E F Dzomba1, M Chimonyo2, R Pierneef3, F C Muchadeyi3. 1. Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa. Dzomba@ukzn.ac.za. 2. Discipline of Animal & Poultry Science; School of Agricultural, Earth & Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa. 3. Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110, South Africa.
Abstract
BACKGROUND: Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1-6 Mb, 6-12 Mb, 12-24 Mb, 24-48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. RESULTS: A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1-6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. CONCLUSIONS: Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.
BACKGROUND: Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1-6 Mb, 6-12 Mb, 12-24 Mb, 24-48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. RESULTS: A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1-6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. CONCLUSIONS: Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.
Entities:
Keywords:
Autozygosity; Production system; ROH island; Runs of Homozygosity; SNP genotypes; Sheep
Authors: Sunduimijid Bolormaa; Ben J Hayes; Julius H J van der Werf; David Pethick; Michael E Goddard; Hans D Daetwyler Journal: BMC Genomics Date: 2016-03-12 Impact factor: 3.969
Authors: Michael N Weedon; Hana Lango; Cecilia M Lindgren; Chris Wallace; David M Evans; Massimo Mangino; Rachel M Freathy; John R B Perry; Suzanne Stevens; Alistair S Hall; Nilesh J Samani; Beverly Shields; Inga Prokopenko; Martin Farrall; Anna Dominiczak; Toby Johnson; Sven Bergmann; Jacques S Beckmann; Peter Vollenweider; Dawn M Waterworth; Vincent Mooser; Colin N A Palmer; Andrew D Morris; Willem H Ouwehand; Jing Hua Zhao; Shengxu Li; Ruth J F Loos; Inês Barroso; Panagiotis Deloukas; Manjinder S Sandhu; Eleanor Wheeler; Nicole Soranzo; Michael Inouye; Nicholas J Wareham; Mark Caulfield; Patricia B Munroe; Andrew T Hattersley; Mark I McCarthy; Timothy M Frayling Journal: Nat Genet Date: 2008-04-06 Impact factor: 38.330
Authors: M R Upadhyay; W Chen; J A Lenstra; C R J Goderie; D E MacHugh; S D E Park; D A Magee; D Matassino; F Ciani; H-J Megens; J A M van Arendonk; M A M Groenen Journal: Heredity (Edinb) Date: 2016-09-28 Impact factor: 3.821
Authors: Lingyang Xu; Guoyao Zhao; Liu Yang; Bo Zhu; Yan Chen; Lupei Zhang; Xue Gao; Huijiang Gao; George E Liu; Junya Li Journal: Sci Rep Date: 2019-11-18 Impact factor: 4.379
Authors: Ivana Drzaic; Ino Curik; Boris Lukic; Mario Shihabi; Meng-Hua Li; Juha Kantanen; Salvatore Mastrangelo; Elena Ciani; Johannes A Lenstra; Vlatka Cubric-Curik Journal: Front Genet Date: 2022-07-15 Impact factor: 4.772