Mitochondrial DNA variation and phylogeography of Old World camels

Ming Liang,Siren Dalai,Yi Li,Hai Le,He Jing,Ji Rimutu 아세아·태평양축산학회 2021 Animal Bioscience Vol.34 No.4

Objective: Old World camels are a valuable genetic resource for many countries around the world due to their adaptation to the desert environment. At present, Old World camels have encountered the challenge of unprecedented loss of genetic resources. Through our research, we would reveal the population structure and genetic variation in Old World camel populations, which provides a theoretical basis for understanding the germplasm resources and origin and evolution of different Old World camel populations. Methods: In the present study, we assessed mtDNA control region sequences of 182 individuals from Old World camels to unravel genetic diversity, phylogeography, and demographic dynamics. Results: Thirty-two haplotypes confirmed by 54 polymorphic sites were identified in the 156 sequences, which included 129 domestic and 27 wild Bactrian camels. Meanwhile, 14 haplotypes were defined by 47 polymorphic sites from 26 sequences in the dromedaries. The wild Bactrian camel population showed the lowest haplotype and nucleotide diversity, while the dromedaries investigated had the highest. The phylogenetic analysis suggests that there are several shared haplotypes in different Bactrian camel populations, and that there has been genetic introgression between domestic Bactrian camels and dromedaries. In addition, positive values of Tajima’s D and Fu’s Fs test demonstrated a decrease in population size and/or balancing selection in the wild Bactrian camel population. In contrast, the negative values of Tajima’s D and Fu’s Fs test in East Asian Bactrian camel populations explained the demographic expansion and/or positive selection. Conclusion: In summary, we report novel information regarding the genetic diversity, population structure and demographic dynamics of Old World camels. The findings obtained from the present study reveal that abundant genetic diversity occurs in domestic Bactrian camel populations and dromedaries, while there are low levels of haplotype and nucleotide diversity in the wild Bactrian camel population. Objective: Old World camels are a valuable genetic resource for many countries around the world due to their adaptation to the desert environment. At present, Old World camels have encountered the challenge of unprecedented loss of genetic resources. Through our research, we would reveal the population structure and genetic variation in Old World camel populations, which provides a theoretical basis for understanding the germplasm resources and origin and evolution of different Old World camel populations.Methods: In the present study, we assessed mtDNA control region sequences of 182 individuals from Old World camels to unravel genetic diversity, phylogeography, and demographic dynamics.Results: Thirty-two haplotypes confirmed by 54 polymorphic sites were identified in the 156 sequences, which included 129 domestic and 27 wild Bactrian camels. Meanwhile, 14 haplotypes were defined by 47 polymorphic sites from 26 sequences in the dromedaries. The wild Bactrian camel population showed the lowest haplotype and nucleotide diversity, while the dromedaries investigated had the highest. The phylogenetic analysis suggests that there are several shared haplotypes in different Bactrian camel populations, and that there has been genetic introgression between domestic Bactrian camels and dromedaries. In addition, positive values of Tajima’s D and Fu’s <i>Fs</i> test demonstrated a decrease in population size and/or balancing selection in the wild Bactrian camel population. In contrast, the negative values of Tajima’s D and Fu’s <i>Fs</i> test in East Asian Bactrian camel populations explained the demographic expansion and/or positive selection.Conclusion: In summary, we report novel information regarding the genetic diversity, population structure and demographic dynamics of Old World camels. The findings obtained from the present study reveal that abundant genetic diversity occurs in domestic Bactrian camel populations and dromedaries, while there are low levels of haplotype and nucleotide diversity in the wild Bactrian camel population.

Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping

Zhang Tao,Wang Zhiying,Li Yaming,Zhou Bohan,Liu Yifan,Li Jinquan,Wang Ruijun,Lv Qi,Li Chun,Zhang Yanjun,Su Rui 아세아·태평양축산학회 2024 Animal Bioscience Vol.37 No.7

Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future.Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations.Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations.Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future. Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

미토콘드리아 Cytb 유전자를 이용한 잔가시고기의 신규 서식지 고령 회천 집단의 유전적 다양성 분석

김강래,성무성,황유진,이명석,정주희,김희수,유정남 한국어류학회 2023 한국어류학회지 Vol.35 No.4

잔가시고기 Pungitius kaibarae의 신규 집단인 고령 (GR) 집단과 야생 집단의 특성을 규명하기 위해 미토콘드리아 cytb 유전자 영역의 886 bp 서열을 이용 총 4개 집단 (경상북도 고령 (회천, GR), 포항 (곡강천, PH), 경산 (오목천, GYSA), 강원도 고성 (배봉천, GS))을 분석하였다. 고령 (GR) 집단에서 가장 낮은 haplotype 다양성을 나타냈고 (Hd=0.000), 고성 (GS) 집단에서 0.755로 가장 높은 haplotype 다양성을 확인하였다. Nucleotide 다양성은 고성 (GS) 집단에서 0.00291로 가장 높은 다양성을 나타냈으며, 고령 (GR) 집단에서 가장 0.00000로 가장 낮은 다양성을 보였다. 유전적 분화도에서 고령 (GR) 집단은 포항 (PH) 집단과 유전적으로 가장 가까운 것으로 나타났다. Haplotype 네트워크는 고령 (GR) 집단이 포항 (PH) 집단과 군집되어 가장 유사한 것으로 나타났다. 고령 (GR) 집단은 계통발생학적 tree에서 높은지지도 (98%)의 값으로 포항 (PH) 집단과 군집됨을 확인하였다. 따라서 고령 (GR) 집단은 포항 (PH) 집단과 유사한 집단에서 유래됨을 추정하였다. The 886-bp sequence of the mitochondrial region encoding the cytb gene was used to identify the origin of the Goryeong (GR) population of Pungitius kaibarae and to characterize genetic diversity and structure among wild populations. The GR population showed the lowest haplotype diversity (Hd=0.000), while the highest haplotype diversity was confirmed at 0.755 among the Goseoung (GS) population. Nucleotide diversity ranged was the highest diversity at 0.00291 inthe GS population and the lowest diversity at 0.00000 in the GR population. The GR population was genetically closest to the Pohang (PH) population. The haplotype network confirmed that the GR population was most similar to the PH population. The GR population also clustered with the PH population with high bootstrap support (98%) in a phylogenetic tree. We thus conclude that the GR population is derived from a population similar to the PH population.

Population genetics analysis based on mitochondrial cytochrome c oxidase subunit I (CO1) gene sequences of Cottus koreanus in South Korea

Yun Bong Han,Kim Yong Hwi,Han Ho-Seop,Bang In-Chul 한국유전학회 2025 Genes & Genomics Vol.47 No.2

Background The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species. Objective To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis. Methods We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea. Results In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (Hd = 0.941) and low nucleotide diversity (π = 0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise FST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak. Conclusions C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately. Background The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species. Objective To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis. Methods We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea. Results In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (Hd = 0.941) and low nucleotide diversity (π = 0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise FST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak. Conclusions C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately.

Genetic diversity and population structure of Lychnis wilfordii (Caryophyllaceae) with newly developed 17 microsatellite markers

김보라,Koh Nakamura,Saya Tamura,이병윤,곽명해 한국유전학회 2019 Genes & Genomics Vol.41 No.4

Lychnis wilfordii (Regel) Maxim. is a perennial plant designated as an endangered species by the Korean government because of rapid reduction in its population size. Thus, a population genetic study of this species is needed to establish the strategy for management and conservation based on scientific evidences. The goals of this study were to develop useful microsatellite markers for L. wilfordii and to understand current genetic status of L. wilfordii in Korean peninsula. Seventeen microsatellite markers were identified using next-generation sequencing and bioinformatic analysis and then analyzed genetic diversity in one hundred forty-five individuals from Korea (KI1, KI2, and KP), China (CX, CF) and Russia (RP). Analysis of molecular variance (AMOVA), principal coordinates analysis (PCoA) and STRU CTU RE results consistently showed discontinuity among L. wilfordii populations. AMOVA showed that the percentage of variation among populations was 53%, which was higher than the variation within populations (19%). PCoA showed that the populations were divided into three genetic clusters, (1) Chinese (CX, CF), (2) Russian (RP) populations and Korean populations (KI1, KI2) excluding KP, and (3) the KP population. In particular, KP, the most southern population on the Korean peninsula, showed significantly lower observed and expected heterozygosity, number of effective alleles, and Shannon index (I) than those of KI1 and KI2. L. wilfordii showed high differentiation between populations with low genetic diversity within populations. Among Korean populations, KP is likely to be affected by genetic drift due to small population size, low genetic diversity and limited gene flow.

