• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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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.

• 한국산림과학회지
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• 제105권4호
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• pp.414-421
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• 2016

국내 당단풍나무 집단의 유전다양성, 유전분화 및 유연관계를 알아보기 위해 AFLP 분석을 실시하였다. 14개 당단풍나무 집단에 대한 7개 AFLP 프라이머 조합을 적용한 결과 유효대립유전자 수($A_e$)가 1.4개, 다형적 유전자좌 비율(%P)이 82.2%, Shannon의 다양성 지수(I)가 0.358, 이형접합도 기대치($H_e$)가 0.231이었고, 베이즈 방법으로 추론한 이형접합도 기대치(Hj)는 0.253으로 나타났다. 당단풍나무의 유전다양성은 단풍나무속 수종들과 비교했을 때 중간수준이었고, 생활사나 생태적 특성이 유사한 수종들에 비해 낮았다. 베이즈 방법으로 추정된 평균 $F_{IS}$값은 0.712로 나타나 자가수분이나 근연관계 개체 간 교배에 의한 동형접합체 증가가 유전다양성에 영향을 준 것으로 생각된다. AMOVA로 추정한 당단풍나무의 유전분화율(${\Phi}_{ST}$)은 0.107이었고, 베이즈 방법으로 추정한 유전분화율(${\Phi}^{II}$)은 0.110이었다. 당단풍나무는 생활사나 생태적 특성이 유사한 종들에 비해 유전분화가 적게 이루어진 것으로 나타났다. 유연 관계 분석에서 울릉도 집단은 내륙의 집단들과 유전적으로 가장 상이한 집단으로 나타났다. 울릉도 집단은 유전다양성이 가장 낮은 집단으로서, 내륙의 집단 일부가 이주하면서 생긴 창시자 효과와 유전적 부동에 의해 유전다양성 감소가 이루어졌고 내륙과의 지리적 격리로 인해 유전자 교류가 감소했기 때문으로 추정된다.

• Genes and Genomics
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• 제40권12호
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• pp.1373-1382
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• 2018

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average $r^2$ values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (-0.015) than Chikso (-0.035). The average $F_{ST}$ value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.

• Asian-Australasian Journal of Animal Sciences
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• 제32권2호
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• pp.176-182
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• 2019

Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

• Animal Bioscience
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• 제35권12호
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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

• Animal Bioscience
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• 제36권3호
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• pp.417-428
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• 2023

Objective: Few studies have genetically monitored chickens over time, and no research has been conducted on ducks. To ensure the sustainable management of key duck breeds, we used microsatellite markers to monitor Brown Tsaiya ducks over time genetically. Methods: The second, fourth, sixth to eighth generations of the Brown Tsaiya duck selected for feeding efficiency and control lines were included in this study to investigate the genetic variations, effective population size, population structure and the differentiation between populations over time with 11 microsatellite markers derived from Brown Tsaiya duck. Results: The results showed there were a slight decrease in the genetic variations and an increase in within-population inbreeding coefficient (F_IS) in both lines, but no consistent increase in F_IS was observed in each line. The effective population size in the second and eighth generations was 27.2 for the selected line and 23.9 for the control line. The change in allele richness showed a downward trend over time, and the selected line was slightly lower than the control line in each generation. The number of private alleles (N_p) in the selected line were higher than in the control line. Moderate differentiation was observed between the second and eighth generations in the selected line (F_ST = 0.0510) and the control line (F_ST = 0.0606). Overall, differentiation tended to increase with each generation, but genetic variation and structure did not change considerably after six generations in the two lines. Conclusion: This study provides a reference for poultry conservation and helps to implement cross-generation genetic monitoring and breeding plans in other duck breeds or lines to promote sustainable management.

