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Lawson JM, Shilton CA, Lindsay-McGee V, Psifidi A, Wathes DC, Raudsepp T, de Mestre AM. Does inbreeding contribute to pregnancy loss in Thoroughbred horses? Equine Vet J 2024; 56:711-718. [PMID: 38221707 DOI: 10.1111/evj.14057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. OBJECTIVES To compare genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL) and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. STUDY DESIGN Observational case-control study. METHODS Allantochorion and fetal DNA from EPL (n = 37, gestation age 14-65 days), MLPL (n = 94, gestational age 70 days-24 h post parturition) and Controls (n = 58) were genotyped on the Axiom Equine 670K SNP Genotyping Array. Inbreeding coefficients using Runs of Homozygosity (FROH) were calculated using PLINK software. ROHs were split into size categories to investigate the recency of inbreeding. RESULTS MLPLs had significantly higher median number of ROH (188 interquartile range [IQR], 180.8-197.3), length of ROH (3.10, IQR 2.93-3.33), and total number of ROH (590.8, IQR 537.3-632.3), and FROH (0.26, IQR 0.24-0.28) when compared with the Controls and the EPLs (p < 0.05). There was no significant difference in any of the inbreeding indices between the EPLs and Controls. The MLPLs had a significantly higher proportion of long (>10 Mb) ROH (2.5%, IQR 1.6-3.6) than the Controls (1.7%, IQR 0.6-2.5), p = 0.001. No unique ROHs were found in the EPL or MLPL populations. MAIN LIMITATIONS SNP-array data does not allow analysis of every base in the sequence. CONCLUSIONS This first study of the effect of genomic inbreeding levels on pregnancy loss showed that inbreeding is a contributor to MLPL, but not EPL in the UK Thoroughbred population. Mating choices remain critical, because inbreeding may predispose to MLPL by increasing the risk of homozygosity for specific lethal allele(s).
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Affiliation(s)
- Jessica M Lawson
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, UK
| | - Charlotte A Shilton
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK
| | - Victoria Lindsay-McGee
- Department of Clinical Science and Services, The Royal Veterinary College, University of London, London, UK
| | - Androniki Psifidi
- Department of Clinical Science and Services, The Royal Veterinary College, University of London, London, UK
| | - D Claire Wathes
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, University of London, Hatfield, UK
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| | - Amanda M de Mestre
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, London, UK
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Carrara ER, Lopes PS, Veroneze R, Pereira RJ, Zadra LEF, Peixoto MGCD. Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle. J Anim Breed Genet 2024; 141:207-219. [PMID: 38010317 DOI: 10.1111/jbg.12836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.
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Affiliation(s)
- E R Carrara
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - P S Lopes
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - R Veroneze
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - R J Pereira
- Mato Grosso Animal Breeding Group, Institute of Agrarian and Technological Sciences, Federal University of Rondonópolis, Rondonópolis, Mato Grosso, Brazil
| | - L E F Zadra
- Brazilian Center for the Genetic Improvement of Guzerá, Belo Horizonte, Minas Gerais, Brazil
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Ristanic M, Zorc M, Glavinic U, Stevanovic J, Blagojevic J, Maletic M, Stanimirovic Z. Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle. Animals (Basel) 2024; 14:669. [PMID: 38473054 DOI: 10.3390/ani14050669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.
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Affiliation(s)
- Marko Ristanic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Minja Zorc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1000 Ljubljana, Slovenia
| | - Uros Glavinic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Jevrosima Stevanovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Jovan Blagojevic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Milan Maletic
- Department of Reproduction, Fertility and Artificial Insemination, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Zoran Stanimirovic
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. Oslobodjenja 18, 11000 Belgrade, Serbia
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Saif-Ur-Rehman M, Hassan FU, Reecy J, Deng T. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan. Anim Biotechnol 2023; 34:1384-1396. [PMID: 35044288 DOI: 10.1080/10495398.2022.2026369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.
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Affiliation(s)
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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Baldrighi GN, Nova A, Bernardinelli L, Fazia T. A Pipeline for Phasing and Genotype Imputation on Mixed Human Data (Parents-Offspring Trios and Unrelated Subjects) by Reviewing Current Methods and Software. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122030. [PMID: 36556394 PMCID: PMC9781110 DOI: 10.3390/life12122030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022]
Abstract
Genotype imputation has become an essential prerequisite when performing association analysis. It is a computational technique that allows us to infer genetic markers that have not been directly genotyped, thereby increasing statistical power in subsequent association studies, which consequently has a crucial impact on the identification of causal variants. Many features need to be considered when choosing the proper algorithm for imputation, including the target sample on which it is performed, i.e., related individuals, unrelated individuals, or both. Problems could arise when dealing with a target sample made up of mixed data, composed of both related and unrelated individuals, especially since the scientific literature on this topic is not sufficiently clear. To shed light on this issue, we examined existing algorithms and software for performing phasing and imputation on mixed human data from SNP arrays, specifically when related subjects belong to trios. By discussing the advantages and limitations of the current algorithms, we identified LD-based methods as being the most suitable for reconstruction of haplotypes in this specific context, and we proposed a feasible pipeline that can be used for imputing genotypes in both phased and unphased human data.
