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Ahn B, Kang M, Jeon H, Kim JS, Jiang H, Ha J, Park C. Origin and population structure of native dog breeds in the Korean peninsula and East Asia. iScience 2023; 26:106982. [PMID: 37378348 PMCID: PMC10291505 DOI: 10.1016/j.isci.2023.106982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/13/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
To study the ancestry and phylogenetic relationships of native Korean dog breeds to other Asian dog populations, we analyzed nucleotide variations in whole-genome sequences of 205 canid individuals. Sapsaree, Northern Chinese indigenous dog, and Tibetan Mastiff were largely related to West Eurasian ancestry. Jindo, Donggyeongi, Shiba, Southern Chinese indigenous (SCHI), Vietnamese indigenous dogs (VIET), and Indonesian indigenous dogs were related to Southeast and East Asian ancestry. Among East Asian dog breeds, Sapsaree presented the highest haplotype sharing with German Shepherds, indicating ancient admixture of European ancestry to modern East Asian dog breeds. SCHI showed greater haplotype sharing with New Guinea singing dogs, VIET, and Jindo than with other Asian breeds. The predicted divergence time of East Asian populations from their common ancestor was approximately 2,000 to 11,000 years ago. Our results expand understanding of the genetic history of dogs in the Korean peninsula to the Asian continent and Oceanic region.
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Affiliation(s)
- Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jong-Seok Kim
- Department of Korean Jindo and Domestic Animal, Jindo 58927, Republic of Korea
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun, Jilin 130119, China
| | - Jihong Ha
- Korean Sapsaree Foundation, Gyeongsan 38412, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea
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Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data. Animals (Basel) 2020; 10:ani10091520. [PMID: 32867351 PMCID: PMC7552306 DOI: 10.3390/ani10091520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023] Open
Abstract
Simple Summary Dogs are an important part of society. The Polish Lowland Sheepdog (PON) is one of 353 of the world’s largest cynological organization listed dog breeds. Breeds with small population sizes, like the PONs, are often characterized by high inbreeding rates and thus an increased risk of congenital diseases. To examine the endangerment of the PONs, measures for genetic diversity and inbreeding were calculated for the German PON population. The study showed that the PONs had to be classified as a minimally endangered population according to threshold values specified by the European Association for Animal Production. However, the very recent trend showed a slight improvement. Abstract Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.
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Vasiliadis D, Metzger J, Distl O. Demographic assessment of the Dalmatian dog - effective population size, linkage disequilibrium and inbreeding coefficients. Canine Med Genet 2020; 7:3. [PMID: 32835229 PMCID: PMC7371805 DOI: 10.1186/s40575-020-00082-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/17/2020] [Indexed: 01/08/2023] Open
Abstract
Background The calculation of demographic measures is a useful tool for evaluating the genomic architecture of dog breeds and enables ranking dog breeds in terms of genetic diversity. To achieve this for the German Dalmatian dog population, 307 purebred animals of this breed were genotyped on the Illumina Canine high density BeadChip. The analysis of pedigree-based inbreeding was performed based on a pedigree with 25,761 dogs including the genotyped dogs. Results The effective population size derived from squared correlation coefficients between SNP alleles (r2) was 69. The maximum value of r2 was 0.56, resulting in a 50% decay value of 0.28 at a marker distance of 37.5 kb. The effective population size calculated from pedigree data using individual increase in inbreeding over equivalent generations was 116. The pedigree inbreeding coefficient was 0.026. The genomic inbreeding coefficient based on the length of runs of homozygosity (ROH) was calculated for seven length categories of ROHs, and ranged from 0.08 to 0.28. The fixation coefficients FIS_PED and FIS_GENO were at 0.017 and 0.004. PANTHER statistical overrepresentation analysis of genes located in consensus ROHs revealed highly underrepresented biological processes in 50% of the investigated dogs. One of those is the 0.28 fold enriched “immune response”, which might be associated to the high prevalence of allergic dermatitis in the breed. Candidate genes for congenital sensorineural deafness (CCSD, a highly prevalent disease in the Dalmatian) were discovered in consensus ROHs. Conclusions The fast decay of r2 and the moderate inbreeding coefficients indicate that the German Dalmatian dog population is rather diverse. Pedigree- and genomic-based inbreeding measures were highly correlated and therefore prove good reliability for the given population. Analyses of consensus ROHs with genes coding for deafness and other breed-defining traits, such as hyperuricosuria, indicate that those ROH became fixed in the Dalmatian population about 500 years ago. In case of the Dalmatian dog, a ROH of 40 SNPs length is enough to investigate signatures of selection (e.g. the ROH with the fixed hyperuricosuria mutation) as far back as the breed formation point approximately 500 years ago.
