Genetic diversity and population structure of Mongolian regional horses with 14 microsatellite markers

윤지혜,Oyungerel Baatartsogt,공홍식 아세아·태평양축산학회 2022 Animal Bioscience Vol.35 No.8

Objective: This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers. Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei’s DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure. Results: On average, the number of alleles, expected heterozygosity (HExp), observed heterozygosity (HObs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei’s DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation. Conclusion: Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships. Objective: This study aimed to identify the genetic diversity and population structure of Mongolian horse populations according to the province of residence (Khentii, KTP; Uvs, USP; Omnogovi and Dundgovi, GOP; Khovsgol, KGP) using 14 microsatellite (MS) markers.Methods: A total of 269 whole blood samples were obtained from the four populations (KTP, USP, GOP, KGP) geographically distinct provinces. Multiplex polymerase chain reaction (PCR) was conducted using 14 MS markers (AHT4, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, and VHL20), as recommended by the International Society for Animal Genetics. Capillary electrophoresis was conducted using the amplified PCR products, alleles were determined. Alleles were used for statistical analysis of genetic variability, Nei’s DA genetic distance, principal coordinate analysis (PCoA), factorial corresponding analysis (FCA), and population structure.Results: On average, the number of alleles, expected heterozygosity (H_Exp), observed heterozygosity (H_Obs), and polymorphic information content among all populations were 11.43, 0.772, 0.757, and 0.737, respectively. In the PCoA and FCA, GOP, and KGP were genetically distinct from other populations, and the KTP and USP showed a close relationship. The two clusters identified using Nei’s DA genetic distance analysis and population structure highlighted the presence of structurally clear genetic separation.Conclusion: Overall, the results of this study suggest that genetic diversity between KTP and USP was low, and that between GOP and KGP was high. It is thought that these results will help in the effective preservation and improvement of Mongolian horses through genetic diversity analysis and phylogenetic relationships.

Genetic Relationships of Panax Species by RAPD and ISSR Analyses

In, Dong-Su,Kim, Young-Chang,Bang, Kyong-Hwan,Chung, Jong-Wook,Kim, Ok-Tae,Hyun, Dong-Yoon,Cha, Seon-Woo,Kim, Tae-Soo,Seong, Nak-Sul The Korean Society of Medicinal Crop Science 2005 韓國藥用作物學會誌 Vol.13 No.5

This study was carried out to develop convenient and reproducible methods for identifying the genetic relationship among germplasms of Panax species based on molecular genetics. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses, genetic polymorphism of the Panax species was investigated with following cultivars and accessions, such as Chunpoong, Yunpoong, Kopoong, Sunpoong, and Kumpoong in domestic cultivars, Hwangsuk, Jakyung and Suckju in domestic accessions, and Panax quinquefolius L. and Panax japonicus C.A. Meyer in foreign introduced accessions, respectively. Specific DNA fragments ranging from 200 to 3,000 base pairs in size could be obtained with various ISSR and RAPD primers under the optimized PCR conditions. The dissimilarity coefficients among the genetic polymorphisms of ginseng cultivars and accessions were calculated from 0.26 to 0.90 in RAPD and from 0.12 to 0.89 in ISSR analysis, respectively. Eleven plant samples were grouped siblings together with cultivars and parents based on cluster analysis of genetic distance depending on genetic property such as origin of the species. In results, both RAPD and ISSR analyses were useful for identifying the genetic relationship among cultivars and accessions of Panax species at DNA level.

Genetic Relationships of Panax Species by RAPD and ISSR Analyses

Dong-Su In,Young-Chang Kim,Kyong-Hwan Bang,Jong-Wook Chung,Ok-Tae Kim,Dong-Yoon Hyun,Seon-Woo Cha,Tae-Soo Kim,Nak-Sul Seong 韓國藥用作物學會 2005 한국약용작물학회지 Vol.13 No.5

This study was carried out to develop convenient and reproducible methods for identifying the genetic relationship among germplasms of Panax species based on molecular genetics. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses, genetic polymorphism of the Panax species was investigated with following cultivars and accessions, such as Chunpoong, Yunpoong, Kopoong, Sunpoong, and Kumpoong in domestic cultivars, Hwangsuk, Jakyung and Suckju in domestic accessions, and Panax quinquefolius L. and Panax japonicus C.A. Meyer in foreign introduced accessions, respectively. Specific DNA fragments ranging from 200 to 3,000 base pairs in size could be obtained with various ISSR and RAPD primers under the optimized PCR conditions. The dissimilarity coefficients among the genetic polymorphisms of ginseng cultivars and accessions were calculated from 0.26 to 0.90 in RAPD and from 0.12 to 0.89 in ISSR analysis, respectively. Eleven plant samples were grouped siblings together with cultivars and parents based on cluster analysis of genetic distance depending on genetic property such as origin of the species. In results, both RAPD and ISSR analyses were useful for identifying the genetic relationship among cultivars and accessions of Panax species at DNA level.