• Fisheries and Aquatic Sciences
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• 제26권12호
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• pp.752-761
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• 2023

Genetic diversity serves as the basis for selecting and genetically enhancing any culturable species in aquaculture. Here, two different strains of wild (River Ravi and River Kabul) and six captive-bred strains of Labeo rohita from various provinces were se- lected, and genetic diversity among them was evaluated using three different microsatellite markers, i.e., Lr-28, Lr-29, and Lr-37, and one mitochondrial CO1 (Cytochrome c oxidase subunit 1) gene. Different strains of L. rohita were collected, and part of their caudal fin was cut and preserved in ethanol for DNA extraction and determination of genetic diversity among them. Results in- dicated that selected markers were polymorphic with polymorphic information content (PIC) content values above 0.5 with the highest in Lr-28 followed by Lr-29 and then Lr-37. The observed heterozygosity (Ho) of all strains was higher (Avg: 0.731) but less than the expected heterozygosity (He). Moreover, TMs and WRs showed the highest He, while TKs showed the lowest, He. Over- all, inbreeding coefficient (FIS) values observed for all strains with selected markers were positive. The DNA barcoding with the CO1 gene revealed genetic variation among various strains, as demonstrated by the clades in the phylogenetic tree separating the strains into two distinct clusters that then divided into sub-clusters. In conclusion, TMs showed the highest heterozygosity as compared to other strains. Overall results provide the baseline data for the initiation of the genetic improvement program.

• Animal Bioscience
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• 제37권4호
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• pp.591-599
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• 2024

Objective: Sumba Ongole (SO) cattle are valuable breed due to their important role in the development of Indonesian cattle. Despite rapid advances in molecular technology, no genomic studies on SO cattle have been conducted to date. The aim of this study is to provide genomic profile related to the population diversity, admixture, and demographic trends of SO cattle. Methods: Genomic information was gathered from 79 SO cattle using the Illumina Bovine SNP50 v3 Beadchip, and for comparative purposes, additional genotypes from 209 cattle populations worldwide were included. The expected and observed heterozygosity, inbreeding coefficient, pairwise fixation indices between-population, and Nei's genetic distance were examined. Multidimensional scaling, admixture, and treemix analyses were used to investigate the population structure. Based on linkage disequilibrium and effective population size calculations, the demographic trend was observed. Results: The findings indicated that the genetic diversity of SO cattle was similar to that of other indicine breeds. SO cattle were genetically related to indicines but not to taurines or Bali cattle. The study further confirmed the close relationship between SO, Ongole, and Nellore cattle. Additionally, a small portion of the Ongole mixture were identified dominant in the SO population at the moment. The study also discovered that SO and Bali cattle (Bos javanicus) could have been ancestors in the development of Ongole Grade cattle, which corresponds to the documented history of Ongolization. Our finding indicate that SO cattle have maintained stability and possess unique traits separate from their ancestors. Conclusion: In conclusion, the genetic diversity of the SO cattle has been conserved as a result of the growing significance of the present demographic trend. Consistent endeavors are necessary to uphold the fitness of the breed.

• 농업과학연구
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• 제9권1호
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• pp.396-450
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• 1982

