Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds

2016 ◽  
Vol 48 (1) ◽  
pp. 85-89 ◽  
Author(s):  
P. Sudrajad ◽  
D. W. Seo ◽  
T. J. Choi ◽  
B. H. Park ◽  
S. H. Roh ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Korean Cattle ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Genome Wide Linkage Disequilibrium

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

scholarly journals Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

2015 ◽  
Vol 6 ◽  
Author(s):  
Sithembile O. Makina ◽  
Jeremy F. Taylor ◽  
Este van Marle-Köster ◽  
Farai C. Muchadeyi ◽  
Mahlako L. Makgahlela ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
South African ◽  
Effective Population ◽  
Cattle Breeds ◽  
Sanga Cattle

scholarly journals Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle

2011 ◽  
Vol 24 (12) ◽  
pp. 1660-1665 ◽  
Author(s):  
S. H. Lee ◽  
Y. M. Cho ◽  
D. Lim ◽  
H. C. Kim ◽  
B. H. Choi ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Effective Population ◽  
Korean Cattle

Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

2006 ◽  
Vol 37 (2) ◽  
pp. 139-144 ◽  
Author(s):  
M. Odani ◽  
A. Narita ◽  
T. Watanabe ◽  
K. Yokouchi ◽  
Y. Sugimoto ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Beef Cattle ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Beef Cattle Breeds ◽  
Genome Wide Linkage Disequilibrium

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 Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0246497
Author(s):  
Vandana Manomohan ◽  
Ramasamy Saravanan ◽  
Rudolf Pichler ◽  
Nagarajan Murali ◽  
Karuppusamy Sivakumar ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
South India ◽  
Genetic Admixture ◽  
Zebu Cattle ◽  
Effective Population ◽  
Cattle Breeds ◽  
South Indian ◽  
Indian Cattle

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

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