• Asian-Australasian Journal of Animal Sciences
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• 제19권10호
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• pp.1394-1398
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• 2006

The complete mtDNA D-loop regions of Japanese and Korean cattle were analyzed for their mtDNA variations and genetic relationships. Sequencing the 30 Higo substrain and 30 Tosa substrain of Japanese Brown, respectively 12 and 17 distinct Bos haplotypes were identified from 77 polymorphic nucleotide sites. In order to focus on the relationships among Japanese and Korean cattle, two types of phylogenetic tree were constructed using individual sequences; first, a neighbor-joining tree with all sequences and second, reduced median networks within each Japanese and Korean cattle group. The trees revealed that two major mtDNA haplotype groups, T3 and T4, were represented in Japanese and Korean cattle. The T4 haplogroup predominated in Japanese Black and Japanese Brown cattle (frequency of 43.3-66.7%), while the T3 haplogroup was predominant (83.3%) and T4 was represented only twice in the Korean cattle. The results suggested that the mitochondrial origins of Japanese Brown were Japanese ancient cattle as well as Japanese Black in despite of the considerable introgression of Korean and European cattle into Japanese Brown.

• Asian-Australasian Journal of Animal Sciences
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• 제20권4호
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• pp.477-481
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• 2007

Korean Ogol chicken has been registered as a natural monument in Korea and regarded as a valuable genetic resource for the world. As an initial step to investigate the genetic structures of this breed, phylogenetic analysis and calculation of genetic diversities have been performed using mitochondrial DNA (mtDNA) sequence variations. A total of 31 Korean Ogol chicken was grouped into four haplotypes and the large haplotype was represented in 12 individuals. The unrooted neighbor-joining tree indicates that the Korean Ogol chicken shared three (A to C) major chicken lineages representing the high genetic variability of this breed. These results can be used for making the breeding and conservation strategies for the Korean Ogol chicken.

• ALGAE
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• 제34권3호
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• pp.229-236
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• 2019

Despite the abundance of seaweeds from Ulleungdo Island, genetic diversity and distribution of edible brown algae from the island remain unstudied. We analyzed mitochondrial cox3 sequences from 86 specimens collected in the island and from the nearby Korean Peninsula. Our cox3 phylogeny for the first time confirmed the occurrence of fives species from Ulleungdo Island; Petalonia binghamiae, P. fascia, Planosiphon zosterifolius, and two cryptic species previously identified as Scytosiphon lomentaria. P. binghamiae was relatively homogeneous with three haplotypes. P. fascia comprised four haplotypes, which were grouped into two genetic lineages. S. lomentaria was heterogeneous with nine haplotypes and was divided into two cryptic species; one species clustered with taxa from cold waters while the other clustered with taxa from temperate and cold waters. Low genetic diversity in P. binghamiae while high genetic diversity in S. lomentaria from Ulleungdo Island are comparable to patterns observed from other species from the Korean peninsula. Ulleungdo Island, although small in size, is an ideal field laboratory to investigate genetic diversity and distributions of economic marine algae.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.220-220
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• 2022

Disproportionating Enzyme 1 (DPE1) is an a-1,4-D-glucanotransferase that cleavages the a-1,4-glucosidic bonds and transfers glucosyl groups. In rice endosperm, it participates in starch synthesis by transferring maltooligosyl groups from amylose and amylopectin to amylopectin. Here, we investigated the haplotype variations and evolutionary indices (e.g., genetic diversity and population structure) for the DPE1 gene in 374 rice accessions representing seven subgroups (wild, indica, temperate japonica, tropical japonica, aus, aromatic, and admixture). Variant calling analysis of DPE1 coding regions leads to the identification of six functional haplotypes representing/occupying 8 nonsynonymous SNPs. Nucleotide diversity analysis revealed the highest pi-value in wild group (0.0556) compared to other cultivated groups, of which temperate japonica showed the most reduction of genetic diversity value (0.003). A significant positive Tajima's D value (1.6330) of admixture highlights sudden population contraction under balancing selection, while temperate japonica with the lowest Tajima's D value (-1.3523) showed a selection signature of DPE1 domestication which might be the cause of excess of rare alleles. Moreover, these two subpopulations exhibits a greater differentiation (F_ST=0.0148), indicating a higher genetic diversity. Our findings on functional DPE1 haplotypes will be useful in future breeding programs, and the evolutionary indices can also be applicable in functional studies of the DPE1 gene.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.216-216
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• 2022

