scholarly journals Estimation of Effective Population Size of Korean Native Black Goat Using Genomic Information

2021 ◽  
Vol 25 (03) ◽  
pp. 575-580
Author(s):  
Kwan-Woo Kim
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Physical Distance ◽  
Capra Hircus ◽  
Systematic Research ◽  
Genomic Information ◽  
Effective Population ◽  
Black Goat

The Korean native black goat (Capra hircus coreanae) is the only goat species to be officially registered in Korea under the Food and Agriculture Organization; however, no systematic research on their genetic diversity has been conducted. Decreased genetic diversity in Korean native black goat leads to an increase in the level of inbreeding across generations. In this study, the genetic parameters and effective population size of three strains of Korean native black goat—82 Dangjin, 87 Jangsu, and 118 Tongyeong individuals—were estimated using their genomic information. The average linkage disequilibrium (r2) between single nucleotide polymorphism markers in the genome was 0.16, 0.14, and 0.13 for the Dangjin, Jangsu, and Tongyeong strains, respectively. The largest linkage disequilibrium was observed in the 14th and 26th chromosomes (r2 = 0.18) of Dangjin individuals. Furthermore, an increase in physical distance between markers decreased the linkage disequilibrium. The effective population size of the three Korean native black goat strains showed a decreasing trend proportional to the decrease in generation. The effective population size was 47, 59 and 56 individuals for the Dangjin, Jangsu and Tongyeong strains, respectively, 13 generations ago. These values could be due to the high level of inbreeding for generating populations to preserve the Korean native black goat genetic resource. © 2021 Friends Science Publishers

scholarly journals Whole genome linkage disequilibrium and effective population size in a coho salmon (Oncorhynchus kisutch) breeding population

2018 ◽  
Author(s):  
Agustín Barría ◽  
Kris A. Christensen ◽  
Grazyella Yoshida ◽  
Ana Jedlicki ◽  
Jean P. Lhorente ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Coho Salmon ◽  
Association Studies ◽  
Breeding Population ◽  
Physical Distance ◽  
Average Density ◽  
Whole Genome ◽  
Effective Population

AbstractThe estimation of linkage disequilibrium between molecular markers within a population is critical when establishing the minimum number of markers required for association studies, genomic selection and for inferring historical events influencing different populations. This work aimed to evaluate the extent and decay of linkage disequilibrium in a coho salmon breeding population using ddRAD genomic markers.Linkage disequilibrium was estimated between a total of 7,505 SNPs found in 62 individuals (33 dams and 29 sires) from the breeding population. The makers encompass all 30 coho salmon chromosomes and comprise 1,655.19 Mb of the genome. The average density of markers per chromosome ranged from 3.45 to 6.11 per 1 Mbp. The minor allele frequency averaged 0.20 (with a range from 0.08 to 0.50). The overall average linkage disequilibrium among SNPs pairs measured as r2 was 0.054. The Average r2 value decreased with increasing physical distance, with values ranging from 0.37 to 0.054 at distances lower than 1 kb and up to 10 Mb, respectively. An r2 threshold of 0.1 was reached at distance of approximately 1.3 Mb. Chromosomes Okis05, Okis15 and Okis28 showed high levels of linkage disequilibrium (> 0.20 at distances lower than 1 Mb). Average r2 values were lower than 0.1 for all chromosomes at distances greater than 4 Mb. Linkage disequilibrium values suggest that whole genome association and selection studies could be performed using about 75,000 SNPs in aquaculture populations (depending on the trait under investigation). From the identified SNPs, an effective population size of 100 was estimated for the population 10 generation ago, and 1,000, for 139 generations ago.Based on the extent of r2 decay, we suggest that at least 75,000 SNPs would be necessary for an association mapping study. Over 100,000 SNPs would be necessary for a high power study, in the current coho salmon population.

scholarly journals Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
Author(s):  
Y. C. Miao ◽  
Z. J. Zhang ◽  
J. R. Su
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Population Bottleneck ◽  
Effective Population ◽  
Taxus Yunnanensis ◽  
Low Genetic Diversity ◽  
Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

scholarly journals Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Vincent Prieur ◽  
Shannon M. Clarke ◽  
Luiz F. Brito ◽  
John C. McEwan ◽  
Michael A. Lee ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
New Zealand ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Maps ◽  
Effective Population

scholarly journals Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

scholarly journals Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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