Genetic Diversity and Phylogenetic Relationships between Chinese Cabbages [B. campestris (syn. rapa) L.] and Cabbages (B. oleracea L.) in Korea

Yan-Lin Sun,Shi-Lin Zheng,Kyong-Cheul Park,Ki-Young Choi,Ho-Min Kang,Soon-Kwan Hong 한국원예학회 2016 원예과학기술지 Vol.34 No.2

Members of the genus Brassica, which are known as oil crops or cruciferous vegetables, are widely cultivated in Canada, Australia, Asian and Europe. Because Brassica species have high yields, are well adapted to their environments, and are self-incompatible, the germplasm is abundant. Previous studies have reported abundant genetic diversity even within Brassica subspecies. In Korea, fresh cabbage leaves are eaten with roast meat, and to meet the current popular demand, new varieties are being increasingly bred. To determine the genetic diversity and relationships among the cabbage vegetables in Korea, we evaluated the genetic variation of 18 accessions based on 5S and 18S ribosomal RNA (rRNA) gene sequences. We detected many variable nucleotide sites, especially in the 5S rRNA gene sequences. Because the length of the 18S rRNA gene might influence the dissimilarity rate statistics, we used both the 5S and 18S sequences to analyze the phylogenetic relationships. S7 (B. oleracea) showed the most distant phylogenetic relationship with the other Brassica species. Interestingly, B2 (B. oleracea), B15, and B18 (B. campestris) have three different types of leaf profiles, and were divided into one group, and the other Brassica species formed another group. Statistical analysis of interspecies and intraspecies genetic distances revealed that B. campestris L. showed higher genetic diversity than B. oleracea L. This work provides additional data that facilitates the evaluation of the genetic variation and relationships among Brassica species. The results could be used in functional plant breeding programs to improve Brassica crops.

Genetic Diversity and Phylogenetic Relationships between Chinese Cabbages [B. campestris (syn. rapa) L.] and Cabbages (B. oleracea L.) in Korea

Sun, Yan-Lin,Zheng, Shi-Lin,Park, Kyong-Cheul,Choi, Ki-Young,Kang, Ho-Min,Hong, Soon-Kwan Korean Society of Horticultural Science 2016 원예과학기술지 Vol.34 No.2

Members of the genus Brassica, which are known as oil crops or cruciferous vegetables, are widely cultivated in Canada, Australia, Asian and Europe. Because Brassica species have high yields, are well adapted to their environments, and are self-incompatible, the germplasm is abundant. Previous studies have reported abundant genetic diversity even within Brassica subspecies. In Korea, fresh cabbage leaves are eaten with roast meat, and to meet the current popular demand, new varieties are being increasingly bred. To determine the genetic diversity and relationships among the cabbage vegetables in Korea, we evaluated the genetic variation of 18 accessions based on 5S and 18S ribosomal RNA (rRNA) gene sequences. We detected many variable nucleotide sites, especially in the 5S rRNA gene sequences. Because the length of the 18S rRNA gene might influence the dissimilarity rate statistics, we used both the 5S and 18S sequences to analyze the phylogenetic relationships. S7 (B. oleracea) showed the most distant phylogenetic relationship with the other Brassica species. Interestingly, B2 (B. oleracea), B15, and B18 (B. campestris) have three different types of leaf profiles, and were divided into one group, and the other Brassica species formed another group. Statistical analysis of interspecies and intraspecies genetic distances revealed that B. campestris L. showed higher genetic diversity than B. oleracea L. This work provides additional data that facilitates the evaluation of the genetic variation and relationships among Brassica species. The results could be used in functional plant breeding programs to improve Brassica crops.

Genetic Diversity and Phenetic Relationships of Genus Oxalis in Korea Using Random Amplified Polymorphic DNA (RAPD) Markers

