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 韓國魚類學會誌 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.

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.

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.

Population Genetic Structure of Potentilla discolor Bunge, Rosaceae in Korea

허만규,Huh, Man-Kyu Korean Society of Life Science 2006 생명과학회지 Vol.16 No.6

한국내 분포하는 장미과의 솜양지꽃(Potentilla discolor Bunge) 15집단에 대한 19 알로자임 대립유전자좌위에서 유전적 다양성과 집단구조를 분석하였다. 조사한 좌위에 대해 약 73.7%가 다형성을 나타내었다. 종과 집단 수준에서 유전적 다양도는 각각 0.215, 0.196이었으며, 집단간 분화정도는 낮았다$(G_{ST}\;=\;0.069)$. 전체 유전적 다양성은 0${\sim}$0.656이며 평균 0.292였다. 유전적 다양도 중 집단내 변이는 높았다$(H_{S}\;=\;0.274)$. 전체 유전적 변이에서 집단간 차이는 Pgm-2에서 0.010, Pgd-2에서 0.261로 평균 0.069였다. 이는 전체 알로자임 변이 중 약 6.9%가 집단간에 있음을 의미한다. 솜양지꽃의 특성으로 광범위한 분포, 다년생 초본, 여러 세대의 존재 등이 높은 유전적 다양성을 나타내는데 기여하는 것으로 설명된다. 조사한 솜양지꽃 집단에서 세대당 이주하는 개체수는 3.36으로 평가되었다. The genetic diversity and population structure of fifteen Potentilla discolor Bunge populations in Korea were determined using genetic variations at 19 allozyme loci. Fourteen of the 19 loci (73.7%) showed detectable polymorphism. Genetic diversity at the species level and at the population level was high ($H_{ES}\;=\;0.215$, $H_{EP}\;=\;0.196$, respectively), whereas the extent of the population divergence was relatively low $(G_{ST}\;=\;0.069)$. Total genetic diversity values $(H_T)$ varied between 0.0 and 0.656, giving an average overall polymorphic loci of 0.292. The interlocus variation of genetic diversity within populations $(H_S)$ was high (0.274). On a per locus basis, the proportion of total genetic variation due to differences among populations $(G_{ST})$ ranged from 0.010 for Pgm-2 to 0.261 for Pgd-2 with a mean of 0.069, indicating that about 6.9% of the total allozyme variation was among populations. Wide geographic ranges, perennial herbaceous nature and the persistence of multiple generations are associated with the high level of genetic variation in P. discolor. The estimate of gene flow based on $G_{ST}$ was high among Korean populations of P. discolor (Nm = 3.36).

가치 다양성에 입각한 도덕과 인구교육: 2022 개정 도덕과 공통 교육과정을 중심으로

김은미 한국초등도덕교육학회 2023 초등도덕교육 Vol.- No.83

This study aimed to examine population education, which is becoming increasingly important, by focusing on its application to the moral education curriculum. Through this examination, I wanted to emphasize the need to treat the phenomenon of the declining birth rate and aging population, which has been treated mainly as a matter of fact, as a matter of value. In particular, I wanted to suggest that there is a distinction between emphasizing the importance of population education and the need for individuals to marry and have children in order to solve the social problems expected from the declining birthrate and aging population. Next, I would like to suggest that population education should attempt to center morality and an approach to pluralistic values, which means that population education should attempt to affirm the increasingly diverse forms of life in the future. Finally, if population education is combined with the process of choosing and affirming various values in life, it can ultimately be expanded to focus on improving the quality of life. 본 연구는 점차 그 중요성이 부각되고 있는 인구교육을 도덕과 교육과정에의 적용을 중심으로 고찰하고자 했다. 이와 같은 고찰을 통해서 그간의 인구교육이 주로 사실의 문제로 다루어온 저출산・고령화 현상을 가치의 문제로 다룰 필요가 있다는 점을 강조하고자 했다. 우선, 인구교육의 중요성을 강조하는 것과 저출산・고령화로 인해 예상되는 사회적인 문제점을 해결하고자 개인에게 결혼과 출산의 필요성을 강조하는 것은 구분되어야 한다는 점을 제시하고자 했다. 다음으로, 인구교육에 있어서 다원화된 가치에 대한 접근을 중심으로 도덕과 교육을 시도할 필요가 있다는 점을 제안하고자 했다. 이는 앞으로 점차 다양해질 삶의 형태를 긍정하면서 인구교육을 시도할 필요가 있다는 점을 제언하는 것이기도 하다. 마지막으로, 인구교육이 삶 속에서의 다양한 가치를 선택하고 이를 긍정한다면 삶의 질을 높이는 것에 관심을 가지는 방향으로 확대될 수 있다는 점을 제시하고자 했다.

Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis

한정은,최병희,곽명해 국립생물자원관 2018 Journal of species research Vol.7 No.4

Population genetic assessment is essential for the conservation and management of endangered and rare plants. Neofinetia falcata is endangered epiphyte orchid and protected by law in Korea. In Korea, this species is only found on islands in the South Sea of Korea (including Jeju-do) and the southern coast of the Korean Peninsula. We developed nine microsatellite makers to assess the genetic diversity and population genetic structure of three populations of N. falcata. The genetic diversity at the species level was low, which can be attributed to inbreeding or fragmentation into small, isolated populations. A recent bottleneck was detected in one population, likely due to overcollection. N. falcata exhibited moderated levels of differentiation among populations, with the three populations were divided into two clusters based on genetic structure. The genetic diversity and structure of N. falcata are affected by restricted gene flow by pollen or seeds due to isolation and geographic distance. Strategies for in situ and ex situ conservation of this species are been proposed based on the results of our study.

Population structure analysis reveals the maintenance of isolated sub-populations of weedy rice

CHUNG, J-W,PARK, Y-J Blackwell Publishing Ltd 2010 Weed research Vol.50 No.6

<P><SMALL>CHUNG</SMALL> J-W & <SMALL>PARK</SMALL> Y-J (2010). Population structure analysis reveals the maintenance of isolated sub-populations of weedy rice. <I>Weed Research</I> <B>50</B>, 606–620.</P><P>Summary</P><P>This study was conducted to assess the genetic diversity, population structure and linkage disequilibrium (LD) of weedy rice in Korea using 73 weedy rice, 24 landrace lines, 12 breeding lines and 24 international varieties. In total, 772 alleles were detected in 63 microsatellite loci. The number of alleles per marker locus ranged from two to 40, with an average of 12.3. The gene diversity and polymorphism information content value averaged 0.694 and 0.668, with a range of 0.016–0.941 and 0.016–0.946 respectively. In a model-based analysis of population structure, Korean rice germplasm was classified into four subpopulations, designated ‘cultivated <I>indica</I>’, ‘cultivated <I>japonica</I>’, ‘weedy <I>indica</I>’, ‘weedy <I>japonica</I>.’ Pair-wise estimates of <I>F</I><SUB>ST</SUB> indicated different degrees of differentiation between the four model-based populations, with values ranging from 0.073 (between cultivated and weedy <I>japonica</I>) to 0.474 (between weedy <I>japonica</I> and weedy <I>indica</I>). The weedy <I>indica</I> population appeared to be highly differentiated, compared with the other populations. The cultivated <I>indica</I> lines had the highest gene diversity (0.58), followed by cultivated <I>japonica</I> (0.50), weedy <I>japonica</I> (0.42) and weedy <I>indica</I> (0.35). The total number of private alleles in weedy <I>indica</I> and <I>japonica</I> populations was 39 (23 markers) and 55 (22 markers) respectively. The average of LD (<I>r</I><SUP>2</SUP>) of weedy <I>indica</I> and <I>japonica</I> types was higher than that of the two cultivated populations, both for inter- and intrachromosome values, indicating the possible reproductive and geographical isolation of sub-populations in cultivated rice fields.</P>