Genetic Diversity and Population Genetic Structure of Black-spotted Pond Frog (Pelophylax nigromaculatus) Distributed in South Korean River Basins

Park, Jun-Kyu,Yoo, Nakyung,Do, Yuno National Institute of Ecology 2021 국립생태원회보(PNIE) Vol.2 No.2

The objective of this study was to analyze the genotype of black-spotted pond frog (Pelophylax nigromaculatus) using seven microsatellite loci to quantify its genetic diversity and population structure throughout the spatial scale of basins of Han, Geum, Yeongsan, and Nakdong Rivers in South Korea. Genetic diversities in these four areas were compared using diversity index and inbreeding coefficient obtained from the number and frequency of alleles as well as heterozygosity. Additionally, the population structure was confirmed with population differentiation, Nei's genetic distance, multivariate analysis, and Bayesian clustering analysis. Interestingly, a negative genetic diversity pattern was observed in the Han River basin, indicating possible recent habitat disturbances or population declines. In contrast, a positive genetic diversity pattern was found for the population in the Nakdong River basin that had remained the most stable. Results of population structure suggested that populations of black-spotted pond frogs distributed in these four river basins were genetically independent. In particular, the population of the Nakdong River basin had the greatest genetic distance, indicating that it might have originated from an independent population. These results support the use of genetics in addition to designations strictly based on geographic stream areas to define the spatial scale of populations for management and conservation practices.

Allozyme Diversity and Population Genetic Structure in Host a Jonesii ( Liliaceae ) , a Korean Endemic Species

정명기 ( Myong Gi Chung ) 한국유전학회 1994 Genes & Genomics Vol.16 No.2

Levels of genetic diversity, population genetic structure, and gene flow in Hosta jonesii, a herbaceous perennial endemic to several islands in southern Korea, were investigated. Starch-gel electrophoresis was conducted on leaves collected from 93 plants in four populations. Nineteen of 25 putative loci examined were polymorphic (Ps=76%) in at least one population and the mean number of alleles per locus was 2.02. In addition, mean expected heterozygosity within populations (HeP=0.273) were higher than average values for species with similar life-history traits. Significant differences in allele frequencies were detected between population at 16 loci (P<0.05), and slightly more than 10% of the genetic variation was found among populations (GST=0.109). Indirect estimate of the number of migrants per generations(Nm) was 1.15, calculated for GST, which indicates that gene flow is high among four populations of H. jonestii. Large population size, predominantly outcross-animal breeding system, seed dispersal by wind, and relatively undisturbed island habitats may result in high levels of genetic diversity within populations and low levels of genetic differentiation among population.

Assessment of genetic diversity and inbreeding in the Okinawa indigenous Agu pig through pedigree analysis

Shihei Touma,Kyota Fusho,Aisaku Arakawa Asian Australasian Association of Animal Productio 2025 Animal Bioscience Vol.38 No.6

Objective: The objective of this study was to clarify the changes in genetic diversity and inbreeding over the years as well as to identify the causes of genetic diversity loss using the pedigree of Okinawa indigenous Agu pigs. Methods: The pedigree of the Agu population consisted of 1,997 animals from 1997 to 2020. The equivalent complete generations (ECG), inbreeding coefficient (F), and effective population size (Ne) were computed using ENDOG v4.8. Genetic diversity parameters, including founders (f), the effective number of founders (f_e), the effective number of ancestors (f_a), and the founder genome equivalent (f_ge), were derived from the probability of gene origin. The study also investigated changes in genetic diversity indices over time. Results: ECG increased from 0.1 in 2003 to 3.87 by 2020, indicating an improved pedigree depth. The F has been on a downward trend since it peaked at 10.5% in 2015. However, the N_e in the reference population was 14.6, which is below the recommended levels. The f, f_e, f_a and f_ge of the reference population were 86, 26, 19, and 11.5, respectively. These values decrease in the order of f>f_e>f_a>f_ge. This indicates that all factors of genetic diversity loss played a role, including the unbalanced contributions of founders, bottlenecks, and random gene losses. Although in recent years efforts have been made to maintain genetic diversity and reduce inbreeding, the Agu pig population exhibited a 5% decrease in genetic diversity over the past 18 years, with both unequal founder contributions and genetic drift identified as significant contributing factors. Conclusion: This study reveals that more favorable breeding strategies (such as optimal contribution and population size expansion) are required to maintain genetic diversity and increase the Ne of the Agu pig population.