The starch-branching enzymes (BEs) are responsible for synthesizing the amylopectin, which plays an important role in determining the structural and physical properties of starch granules. BE has two differently functioning isoforms (BEI and BEIIa/b) based on their difference in the chain-length pattern by the degree of polymerization (DP), which mainly contributes to the amylopectin chain length distribution in starch biosynthesis. In this study, we investigated functional haplotypes and evolutionary analyses of SBE1 in 374 rice accessions (320 Korean bred and 54 wild). The analyses were performed based on the classified subpopulations. Haplotype analysis generates a total of 8 haplotypes, of which only four haplotypes were functional carrying four functional SNPs in four different exons of SBE1 on chromosome 6. Nucleotide diversity analysis showed a highest pi-value in aromatic group (0.0029), while the lowest diversity value was in temperate japonica (0.0002), indicating the signal of this gene evolution origin. Different directional selections could be estimated by negative Tajima's D value of temperate japonica (-1.1285) and positive Tajima's D value of tropical japonica (0.9456), where the selective sweeps were undergone by both positive purifying and balancing selections. Phylogenetic analysis indicates a closer relationship of the wild with most of the cultivated subgroups indicating a common ancestor for SBE1 gene. FST-values indicate distant genetic relationships of temperate japonica from all other classified groups. PCA and population structure analysis show an admixed structure of wild and cultivated subpopulations in some proportions.

• 한국육종학회지
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• 제41권4호
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• pp.397-402
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• 2009

Self-incompatibility (SI) prevents self-fertilization by inhibiting the pollen tube growth of self-pollen. Molecular analysis has revealed that the S locus comprises a number of genes, such as the S-locus glycoprotein (SLG), the S-locus receptor kinase (SRK), and SP11 (SCR). Although molecular markers related to those genes have been developed, a simple S-haplotype detecting method has not been reported due to the highly polymorphic and relatively small coding regions. In this study, the sequence characterized amplified region (SCAR) markers were used to establish an efficient radish genotyping method. We identified the S-haplotypes of 192 radish accessions using 19 different markers, which proved to be highly reliable. The accessions were assigned to 17 types of S-haplotypes, including 8 types of SRKs and 9 types of SLGs. Since the developed SCAR markers are based on their gene sequences, we could easily identify the S-haplotypes by a single specific band, with the highest frequencies detected for SLG 5, SRK 1, and SLG 1, in order. Among the tested markers, the SLG 1, SRK 1, and SRK 5 markers exhibited high reliability, compared to phenotypic results. Furthermore, we identified the seven types of unreported SLGs using SLG Class -I and -II specific markers. Although the developed SCAR markers still need to be improved for the genotyping of all S-haplotypes, these markers could be helpful for monitoring inbred lines, and for developing the MAS in radish breeding programs.

• Asian-Australasian Journal of Animal Sciences
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• 제20권12호
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• pp.1812-1819
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• 2007

Heart fatty acid-binding protein gene (H-FABP) is an important candidate gene for meat quality. One of the objectives of this study was to screen single nucleotide polymorphisms (SNP) of chicken H-FABP gene among 252 individuals that included 4 Chinese domestic chicken breeds (Fengkai Xinghua (T04), Huiyang Huxu (H), Qingyuan Ma (Q), Guangxi Xiayan (S1)), 2 breeds developed by the Institute of Animal Science, Guangdong Academy of Agricultural Sciences (Lingnan Huang (DC), dwarf chicken (E4)) and one introduced broiler (Abor Acre (AA)). Another objective of this study was to analyze the associations between polymorphisms of the H-FABP gene and fat deposition traits in chickens. PCR-SSCP was used to analyze SNPs in H-FABP and 4 SNPs (T260C, G675A, C783T and G2778A) were detected. Associations between polymorphic loci and intramuscular fat (IMF), abdominal fat weight (AFW) and abdominal fat percentage (AFP) were analyzed by ANCOVA method. The results showed that the T260C genotypes were significantly associated with IMF (p = 0.0233) and AFP (p = 0.0001); the G675A genotypes were significantly associated with AFW, AFP (p<0.01) and IMF (p<0.05); at the C783T locus, AFW and AFP differed highly between genotypes. However, the G2778A loci did not show any significant effect on fat deposition traits in this study. In addition, we found that there were some differences between AFP and definite haplotypes through a nonparametric statistical method, so the haplotypes based on the SNPs except G2778A loci were also significantly associated with IMF, AFW (g) (p<0.05) and AFP (%) (p<0.001). Significantly and suggestively dominant effects of H4H4 haplotype were observed for IMF and the H2H3 was dominant for AFW (g) and AFP (%). The results also revealed that H5H7 haplotype had a negative effect on IMF, while the H5H6 had a positive effect on AFW (g) and AFP (%).

