The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Nosrati, Maryam; Nanaei, Hojjat Asadollahpour; Javanmard, Arash; Esmailizadeh, Ali

doi:10.1016/j.ygeno.2021.03.005

Cited by 29 publications

(30 citation statements)

References 49 publications

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“…Nosrati et al [ 48 ] detected on average 50.38 ROH in individuals from the same Soay population used in the present study, which corresponds to roughly one-quarter of the runs detected herein (188.4). This divergence in the results could be attributed to the differences in the detection parameters, such as higher values of minimal number of SNPs in an ROH (40) and maximal gap between adjacent SNPs (1 Mb), as well as lower SNP density (100 kb/SNP).…”

Section: Discussionsupporting

confidence: 73%

“…Many studies also reported the prevalence of ROH in the shortest length category for several sheep breeds [ 27 , 44 , 45 , 46 , 47 ]. It has been reported that modern populations of sheep usually present higher effective population sizes (Ne) and SNP diversity than cattle populations [ 11 , 27 , 32 , 48 ], which could be related to the prevalence of short over long ROH in sheep. Moreover, Ferenčaković et al [ 17 ] reported that the use of low-density SNP chips for the detection of ROH may lead to an overestimation of the number of ROH shorter than 4 Mb.…”

Section: Discussionmentioning

confidence: 99%

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Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Selli

Ventura

Fonseca

et al. 2021

Animals

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In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.

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Section: Discussionsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Selli

Ventura

Fonseca

et al. 2021

Animals

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show abstract

“…The percentage of SNP occurrences in ROHs was calculated to characterize the genomic regions of ROH hotspots. In previous studies ( 7 , 8 , 11 , 15 , 42 ), the threshold of ROH hotspots was usually set as the top 1% and 5% of the SNP occurrences. For a better comparison, similar to a previous study ( 30 ), we defined the ROH hotspots with a frequency of SNP occurrences exceeding 80% (top 1.96% in AD pigs and top 1.46% in CD pigs) as significant regions putatively under selection.…”

Section: Methodsmentioning

confidence: 99%

“…Selection may strongly affect the distribution of ROH, and regions of genomic loci under selection tend to generate a high frequency of ROH (hotspots) (5). An increasing number of studies have confirmed that ROH hotspots are due to positive selection for economically important traits in cattle (6,7), pigs (8)(9)(10), chickens (11,12), goats (13,14), and sheep (15,16). Therefore, the identification and characterization of ROH in a population can provide new insights for uncovering the demographic history and the genetic basis of germplasm characteristics.…”

Section: Introductionmentioning

confidence: 99%

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Wang

Ruan

et al. 2022

Front. Vet. Sci.

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Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

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“…It is worth noting that loss of genetic diversity within species and among populations is harmful not only in the context of conservation and current productivity but also for future utilization, as some genes lost at present might be vital in the future [ 18 ], under the dynamic global economic and social status and climate change as well. Perhaps it is also worth noting that species lose their genetic diversity through uncontrolled gene flow between and within populations leading to inbreeding, reduced effective population size, consequently causing inbreeding depression e.g., [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep (Ovis aries) Breeds

Wanjala

Bagi²,

Kusza³

2021

Biology

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To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.

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The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Cited by 29 publications

References 49 publications

Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep (Ovis aries) Breeds

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