Effect of Population Reduction on mtDNA Diversity and Demographic History of Korean Cattle Populations

Dadi, Hailu,Lee, Seung-Hwan,Jung, Kyoung-Sup,Choi, Jae-Won,Ko, Moon-Suck,Han, Young-Joon,Kim, Jong-Joo,Kim, Kwan-Suk Asian Australasian Association of Animal Productio 2012 Animal Bioscience Vol.25 No.9

The population sizes of three Korean indigenous cattle populations have been drastically reduced over the past decades. In this study, we examined the extent to which reduction in populations influenced genetic diversity, population structure and demographic history using complete mitochondrial DNA (mtDNA) control region sequences. The complete mtDNA control region was sequenced in 56 individuals from Korean Black (KB), Jeju Black (JEB) and Korean Brindle (BRI) cattle populations. We included 27 mtDNA sequences of Korean Brown (BRO) from the GenBank database. Haplotype diversity estimate for the total population was high (0.870) while nucleotide diversity was low (0.004). The KB showed considerably low nucleotide (${\pi}$ = 0.001) and haplotype (h = 0.368) diversities. Analysis of molecular variance revealed a low level of genetic differentiation but this was highly significant (p<0.001) among the cattle populations. Of the total genetic diversity, 7.6% was attributable to among cattle populations diversity and the rest (92.4%) to differences within populations. The mismatch distribution analysis and neutrality tests revealed that KB population was in genetic equilibrium or decline. Indeed, unless an appropriate breeding management practice is developed, inbreeding and genetic drift will further impoverish genetic diversity of these cattle populations. Rational breed development and conservation strategy is needed to safeguard these cattle population.

Microsatellite Genetic Diversity and Population Structure of the Endangered Reeves’ Turtles (Mauremys reevesii) in South Korea

문광선,이영구,김인엽,김태욱,이사현,양두하,한상현,성하철 한국동물유전육종학회 2025 한국동물유전육종학회지 Vol.9 No.2

To understand the genetic diversity and population structure this study were examined using microsatellite (MS) genotypes in two Reeves’ turtle populations in South Korea. Mean observed and expected heterozygosities and polymorphic information content were 0.555, 0.595 and 0.564 in Geumgok population and 0.550, 0.633 and 0.591 in Gangjin-Yeongam population, respectively. Genetic diversity levels of Korean turtles showed higher than those of Chinese and Taiwanese captive breeding populations but lower than those of two Chinese populations collected from broad geographic range. Among nine MS loci tested, six loci in Geumgok population and two loci in Gangjin-Yeongam population showed significantly departed from Hardy-Weinberg equilibrium (PHW<0.05). Positive inbreeding coefficient (FIS) values were found, estimating that inbreeding occurred. On the other hand, negative FIS estimated to be introgression of exotic gene pools at the past. The genetic structure exhibited a fitting constant K=2, along with separation between both populations. The results from FCA, structure and phylogenetic analyses showed that these populations shared almost alleles except for several individuals but clustered into different branches on the phylogenetic tree, indicating that both populations had the similar ancestral origins but current populations formed by different reproduction processes. Our findings suggest that the two populations have experienced severe genetic bottlenecks in the past and have been growing their populations through a breeding process including inbreeding since the introgression of exotic gene pools. This study will provide important information for developing management programs for enhancing the genetic diversity and the population stability of the endangered Reeves’ turtle in South Korea.