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Affiliation(s)
- Danae Vasiliadis
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
| | - Ottmar Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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Amiri Ghanatsaman Z, Wang GD, Asadollahpour Nanaei H, Asadi Fozi M, Peng MS, Esmailizadeh A, Zhang YP. Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication. BMC Genomics 2020; 21:207. [PMID: 32131720 PMCID: PMC7057629 DOI: 10.1186/s12864-020-6619-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/25/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. RESULTS Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10,571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3'-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. CONCLUSIONS Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
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Gajaweera C, Kang JM, Lee DH, Lee SH, Kim YK, Wijayananda HI, Kim JJ, Ha JH, Choi BH, Lee SH. Genetic diversity and population structure of the Sapsaree, a native Korean dog breed. BMC Genet 2019; 20:66. [PMID: 31382890 PMCID: PMC6683530 DOI: 10.1186/s12863-019-0757-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 06/20/2019] [Indexed: 01/14/2023] Open
Abstract
Background The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed was rescued from extinction and population sizes have been gradually increasing over the past few decades. The aim of this study was to ascertain novel information about the genetic diversity, population structure, and demographic history of the Sapsaree breed using genome-wide single nucleotide polymorphism data. We characterized the genetic profile of the Sapsaree breed by comparison with seven foreign dog breeds with similar morphologies to estimate genetic differentiation within and among these breeds. Results The results suggest that Sapsarees have higher genetic variance compared with the other breeds analyzed. The majority of the Sapsarees in this study share a discrete genetic pattern, although some individuals were slightly different, possibly as a consequence of the recent restoration process. Concordant results from analyses of linkage disequilibrium, effective population size, genetic diversity, and population structural analyses illustrate a relationship among the Sapsaree and the Tibetan breeds Tibetan terrier and Lhasa Apso, and a small genetic introgression from European breeds. The effective population size of the Sapsaree has contracted dramatically over the past generations, and is currently insufficient to maintain long-term viability of the breed’s genetic diversity. Conclusions This study provides novel insights regarding the genetic diversity and population structure of the native Korean dog breed Sapsaree. Our results suggest the importance of a strategic and systematic approach to ensure the genetic diversity and the authenticity of the Sapsaree breed. Electronic supplementary material The online version of this article (10.1186/s12863-019-0757-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chandima Gajaweera
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Animal Science, Faculty of Agriculture, University of Ruhuna, Matara, Sri Lanka
| | - Ji Min Kang
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Doo Ho Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Soo Hyun Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yeong Kuk Kim
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hasini I Wijayananda
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Gyeongsan, 712-749, Republic of Korea
| | - Ji Hong Ha
- School of Life Science, Kyungpook National University, Daegu, 41940, Republic of Korea
| | - Bong Hwan Choi
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Seung Hwan Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Talenti A, Dreger DL, Frattini S, Polli M, Marelli S, Harris AC, Liotta L, Cocco R, Hogan AN, Bigi D, Caniglia R, Parker HG, Pagnacco G, Ostrander EA, Crepaldi P. Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution. Ecol Evol 2018; 8:2911-2925. [PMID: 29531705 PMCID: PMC5838073 DOI: 10.1002/ece3.3842] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/27/2017] [Indexed: 01/16/2023] Open
Abstract
Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome-wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.
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Affiliation(s)
- Andrea Talenti
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Dayna L. Dreger
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Stefano Frattini
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Michele Polli
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Stefano Marelli
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Alexander C. Harris
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Luigi Liotta
- Dipartimento di Scienze VeterinarieUniversity of MessinaMessinaItaly
| | - Raffaella Cocco
- Dipartimento di Medicina VeterinariaUniversity of SassariSassariItaly
| | - Andrew N. Hogan
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Daniele Bigi
- Dipartimento di Scienza e Tecnologie Agro‐AlimentariAlma Mater Studiorum University of BolognaBolognaItaly
| | - Romolo Caniglia
- Area per la Genetica della ConservazioneIstituto Superiore per la Protezione e la Ricerca AmbientaleOzzano dell'EmiliaBolognaItaly
| | - Heidi G. Parker
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Giulio Pagnacco
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
| | - Elaine A. Ostrander
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Paola Crepaldi
- Dipartimento di Medicina VeterinariaUniversità di MilanoMilanoItaly
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Choi BH, Wijayananda HI, Lee SH, Lee DH, Kim JS, Oh SI, Park EW, Lee CK, Lee SH. Genome-wide analysis of the diversity and ancestry of Korean dogs. PLoS One 2017; 12:e0188676. [PMID: 29182674 PMCID: PMC5705110 DOI: 10.1371/journal.pone.0188676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/10/2017] [Indexed: 01/22/2023] Open
Abstract
There are various hypotheses on dog domestication based on archeological and genetic studies. Although many studies have been conducted on the origin of dogs, the existing literature about the ancestry, diversity, and population structure of Korean dogs is sparse. Therefore, this study is focused on the origin, diversity and population structure of Korean dogs. The study sample comprised four major categories, including non-dogs (coyotes and wolves), ancient, modern and Korean dogs. Selected samples were genotyped using an Illumina CanineHD array containing 173,662 single nucleotide polymorphisms. The genome-wide data were filtered using quality control parameters in PLINK 1.9. Only autosomal chromosomes were used for further analysis. The negative off-diagonal variance of the genetic relationship matrix analysis depicted, the variability of samples in each population. FIS (inbreeding rate within a population) values indicated, a low level of inbreeding within populations, and the patterns were in concordance with the results of Nei's genetic distance analysis. The lowest FST (inbreeding rate between populations) values among Korean and Chinese breeds, using a phylogenetic tree, multi-dimensional scaling, and a TreeMix likelihood tree showed Korean breeds are highly related to Chinese breeds. The Korean breeds possessed a unique and large diversity of admixtures compared with other breeds. The highest and lowest effective population sizes were observed in Korean Jindo Black (485) and Korean Donggyeong White (109), respectively. The historical effective population size of all Korean dogs showed declining trend from the past to present. It is important to take immediate action to protect the Korean dog population while conserving their diversity. Furthermore, this study suggests that Korean dogs have unique diversity and are one of the basal lineages of East Asian dogs, originating from China.
