessary to genetically characterize the local duck breeds for aiding conservation and future improvement strategies. Thus, this study was carried out to assess genetic diversity and phylogenetic relationship of eight local duck populations of Indonesia using microsatellite markers. Methods: In total, 240 individuals (30 individuals each population) from Alabio (AL), Bayang (BY), Magelang (MG), Mojosari (MJ), Pegagan (PG), Pitalah (PT), Rambon (RM), and Turi (TR) duck populations were genotyped using 22 microsatellite markers. Results: The results showed a moderate level of genetic diversity among populations, with a total of 153 alleles detected over all loci and populations, ranging from 3 to 22 alleles per locus. Observed (Ho) and expected heterozygosity (He), as well as polymorphism information content over all loci and populations were 0.440, 0.566, and 0.513, respectively. Heterozygote deficiency in the overall populations ($F_{IT}=0.237$), was partly due to the heterozygote deficiency within populations ($F_{IS}=0.114$) and moderate level of genetic differentiation among populations ($F_{ST}=0.137$). The most diverse population was MG (He = 0.545) and the least diverse population was AL (He = 0.368). The majority of populations were relatively in heterozygote deficiency (except AL), due to inbreeding. The genetic distances, phylogenetic trees, and principal coordinates analysis concluded that the populations can be grouped into two major clusters, resulting AL, MG, and MJ in one cluster separated from the remaining populations. Conclusion: The present study revealed a considerable genetic diversity of studied populations and thus, proper management strategies should be applied to preserve genetic diversity and prevent loss of alleles.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.267-267
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• 2022

Glutinous rice is a key grain quality trait occupying an important part during rice processing in most rice growing areas. Amylose content (AC) of rice determine eating quality which is one of the major traits in rice breeding program. In this study, a gene pyramiding approach was used to introduce two dull genes, responsible for low amylose contents, for glutinous rice breeding using marker assisted selection (MAS). Two dull genes were located on chromosome 6 (wx-mq, AC: 12.7 %) and chromosome 10 (du1, AC: 10.3%), respectively. To test whether these two dull genes have an epistatic interaction, we developed an F₂ population by crossing two nearly isogenic lines(NILs) harboring wx-mq and du1. Gene based marker and KASP marker were used to select NILs(NIL-nor, NIL-wxmq, NIL-du1, and NIL-wxmq/du1) from the F2 population. A two-way ANOVA revealed an epistatic interaction between the two genes in the F2 population. The mean of Amylose contents for NIL-nor, NIL-wxwq, NIL-(du1, and NIL-wxmq/du1 were 17.3%, 12.5%, 9.7%, and 7.2%, respectively. This interaction was confirmed by an analysis of NILs indicating that both genes are involved in the same genetic mechanism controlling amylose contents. This result will be useful for rice breeding related to amylose content.