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Jaafar MA, Heins BJ, Dechow C, Huson HJ. The impact of using different ancestral reference populations in assessing crossbred population admixture and influence on performance. Front Genet 2022; 13:910998. [PMID: 36226168 PMCID: PMC9549382 DOI: 10.3389/fgene.2022.910998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Crossbreeding is a process in which animals from different breeds are mated together. The animals produced will exhibit a combination of both additive and non-additive genetic improvement from parental breeds that increase heterozygosity and negate inbreeding depression. However, crossbreeding may also break up the unique and often beneficial gene combinations in parental breeds, possibly reducing performance potential as the benefits of heterosis depends on the type of crossbreeding systems used and heritability of the traits. This effect of crossbreeding, especially on the genome architecture, is still poorly understood with respect to 3-breed crossbreeding systems. Thus, this study examined variation in genomic ancestry estimations relative to pedigree-based estimations and correlated breed composition to key production and health traits. Two rotational crossbred populations, referenced as ProCROSS and Grazecross were assessed and totaled 607 crossbred cattle. ProCROSS is a product of rotational crossbreeding of Viking Red (VKR), Holstein (HOL), and Montbeliarde (MON). In contrast, Grazecross consists of Viking Red (VKR), Normande (NOR), and Jersey (JER). Both breeding programs were aimed at capitalizing on the positive effect of heterosis. The VKR is a marketing term for Swedish Red, Danish Red, and Finnish Ayrshire breed which complicated breed determination. Therefore, genomic breed composition estimates were compared using two different representations of VKR, one of which was based on parents used in the crossing system and a second based on genotypes from the ancestral breeds that comprise VKR. Variation of breed composition estimates were assessed between pedigree and genome-based predictions. Lastly, Genomic estimations were correlated with production and health traits by comparing extreme performance groups to identify the relationship between breed ancestry and performance. With the exception of the JER breed composition in Grazecross, all other estimates of the purebred contribution to the ProCROSS and Grazecross showed a significant difference in their genomic breed estimation when using the VKR ancestral versus the VKR parental reference populations for admixture analysis. These observations were expected given the different relationship of each VKR representation to the crossbred cattle. Further analysis showed that regardless of which VKR reference population was used, the degree of MON and HOL breed composition plays a significant role in milk and fat production in ProCROSS, while the degree of VKR and NOR ancestry were related to improved health performance in Grazecross. In all, identifying the most appropriate and informative animals to use as reference animals in admixture analysis is an important factor when interpreting results of relationship and population structure, but some degree of uncertainty exists when assessing the relationship of breed composition to phenotypic performance.
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Affiliation(s)
- Mohd A. Jaafar
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Bradley J. Heins
- West Central Research and Outreach Centre, University of Minnesota, Morris, MN, United States
| | - Chad Dechow
- Department of Animal Science, Penn State University, State College, University Park, PA, United States
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Heather J. Huson,
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Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12182365. [PMID: 36139225 PMCID: PMC9495118 DOI: 10.3390/ani12182365] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the genetic composition of indigenous goats is essential to promote the scientific conservation and sustainable utilization of these breeds. The Jianchang Black (JC) goat, a Chinese native breed, is solid black and exhibits crude feed tolerance, but is characterized by a low growth rate and small body size. Based on the whole-genome sequencing data for 30 JC, 41 Jintang Black (JT), and 40 Yunshang Black (YS) goats, and 21 Bezoar ibexes, here, we investigated the genetic composition of JC goats by conducting analyses of the population structure, runs of homozygosity (ROH), genomic inbreeding, and selection signature. Our results revealed that JT and YS showed a close genetic relationship with a non-negligible amount of gene flows but were genetically distant from JC, apart from Bezoars. An average of 2039 ROHs were present in the autosomal genome per individual. The ROH-based inbreeding estimates in JC goats generally showed moderate values ranging from 0.134 to 0.264, mainly due to rapid declines in the effective population size during recent generations. The annotated genes (e.g., IL2, IL7, and KIT) overlapping with ROH islands were significantly enriched in immune-related biological processes. Further, we found 61 genes (e.g., STIM1, MYO9A, and KHDRBS2) under positive selection in JC goats via three complementary approaches, which may underly genetic adaptations to local environmental conditions. Our findings provided references for the conservation and sustainable utilization of JC goats.
