• Animal Bioscience
• /
• v.35 no.8
• /
• pp.1141-1150
• /
• 2022

Objective: To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea. Methods: We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software. Results: By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia. Conclusion: The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2023.04a
• /
• pp.11-11
• /
• 2023

Due to the abundance of information in Nuclear DNA, it has a magnificent phylogenetic resolution. Moreover, because they show biparental inheritance, it has proven to be superior to organelle DNA, which has a limited number of genes and only shows maternal lineage. In particular, the transcriptome, which includes much nuclear DNA but is relatively inexpensive to analyze, can provide valuable insights into evolution through selection analysis and enable gene function research. This study's dataset includes 45 transcriptomes (16 generated for this study). It aims to explore the evolutionary history of Apioideae by comparing the results of the phylogenetic analysis with gene tree discordance and chloroplast phylogeny. The results confirmed the taxonomic positions of Peucedanum terebinthaceum, Ligusticum tachiroei, and Cymopterus melanotilingia and proposed a genus change for Glehnia littoralis. High gene tree discordances were identified in recently diverged clades, suggesting frequent hybridization and introgression. In the most recently diverged tribe of Selineae, the highest number of PSGs (positively selected genes) has been confirmed, which is inferred to be due to the geological and climatic diversity of their originated habitat, Central Asia. These genes include those related to responses to growth and drought, oxidative, and salt stress. In particular, the CYP97A gene confirmed as PSGs in Bupleurum latissimum is inferred to be a result of adaptation to the light-limited environment of Ulleungdo Island, as it is associated with the efficiency of photosynthesis.

• Molecules and Cells
• /
• v.26 no.6
• /
• pp.566-575
• /
• 2008

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia - northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia - northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.

• Journal of Life Science
• /
• v.26 no.7
• /
• pp.749-757
• /
• 2016

This study was carried out to reveal the genetic population structure of the Jeju Island population and the phylogenetic relationship of East Asian populations of the large-footed bat (Myotis macrodactylus) based on the genetic polymorphisms of mitochondrial cytochrome B (CYTB) and NADH dehydrogenase subunit 1 (ND1) gene sequences. A total of fourteen and nine haplotypes were found in the CYTB and ND1 sequences from East Asian bats, respectively. Haplotype distribution showed locality specific patterns. The results from ND1 haplotype analysis showed that the Jeju Island population has four haplotypes: the Mt. Halla and Western subpopulations have three ND1 haplotypes, but the Eastern subpopulation has just a single haplotype Nd03, which is commonly found on this island. The neighbor-joining (NJ) tree showed the closer relationship between Jeju Island and Japan rather than that between Jeju and Gangwon-do Province. The divergence time between the maternal ancestor lineages of Japanese and Chinese populations was estimated to be 0.789±0.063 MYBP. The secondary divergence between Jeju and Japanese bats was calculated about to be 0.168±0.013 MYBP. The Jeju population has immigrated to the island at least fifty thousand years ago. In addition, ND1 haplotype analysis suggested that the insular bats have experienced at least two further genetic differentiation events within this island. Consequently, these findings suggested that the results of this study may play a critical role in understanding the phylogenetic relationship among East Asian bat populations of M. macrodactylus. To prepare more explainable information on evolutionary correlation, analysis is still required to examine using expanded samples from China, Russia, and southern parts of the Korean Peninsula.

• BMB Reports
• /
• v.40 no.4
• /
• pp.577-587
• /
• 2007

Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Cola(A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