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Affiliation(s)
- Bong Hwan Choi
- Animal Genome & Bioinformatics, National Institute of Animal Science, RDA, WanJu, Korea
| | | | - Soo Hyun Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Doo Ho Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Jong Seok Kim
- Korean Jindo and Domestic Animal Center, Jindo, Korea
| | - Seok Il Oh
- Korean Jindo and Domestic Animal Center, Jindo, Korea
| | - Eung Woo Park
- Animal Genome & Bioinformatics, National Institute of Animal Science, RDA, WanJu, Korea
| | - Cheul Koo Lee
- Department of Biotechnology, Korea University, Seoul, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
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A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci. Heredity (Edinb) 2016; 117:207-16. [PMID: 27165767 DOI: 10.1038/hdy.2016.30] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 03/14/2016] [Accepted: 03/29/2016] [Indexed: 12/29/2022] Open
Abstract
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of single-nucleotide polymorphism (SNP) loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP data set are unlinked. The approach is applied to an empirical data set of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.
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Do KT, Lee JH, Lee HK, Kim J, Park KD. Estimation of effective population size using single-nucleotide polymorphism (SNP) data in Jeju horse. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2014; 56:28. [PMID: 26290717 PMCID: PMC4540288 DOI: 10.1186/2055-0391-56-28] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 10/29/2014] [Indexed: 01/20/2023]
Abstract
This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy–Weinberg equilibrium test P-value of <10–6) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient (r2) between SNP pairs, were calculated for each allele and the effective population size was determined based on r2 measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But r2 decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average r2 between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average r2 between all SNP pairs was 0.02. We observed an initial pattern of decreasing Ne and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse’s population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.
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Affiliation(s)
- Kyoung-Tag Do
- Department of Equine Sciences, Sorabol College, Gyeongju, 780-711 Republic of Korea
| | - Joon-Ho Lee
- The Animal Genomics and Breeding Center, Hankyong National University, Anseong, 456-749 Republic of Korea
| | - Hak-Kyo Lee
- The Animal Genomics and Breeding Center, Hankyong National University, Anseong, 456-749 Republic of Korea
| | - Jun Kim
- Provincial Livestock Promotion, Jeju, 690-802 Republic of Korea
| | - Kyung-Do Park
- The Animal Genomics and Breeding Center, Hankyong National University, Anseong, 456-749 Republic of Korea
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Kang JH, Lim HJ, Kang HS, Lee JM, Baby S, Kim JJ. Development of Genetic Markers for Triploid Verification of the Pacific Oyster, Crassostrea gigas. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:916-20. [PMID: 25049868 PMCID: PMC4093491 DOI: 10.5713/ajas.2013.13108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/06/2013] [Accepted: 04/02/2013] [Indexed: 12/04/2022]
Abstract
The triploid Pacific oyster, which is produced by mating tetraploid and diploid oysters, is favored by the aquaculture industry because of its better flavor and firmer texture, particularly during the summer. However, tetraploid oyster production is not feasible in all oysters; the development of tetraploid oysters is ongoing in some oyster species. Thus, a method for ploidy verification is necessary for this endeavor, in addition to ploidy verification in aquaculture farms and in the natural environment. In this study, a method for ploidy verification of triploid and diploid oysters was developed using multiplex polymerase chain reaction (PCR) panels containing primers for molecular microsatellite markers. Two microsatellite multiplex PCR panels consisting of three markers each were developed using previously developed microsatellite markers that were optimized for performance. Both panels were able to verify the ploidy levels of 30 triploid oysters with 100% accuracy, illustrating the utility of microsatellite markers as a tool for verifying the ploidy of individual oysters.
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Affiliation(s)
- Jung-Ha Kang
- Biotechnology Research Division, NFRDI, Busan 619-705, Korea
| | - Hyun Jeong Lim
- Biotechnology Research Division, NFRDI, Busan 619-705, Korea
| | - Hyun-Soek Kang
- Biotechnology Research Division, NFRDI, Busan 619-705, Korea
| | - Jung-Mee Lee
- Biotechnology Research Division, NFRDI, Busan 619-705, Korea
| | - Sumy Baby
- Biotechnology Research Division, NFRDI, Busan 619-705, Korea
| | - Jong-Joo Kim
- Biotechnology Research Division, NFRDI, Busan 619-705, Korea
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