육종(育種) 자료(資料)를 얻기위해 수집(蒐集)한 한국(韓國) 재래종(在來種) 옥수수 57계통(系統)에 대(對)하여 주성분(主成分) 분석(分析)을 이용(利用)하여 재래종(在來種) 옥수수를 해석(解析)하고 계통분류(系統分類)를 하고 분류(分類)된 계통군별(系統群別)로 주요(主要) 특성(特性)에 대(對)한 유전적(遺傳的) 특성(特性)을 구명(究明)하고자 본(本) 연구(硏究)를 수행(修行)하였던 바 그 결과(結果)를 요약(要約)하면 다음과 같다. 1. 특성(特性)들의 평균치(平均値)는 모든 특성(特性)에서 계통간(系統間) 차이(差異)가 있었으며 비중(比重)을 제외(除外)한 모든 특성(特性)에서 교배유형별(交配類型別)로 차이(差異)가 있었는데 출수기(出穗期)까지의 일수(日數)를 제외(除外)한 모든 특성(特性)에서 자식(自殖)된 계통(系統)의 것은 세력(勢力)이 감소(減少)되었고 톱교배(交配)된 계통(系統)의 것은 세력(勢力)이 증대(增大) 되었다. 2. 특성간(特性間)의 상관계수(相關係數)는 0.99~-0.59 사이에 분포(分布)하였는데 특성간(特性間)의 상관(相關)은 대체(大體)로 낮은 것이 많았다. 그러나 수량구성요소(收量構成要素)와 관련(關聯)된 주요특성(主要特性)에서는 상관(相關)이 높았고 교배유형(交配類型)에 따른 특성간(特性間)의 상관계수(相關係數)의 크기는 별(別) 차이(差異)가 없었다. 3. 27개(個) 특성(特性) 가운데서 12개(個)의 주요특성(主要特性)을 이용(利用)한 주성분(主成分) 분석(分析)에서 제(第)4 주성분(主成分)까지를 가지고 전(全) 변동(變動)의 86.4%를 형매교배(兄妹交配)에서, 84.3%를 자식교배(自殖交配)에서 81.1%를 톱교배(交配)에서 각각(各各) 설명(說明)할 수 있었다. 4. 주성분(主成分)에 대(對)한 특성(特性)의 기여율(寄與率)은 특성(特性)에 따라 달랐고 상위(上位) 주성분(主成分)에서 컸으며 하위(下位) 주성분(主成分)에서 작았다. 5. 주성분(主成分)과 특성간(特性間)의 상관계수(相關係數)는 주성분(主成分)의 생물학적(生物學的) 의의(意義)와 주성분(主成分)에 대응(對應)한 식물체(植物體)의 형(型)을 명확(明確)히 하였는데 제(第)1 주성분(主成分)은 식물체(植物體)의 크기에 관련(關聯)된 주성분(主成分)이었고, 제(第)2 주성분(主成分)은 식물체(植物體)의 분화(分化) 및 생장기간(生長期間)에 관련(關聯)된 주성분(主成分)이었고, 제(第)3 주성분(主成分)과 제(第)4 주성분(主成分)은 형매교배(兄妹交配)된 계통(系統) 및 자식계통(自殖系統)에서는 뚜렷한 특징(特徵)이 없었으나 톱교배(交配)된 계통(系統)에서는 엽(葉)의 크기에 관련(關聯)된 주성분(主成分)이었다. 6. 계통간(系統間) 거리(距離)에 의(依)해 57계통(系統)은 4개(個)의 계통군(系統群)으로 분류(分類)되었으나 전계통(全系統)의 91.1%인 52계통(系統)이 계통군(系統群) I로 분류(分類)되어 수집(蒐集)된 재래종(在來種) 옥수수의 대부분(大部分)이 동일계통(同一系統)인 것으로 나타났고, 계통군(系統群) II에는 3계통(系統)이, 계통군(系統群) III과 계통군(系統群) IV에는 각각(各各) 1계통(系統)이 속(屬)하였다. 계통군(系統群) I은 조생(早生), 단간(短稈), 중형자수(中型雌穗), 중립(中粒) 및 중수(中收) 계통(系統)들이었고, 계통군(系統群) II는 만생(晩生), 중간(中稈), 소형자수(小型雌穗), 소립(小粒), 다자수(多雌穗) 및 다수(多收) 계통(系統)들이었다. 계통군(系統群) III은 중생(中生), 장간(長稈), 소형자수(小型雌穗) 및 소립(小粒), 소수(少收) 계통(系統)들이었고, 계통군(系統群) IV는 중생(中生), 장간(長稈), 대형자수(大型雌穗), 소자수(少雌穗) 및 중수계통(中收系統)이었다. 7. 특성(特性)들의 자식열세도(自殖劣勢度)는 계통(系統)에 따라 차이(差異)가 있었으며 수량(收量), 이삭중(重), 초장(草長) 등(等)에서 비교적(比較的) 크게 나타났고, 분류(分類)된 군별(群別) 자식열세도(自殖劣勢度)는 100 입중(粒重), 엽수(葉數), 엽장(葉長) 및 출수기(出穗期)까지의 일수(日數) 등(等)의 특성(特性)이 계통군(系統群) I에서 컸고, 기타의 특성(特性)은 계통군(系統群) II에서 컸다. 8. 특성(特性)들의 잡종강세도(雜種强勢度)는 계통간(系統間) 차이(差異)가 있었으며 이삭중(重), 이삭당(當) 입중(粒重), 100입중(粒重) 및 엽장(葉長) 등(等)에서 높았으며 분류(分類)된 군별(群別)로 보면 이삭길이, 이삭직경(直徑), 이삭중(重), 이삭당(當) 입중(粒重), 100 입중(粒重) 및 엽장(葉長) 등(等)의 특성(特性)은 계통군(系統群) II에서 높았고 기타의 특성(特性)은 계통군(系統群) I에서 높았다. 9. 특성(特性)들의 동질접합체(同質接合體) 정도(程度)는 이삭중(重)(79.1%)에서 가장 높았으며 이삭 수(數)(-2.1%)에서 가장 낮았는데 특성별(特性別)로 큰 차이(差異)가 있었다. 분류(分類)된 군별(群別)에 있어서도 동질접합체(同質接合體) 정도(程度)는 특성(特性)에 따라 차이(差異)가 있었는데 계통군(系統群) II에서 높은 것이 많았고 계통군(系統群) I에서 낮은 것이 많았다. 10. 형매교배(兄妹交配)된 계통(系統)의 특성(特性)과 톱 교배(交配)된 계통(系統)의 특성(特性)과의 상관관계(相關關係)는 모든 특성(特性)에서 정(正)의 상관(相關)을 나타내었으며 이삭수(數), 초장(草長), 엽장(葉長), 수량(收量) 및 단백질(蛋白質) 함량(含量) 등(等)에서 높은 상관(相關)을 나타내었으며 이삭 직경(直徑), 100입중(粒重) 및 엽수(葉數) 등(等)에서는 유의성(有意性)이 인정(認定)되지 않았다.