Man Kyu Huh(허만규),Byoung-Ki Choi(최병기) 한국생명과학회 2014 생명과학회지 Vol.24 No.7

RAPD마크를 이용한 한국 내 괭이밥속(Oxalis L.) 식물의 유전적 다양성과 표현형 관계를 평가하였다. 10개의 시발체로 125개의 밴드를 얻었으며 시발체당 12.5개였다. 이들 밴드 중 121개(96.8%)는 다형성을 나타내었으며 단지 4개만 단형성을 나타내었다. 6개 분류군에서 RAPD 표현형의 평균은 3.6개(선괭이밥, 괭이밥)에서 4.8개(붉은괭이밥)였다. 종간 변이에서 선괭이밥과 자주괭이밥이 가장 낮은 변이를 나타내었으며(28.8%), 붉은괭이밥이 가장 높은 변이를 나타내었다(38.4%). 분류군 내 대립유전자좌위는 평균 32.7%였다. 종 간 전체 유전적 다양도와 종내 유전적 다양도는 각각 0.362와 0.122였다. 종간 분화에 근거한 전체 변이의 몫(GST)은 0.663이였다. 이는 전체변이의 66.3%는 종간에 있음을 나타낸다. NJ tree에서 선괭이밥과 붉은괭이밥의 분지군은 높은 지지도를 가지며 괭이밥과 자매군을 형성하였다. 염색체의 수와 RAPD의 표현형적 관계와 일치하지 않았다. We evaluated the phenetic relationships within six taxa of genus Oxalis L. in Korea with random amplified polymorphic DNA (RAPD) markers. Ten primers produced 125 bands for six taxa, and the mean number of bands per primer was 12.5. Across the six taxa, 121 (96.8%) bands were polymorphic, and only four were monomorphic. The mean number of RAPD phenotypes across the six taxa varied from 3.6 (O. stricta and O. corymbosa) to 4.8 (O. corniculata for. rubrifolia). In a simple measure of intraspecies variability according to the percentage of polymorphic bands, O. stricta and O. corymbosa exhibited the lowest variation (28.8%), and O. corniculata for. rubrifolia showed the highest (38.4%). A mean of 32.7% of the loci was polymorphic within taxa. The total interspecies genetic diversity (HT) and intraspecies genetic diversity (HS) was 0.362 and 0.122, respectively. On a per-locus basis, the proportion of total genetic variation due to differences among species (GST) was 0.663. This indicates that about 66.3% of the total variation was among species. The node of O. stricta and O. corniculata for. rubrifolia was strongly supported, with a high bootstrap value in the NJ tree and sistered with O. corniculata. According to RAPD analysis, the number of chromosomes was not congruent with a phenetic relationship.

Genetic Relationships of Lactuca spp. Revealed by RAPD, Inter-SSR, AFLP, and PCR-RFLP Analyses

Yang, Tae-Jin,Jang, Suk-Woo,Kim, Won-Bae The Korean Society of Crop Science 2007 Journal of crop science and biotechnology Vol.10 No.1

RAPD, Inter-SSR, and AFLP markers were used to assess the genetic diversity of lettuce cultivars and the phylogenetic relationships in Lactuca spp. A total of 216 polymorphic bands from seven RAPD primers, four Inter-SSR primers, and five AFLP primer combinations were used to elucidate the genetic similarity among lettuce cultivars. Forty-four lettuce accessions were subdivided into discrete branches according to plant type: crisphead, butterhead, and stem type, with some exceptions. The leafy- and cos-type accessions were intermingled in other groups with no discrete branch indicating that these are more diverse than others. Three accessions, including the Korean cultivar 'Cheongchima', the Korean local landrace 'Jinjam', and the German cultivar 'Lolla Rossa' were classified as the most diverse accessions. Twenty bands were unique in specific cultivars. Among these, three were specific in a plant type; one in Korean leafy type, one in crisphead type, and one in cos type lettuce. In the phylogenetic analysis among Lactuca species, L. saligna, L. serriola, and L. georgica clustered in a sister branch of the L. sativa complex. Two L. virosa accessions show the highest intra-specific relationships. L. perennis outlied from all the other Lactuca species at a genetic similarity of 0.53 and clustered with two Cichorium species, C. intybus and C. endivia, with genetic similarity of 0.67. The phylogenetic tree was supported by data from polymorphism of chloroplast genome which was revealed by PCR-RFLP.

AFLP 분석을 이용한 배추과 식물의 종속간 분자유전연구

권수진(Soo-Jin Kwon),임기병(Ki-Byung Lim),임명호(Myung-Ho Lim),박지영(Jee-Young Park),김진아(Jin-A Kim),김정선(Jung Sun Kim),이수성(Soo-Seong Lee),박범석(Beom-Seok Park),진용문(Yong-Moon Jin) 한국원예학회 2007 원예과학기술지 Vol.25 No.2