• Development and Reproduction
• /
• v.18 no.3
• /
• pp.139-143
• /
• 2014

Different with other fishes, the guppies (Poecilia reticulata) is ovoviviparity, which retain their fertilized eggs within the follicle throughout gestation. The synchronously growing diplotene oocytes store nutrients in droplets and yolk, before their maturation and fertilization. The lecithotrophic strategy of development entails the provisioning of embryos with resources from the maternal yolk deposit rather than from a placenta, it allows the extracorporeal culture of guppy embryo. Studies on their early development of live bearers like the guppy including lineage tracing and genetic manipulations, have been limited. Therefore, to optimize conditions of embryo in vitro culture, explanted embryos from pregnant females were incubated in embryo medium (L-15 medium, supplemented with 5, 10, 15, 20% fetal bovine serum, respectively). We investigated whether the contents of FBS in vitro culture medium impact the development of embryos, and whether they would hatch in vitro. Our study found that in 5% of FBS of the medium, although embryos developed significantly slower in vitro than in the ovary, it was impossible to exactly quantify the developmental delay in culture, due to the obvious spread in developmental stage within each batch of eggs, and embryos can only be maintained until the early-eyed. And although in culture with 20% FBS the embryos can sustain rapid development of early stage, but cannot be cultured for the entire period of their embryonic development and ultimately died. In the medium with 10% and 15% FBS, the embryos seems well developed, even some can continue to grow after follicle ruptures until it can be fed. We also observed that embryonic in these two culture conditions were significantly different in development speed, in 15% it is faster than 10%. But 10% FBS appears to be more optimizing condition than 15% one on development process of embryos and survival rate to larvae stage.

• Asian-Australasian Journal of Animal Sciences
• /
• v.28 no.4
• /
• pp.457-466
• /
• 2015

Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan's early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value ($F_{IS}$) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high $F_{ST}$ values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.

• Journal of Animal Science and Technology
• /
• v.46 no.6
• /
• pp.917-924
• /
• 2004

Using PCR-RFLP haplotyping for the mitochondrial DNA(mtDNA) fragment containing the NADH dehydrogenase 2 gene(ND2) and three tRNA genes(tRNA-Met, tRNA-Trp and tRNA-Ala), we characterized the genetic diversity of five pig breeds including Jeju native pigs. mtDNA polymorphisms showing distinct cleavage patterns were found in the pig breeds. Two digestion patterns were detected when HaeIII- and Hinfl-RFLP, and four in the Tsp5091-RFLP analyses. Combining the three restriction enzyme digestion patterns found in five different pig breeds, four mtDNA haplotypes were observed and the haplotype frequencies were significantly different by the pig breeds. A monomorphic haplotype, mtWB, was observed in both Korean wild boars and Large White pigs. Both Duroc and Landrace pigs contained two haplotypes suggesting their multiple maternal lineages. Jeju native pig has two haplotypes(mtJN and mtJD). Of these, mtJN is identified as a Jeju native pig specific haplotype. This study suggested that more than two progenitor populations have been taken part in the domestication process of the Jeju native pig population, and/or probably subsequent crossing with other pig breeds from near east Asia. Unlike with our prediction, there was no direct evidence under molecular levels on the maternal introgression of Korean wild boar in the domestication of Jeju native pigs. In conclusion, specificity of mtDNA haplotypes related to pig breeds win be useful for identifying the maternal lineage as wen as constructing the genealogical pedigree in pigs.

• Journal of Animal Science and Technology
• /
• v.45 no.6
• /
• pp.933-938
• /
• 2003

This study was performed to analyse the sequences of variations of mtDNA D-loop and their effects on carcass traits in Hnawoo(Korean cattle). The resulting sequences were compared with previously published sequences for other cattle breeds(GenBank J01394). The PCR was used to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Twenty five polymorphic sites by nucleotide substitution were found in mtDNA of Hanwoo. The frequencies of positions at 169, 16042, 16093, 16119, 16255 and 16302 nt with high levels of sequence polymorphism were 0.891, 0.117, 0.109, 0.182, 0.197 and 0.117, respectively. The substitution effect at 169 and 16119 nt was found significant on marbling score. Also substitution effect at 169 and 16042 nt was highly significant(p〈0.01) on backfat. thickness. Polymorphism of mtDNA sequence in D-loop region could be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Hanwoo.

• Reproductive and Developmental Biology
• /
• v.29 no.1
• /
• pp.9-13
• /
• 2005

This study was performed to analyze the sequence variation in mtDNA D-loop and their effects on milk and milk fat production in Holstein cows. The analyzed sequences were compared with previously published sequences from other cattle breeds (GenBank J01394). PCR was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Thirty five polymorphic sites by nucleotide substitution were found in mtDNA. The frequencies of positions at 106, 169, 16057, 16231 and 16255 nt with high levels of sequence polymorphism were 0.090, 0.555, 0.055, 0.090 and 0.050, respectively. The substitution effect at 169 nt was found significant on milk production, and substitution effect at 16118, 16139 and 16302 nt was highly significant (p<0.1) on milk fat production. Polymorphism of mtDNA sequence in D-loop region might be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Holstein cows.