publication . Article . 2021

A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

Wim Gorssen; Roel Meyermans; Steven Janssens; Nadine Buys;
Open Access
  • Published: 01 Dec 2021
  • Publisher: BioMed Central
Abstract
Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make ...
Persistent Identifiers
Subjects
free text keywords: Animal Science and Zoology, Genetics, Ecology, Evolution, Behavior and Systematics, General Medicine, [SDV]Life Sciences [q-bio], Research Article, Livestock, business.industry, business, SNP, Population, education.field_of_study, education, Evolutionary biology, Inbreeding, Genome-wide association study, Runs of Homozygosity, Biology, Single-nucleotide polymorphism, Genetic association, lcsh:Animal culture, lcsh:SF1-1100, lcsh:Genetics, lcsh:QH426-470
58 references, page 1 of 4

1. Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: Windows into population history and trait architecture. Nat Rev Genet. 2018;19:220-34.

2. Broman KW, Weber JL. Long homozygous chromosomal segments in reference families from the Centre d'Étude du Polymorphisme Humain. Am J Hum Genet. 1999;65:1493-500.

3. Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006;15:789-95.

4. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, et al. Runs of homozygosity in European populations. Am J Hum Genet. 2008;83:359-72.

5. Sölkner J, Ferenčaković M, Fürst C, Čurik I. Genomic metrics of individual autozygosity, applied to a cattle population. In Proceedings of the 61st Annual Meeting of the European Association for Animal Production: 23-27 August 2010; Heraklion. 2010. [OpenAIRE]

6. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, et al. A simple genetic architecture underlies morphological variation in dogs. PLoS Biol. 2010;8:e1000451.

7. Bosse M, Megens HJ, Madsen O, Paudel Y, Frantz LAF, Schook LB, et al. Regions of homozygosity in the porcine genome: Consequence of demography and the recombination landscape. PLoS Genet. 2012;8:e1003100.

8. Khanshour AM. Genetic diversity and population structure of the Arabian horse populations from Syria and other countries. PhD thesis, Texas A&M University. 2013.

9. Guangul SA. Design of community based breeding programs for two indigenous goat breeds of Ethiopia. PhD thesis, University of Natural Resources and Life Sciences Vienna. 2014.

10. Beynon SE, Slavov GT, Farré M, Sunduimijid B, Waddams K, Davies B, et al. Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genet. 2015;16:65. [OpenAIRE]

11. Bertolini F, Gandolfi B, Kim ES, Haase B, Lyons LA, Rothschild MF. Evidence of selection signatures that shape the Persian cat breed. Mamm Genome. 2016;27:144-55.

12. Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, et al. Genomic measures of inbreeding coeficients and genome-wide scan for runs of homozygosity islands in Iranian river bufalo Bubalus bubalis. BMC Genet. 2020;21:16. [OpenAIRE]

13. Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet. 2017;48:255-71.

14. Curik I, Ferenčaković M, Sölkner J. Inbreeding and runs of homozygosity: a possible solution to an old problem. Livest Sci. 2014;166:26-34. [OpenAIRE]

15. Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One. 2017;12:e0176780.

58 references, page 1 of 4
Abstract
Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make ...
Persistent Identifiers
Subjects
free text keywords: Animal Science and Zoology, Genetics, Ecology, Evolution, Behavior and Systematics, General Medicine, [SDV]Life Sciences [q-bio], Research Article, Livestock, business.industry, business, SNP, Population, education.field_of_study, education, Evolutionary biology, Inbreeding, Genome-wide association study, Runs of Homozygosity, Biology, Single-nucleotide polymorphism, Genetic association, lcsh:Animal culture, lcsh:SF1-1100, lcsh:Genetics, lcsh:QH426-470
58 references, page 1 of 4

1. Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: Windows into population history and trait architecture. Nat Rev Genet. 2018;19:220-34.

2. Broman KW, Weber JL. Long homozygous chromosomal segments in reference families from the Centre d'Étude du Polymorphisme Humain. Am J Hum Genet. 1999;65:1493-500.

3. Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006;15:789-95.

4. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, et al. Runs of homozygosity in European populations. Am J Hum Genet. 2008;83:359-72.

5. Sölkner J, Ferenčaković M, Fürst C, Čurik I. Genomic metrics of individual autozygosity, applied to a cattle population. In Proceedings of the 61st Annual Meeting of the European Association for Animal Production: 23-27 August 2010; Heraklion. 2010. [OpenAIRE]

6. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, et al. A simple genetic architecture underlies morphological variation in dogs. PLoS Biol. 2010;8:e1000451.

7. Bosse M, Megens HJ, Madsen O, Paudel Y, Frantz LAF, Schook LB, et al. Regions of homozygosity in the porcine genome: Consequence of demography and the recombination landscape. PLoS Genet. 2012;8:e1003100.

8. Khanshour AM. Genetic diversity and population structure of the Arabian horse populations from Syria and other countries. PhD thesis, Texas A&M University. 2013.

9. Guangul SA. Design of community based breeding programs for two indigenous goat breeds of Ethiopia. PhD thesis, University of Natural Resources and Life Sciences Vienna. 2014.

10. Beynon SE, Slavov GT, Farré M, Sunduimijid B, Waddams K, Davies B, et al. Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genet. 2015;16:65. [OpenAIRE]

11. Bertolini F, Gandolfi B, Kim ES, Haase B, Lyons LA, Rothschild MF. Evidence of selection signatures that shape the Persian cat breed. Mamm Genome. 2016;27:144-55.

12. Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, et al. Genomic measures of inbreeding coeficients and genome-wide scan for runs of homozygosity islands in Iranian river bufalo Bubalus bubalis. BMC Genet. 2020;21:16. [OpenAIRE]

13. Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet. 2017;48:255-71.

14. Curik I, Ferenčaković M, Sölkner J. Inbreeding and runs of homozygosity: a possible solution to an old problem. Livest Sci. 2014;166:26-34. [OpenAIRE]

15. Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One. 2017;12:e0176780.

58 references, page 1 of 4
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