식물의 유전적 다양성과 유연관계 분석은 작물개량의 기 본이다. AFLP를 이용한 핵산지문분석법은 식물 뿐 아니라 다른 생물체의 유전자지도 작성에서부터 유전적 다양성 조 사에까지 널리 응용되고 있는 강력한 기술 중 하나이다. 배추속 작물 중 2배체인 기본종과 기본종들간 교잡에 의해 생성된 이질4배체, 종간 혹은 속간 잡종 그리고 이들의 양친을 대상으로 AFLP 양상을 관찰하였다. AFLP 반응에는 두개의 프라이머 쌍이 사용되었고 7개의 EcoRI(+2)/MseI(+3) 프라이머 조합이 유전적 유연관계의 측정에 이용되었다. 9개 accession 간의 유전적 유사도는 Nei의 유전적 거리 산출식에 의해서, 이들간 군집분석은 NTSYS-pc 프로그램의 UPGMA를 이용하였다. FISH를 통해 배추(Brassica)와 무(Raphanus)의 속간 잡종 1세대(배무채)의 염색체를 관찰한 결과 배추와 무의 염색체 수가 일치한 19쌍의 염색체(2n=4x=38)가 관찰되었으며 배추 염색체내에 무염색체 일부가 치환되었음을 확인할 수 있었다. Genetic diversity and relationship in the related plant taxa is a prerequisite for crop improvement. Amplified fragment length polymorphism (AFLP) fingerprinting is one of the powerful and widely used tools, which has found wide spread application in numerous studies ranging from genetic mapping to diversity surveys in plants and other organisms. Genome relationship among diploid and allotetraploid Brassica taxa, and between interspecific hybrid or intergeneric hybrid and their parental species were investigated using AFLP display. The two primer pairs for AFLP reactions and seven EcoRI (+2) and M5eI (+3) primer combinations were used in the measurement of genetic relationships. Genetic similarities among nine accessions were estimated by Nei’s distance equation, and cluster analysis was performed using the unweighed pair group method (UPGMA) in the computer program NTSYS-pc. One intergeneric hybrid between Brassica and Raphanus showed 2n=4x=38 chromosomes, of which Raphanus chromosome segment were translocated with B. rapa chromosome.

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers

Suh, Sangwon,Kim, Young-Sin,Cho, Chang-Yeon,Byun, Mi-Jeong,Choi, Seong-Bok,Ko, Yeoung-Gyu,Lee, Chang Woo,Jung, Kyoung-Sub,Bae, Kyoung Hun,Kim, Jae-Hwan Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.11

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

I-SSR 標識子를 利用한 호도나무屬의 識別 및 類緣關係 分析

黃錫仁,曺炅眞,李文鎬,李在善,李炳實,李郁 한국임학회 2004 한국산림과학회지 Vol.93 No.7

DNA 표지자를 이용한 호도나무 품종의 유연관계 및 품종구분을 위하여 I-SSR 9개 표지를 이용하여 104개의 유의적인 표지가 얻어졌으며, 신품종 호도나무를 포함한 83개 국내외 품종(종)에 대해 DNA 지문에 의한 품종식별이 가능하였다. 수원 1호, 수원 2호, 왕호도는 모두 Conrord, McKinster 등 미국에서 도입된 대립성 품종과의 인공교배로 육성된 품종으로 유전적 유연관계가 상촌 4호 등 국내 선발종보다는 산성 4호×Concord의 교배종과 더 가까웠다. 국내 선발종 호도나무인 상촌 2호, 상촌 4호 및 산성 4호 이들 끼리 한 그룹을 이루고 있는데 이는 국내의 호도나무가 외국품종과 구분되는 유전적 동질성이 있음을 보여주었다. 영동은 개체선발로 육성되었으나 외국종과 교배에 의하여 육성된 교잡종들과 같은 무리에 속하였는데, 이는 영동 품종은 외국 품종의 교배에 의해 외래 유전자 일부가 유입된 것이 아닌가 추정된다. Concord×상촌 1호., Concord×상촌 2호, Concord×대부 1호가 한 무리를 이루었고 Lake×상촌 2호가 이들과 구분되는 것은 교배차대가 유전적으로 화분수보다는 모수의 영향을 더 많이 받고 있음을 보여준다. Using 104 fragments amplified from 9 I-SSR primers, a total of 83 cultivars in Juglans spp. including new cultivars used for the present study were identified. The new cultivars 'Suwon No.1', 'Suwon No.2', and 'Wanghodo' are hybrids between the domestic cultivars and the introduced cultivars such as 'Concord' and 'McKinster' bearing big nuts. Consequently, these cultivars were closer to the hybrid between 'Sansung 4×Concord' than to domestically selected cultivars such as 'Sangehon 4' from the viewpoint of genetic relationship. The domestic cultivars such as 'Sangchon 2', 'Sangchon 4', and 'Sansung 4' belonged to the same group and were genetically distinctive from the introduced cultivars. This suggests that there would be difference in genetic structure between the domestic and the introduced cultivars. The cultivar 'Yeongdong' was clustered into the group of hybrids between the domestic and the introduced cultivars although it was developed by the selection of a tree from a domestic population. This might be because the genes were introduced from the introduced cultivars into the domestic population via open-pollination. The 'Concordx×Sangchon 1', 'Concord×Sangchon 2', and 'Concord×Daebu 1' were Clustered into the same group whereas 'Lake×Sangchon 2' was clustered into the different group. This ndicates that the genetic characteristics of hybrids may be influence more strongly by the mother tree than by the father tree.