• 생명과학회지
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• 제20권3호
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• pp.462-465
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• 2010

단맛은 인간이 느낄 수 있는 다섯 가지 감각 중 하나로, 열량을 제공하며 식욕을 결정하는데 중요한 요인이다. 인간이 맛물질을 느끼는 민감도 차이에 유전적인 요인이 중요한 역할을 한다는 사실이 알려진 바, 본 연구에서는 한국인 98명을 대상으로 단맛을 결정하는 미각수용체 TAS1R2 유전자에 대해 염기서열분석법을 이용한 단일염기 다형성 종류 및 빈도, 그리고 일배체형 분석을 수행하였다. 그 결과, TAS1R2 유전자로부터 총 12종류의 SNP이 검출되었으며 약 70%는 아미노산 치환을 일으키는 변이로 확인되었다. 특히, 231번째와 950번째 변이는 본 연구를 통해 처음으로 발견된 새로운 것으로 한국인 집단에서 특이적으로 존재하는 SNP일 가능성이 높다고 판단된다. 일배체형 분석결과에 따르면, 발견된 20 종류 일배체형 중 세 가지가 주로 한국인이 가지는 것으로 확인되었다. 본 연구결과 발견된 TAS1R2 유전자의 SNP은 향후 단맛물질을 감지하는 인간의 민감도차이를 결정하는데 유전적 요인으로 작용하는지 알아보는데 중요한 기초자료를 제시해 주리라 생각되며 맞춤형 식단 등 영양유전학 분야에 응용될 수 있을 것이다.

• Asian-Australasian Journal of Animal Sciences
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• 제26권6호
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• pp.780-787
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• 2013

The objective of this study was to investigate single nucleotide polymorphisms (SNPs) in the bovine nephroblastoma overexpressed (NOV) gene and to evaluate whether these polymorphisms affect carcass traits in the Korean cattle population. We resequenced to detect SNPs from 24 unrelated individuals and identified 19 SNPs within the full 8.4-kb gene, including the 1.5-kb promoter region. Of these 19 SNPs, four were selected for genotyping based on linkage disequilibrium (LD). We genotyped 429 steers to assess the associations of these four SNPs with carcass traits. Statistical analysis revealed that g.7801T>C and g.8379A>C polymorphisms in the NOV gene were associated with carcass weight (p = 0.012 and 0.008, respectively), and the g.2005A>G polymorphism was associated with the back fat thickness (BF) trait (p = 0.0001). One haplotype of the four SNPs (GGTA) was significantly associated with BF (p = 0.0005). Our findings suggest that polymorphisms in the NOV gene may be among the important genetic factors affecting carcass yield in beef cattle.

• Animal Systematics, Evolution and Diversity
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• 제16권2호
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• pp.169-176
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• 2000

제주도산 노루 (C. Pygargus tianschanicus)의 분류학적 위치를 규명하기 위한 연구의 일환으로, 한국의 제주도에서 채집된 6마리의 노루 표본들을 이용하여 mtDNA의 cytochrome b 유전자의 부분적인 염기서열의 분석을 하였다. 밝혀진 세 haplotype간의 nucleotide Tamura & Nei's distance는 최대 0.005로써, 노루의 다른 아종 내의 다양성과 비슷한 정도였다. 또한 제주도산 노루의 cytochrome b 염기서열들과 GenBank에서 얻은 서 시베리아 지역의 노루인 C. p. Pygargus의 cytochrome b 염기서열간의 nucleotide distance는 평균 0.013였으며, C. p. tianschanicus는 65만년 전에 서 시베리아 지역의 노루인 C. p. Pygargus에서 분화되었을 것으로 판단된다.