• 한국어류학회지
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• 제27권1호
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• pp.10-15
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• 2015

현재 IUCN의 취약 등급인 대왕바리(giant grouper, Epinephelus lanceolatus) 친어의 효율적인 관리 시스템 구축을 위한 기반연구로서 기 개발되어 있는 동종의 microsatellite 마커를 이용한 가계도 분석 효율을 조사하였다. 대왕바리 친어 32마리를 8개의 microsatellite 마커로 분석한 결과 총 52개의 대립유전자가 검출되었으며, 기대치 이형접합율은 0.663, 근친교배계수는 0.011로 조사되어 현재 확보된 대왕바리 친어는 유전 다양성이 비교적 잘 유지되고 있었다. 하지만 유효집단 크기가 35로 추정됨으로써 지속적인 친어 확보의 필요성을 보였다. 해당 마커를 이용한 동일 유전자형 출현 확률은 무작위 집단에서 $6.85{\times}10^{-11}$ 그리고 한쪽 부모의 유전자형 확보 및 양친의 유전자형이 확보된 상태에서의 부권 부정률은 각각 0.00835, 0.00027로 나타났으며, 주좌표 분석 결과 친어의 유전자형은 중복되지 않았다. 따라서 본 연구에 이용한 8개의 microsatellite 마커로도 유전자형 데이터베이스를 기반으로 한 대왕바리 친어 관리 시스템 구축이 가능할 것이며, 이를 활용한 유전 다양성이 높은 자손 생산 및 유전적으로 유사한 개체의 중복 확보를 방지할 수 있어 친어 확보의 효율성을 높일 수 있을 것이다.