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Wolf M, de Jong M, Daníel Halldórsson S, Árnason Ú, Janke A. Genomic impact of whaling in North Atlantic fin whales. Mol Biol Evol 2022; 39:6580755. [PMID: 35512360 PMCID: PMC9113106 DOI: 10.1093/molbev/msac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained largely unaddressed because of the paucity of adequate samples and the limitation of applicable techniques. Here, we have examined the effect of whaling on the North Atlantic fin whale based on genomes of 51 individuals from Icelandic waters, representing three temporally separated intervals, 1989, 2009 and 2018 and provide a reference genome for the species. Demographic models suggest a noticeable drop of the effective population size of the North Atlantic fin whale around a century ago. The present results suggest that the genome-wide heterozygosity is not markedly reduced and has remained comparable with other baleen whale species. Similarly, there are no signs of apparent inbreeding, as measured by the proportion of long runs of homozygosity, or of a distinctively increased mutational load, as measured by the amount of putative deleterious mutations. Compared with other baleen whales, the North Atlantic fin whale appears to be less affected by anthropogenic influences than other whales such as the North Atlantic right whale, consistent with the presence of long runs of homozygosity and higher levels of mutational load in an otherwise more heterozygous genome. Thus, genome-wide assessments of other species and populations are essential for future, more specific, conservation efforts.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany
| | - Menno de Jong
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany
| | | | - Úlfur Árnason
- Department of Clinical Sciences Lund, Lund University, Sweden, Department of Neurosurgery, Skane University Hospital in Lund, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany.,LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, Germany
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Mulim HA, Brito LF, Pinto LFB, Ferraz JBS, Grigoletto L, Silva MR, Pedrosa VB. Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals. BMC Genomics 2022; 23:209. [PMID: 35291953 PMCID: PMC8925140 DOI: 10.1186/s12864-022-08384-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/10/2022] [Indexed: 01/12/2023] Open
Abstract
Background A decline in the level of genetic diversity in livestock can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, various metrics have been proposed to assess the level of genetic diversity in selected populations. Therefore, the main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four ROH islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system, indicating potential balancing selection. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data. Conclusions The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08384-0.
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Affiliation(s)
| | - Luiz F Brito
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA
| | | | - José Bento Sterman Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Lais Grigoletto
- Department of Animal Science, Purdue University, West Lafayette, Indiana, USA.,Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Victor Breno Pedrosa
- Department of Animal Science, Federal University of Bahia, Salvador, Bahia, Brazil. .,Department of Animal Science, State University of Ponta Grossa, Av. General Carlos Cavalcanti, 4748 - Uvaranas, Ponta Grossa, PR, 84030-900, Brazil.
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Schiavo G, Bovo S, Ribani A, Moscatelli G, Bonacini M, Prandi M, Mancin E, Mantovani R, Dall'Olio S, Fontanesi L. Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region. J Dairy Sci 2021; 105:2408-2425. [PMID: 34955250 DOI: 10.3168/jds.2021-20915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Reggiana and Modenese are autochthonous cattle breeds, reared in the North of Italy, that can be mainly distinguished for their standard coat color (Reggiana is red, whereas Modenese is white with some pale gray shades). Almost all milk produced by these breeds is transformed into 2 mono-breed branded Parmigiano-Reggiano cheeses, from which farmers receive the economic incomes needed for the sustainable conservation of these animal genetic resources. After the setting up of their herd books in 1960s, these breeds experienced a strong reduction in the population size that was subsequently reverted starting in the 1990s (Reggiana) or more recently (Modenese) reaching at present a total of about 2,800 and 500 registered cows, respectively. Due to the small population size of these breeds, inbreeding is a very important cause of concern for their conservation programs. Inbreeding is traditionally estimated using pedigree data, which are summarized in an inbreeding coefficient calculated at the individual level (FPED). However, incompleteness of pedigree information and registration errors can affect the effectiveness of conservation strategies. High-throughput SNP genotyping platforms allow investigation of inbreeding using genome information that can overcome the limits of pedigree data. Several approaches have been proposed to estimate genomic inbreeding, with the use of runs of homozygosity (ROH) considered to be the more appropriate. In this study, several pedigree and genomic inbreeding parameters, calculated using the whole herd book populations or considering genotyping information (GeneSeek GGP Bovine 150K) from 1,684 Reggiana cattle and 323 Modenese cattle, were compared. Average inbreeding values per year were used to calculate effective population size. Reggiana breed had generally lower genomic inbreeding values than Modenese breed. The low correlation between pedigree-based and genomic-based parameters (ranging from 0.187 to 0.195 and 0.319 to 0.323 in the Reggiana and Modenese breeds, respectively) reflected the common problems of local populations in which pedigree records are not complete. The high proportion of short ROH over the total number of ROH indicates no major recent inbreeding events in both breeds. ROH islands spread over the genome of the 2 breeds (15 in Reggiana and 14 in Modenese) identified several signatures of selection. Some of these included genes affecting milk production traits, stature, body conformation traits (with a main ROH island in both breeds on BTA6 containing the ABCG2, NCAPG, and LCORL genes) and coat color (on BTA13 in Modenese containing the ASIP gene). In conclusion, this work provides an extensive comparative analysis of pedigree and genomic inbreeding parameters and relevant genomic information that will be useful in the conservation strategies of these 2 iconic local cattle breeds.
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Affiliation(s)
- Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Giulia Moscatelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Massimo Bonacini
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Marco Prandi
- Associazione Nazionale Allevatori Bovini di Razza Reggiana (ANABORARE), Via Masaccio 11, 42124 Reggio Emilia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy.
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12
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Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations. Animals (Basel) 2021; 11:ani11113234. [PMID: 34827966 PMCID: PMC8614534 DOI: 10.3390/ani11113234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary This study aimed to evaluate the consistency of different methodologies and sources of information used to estimate inbreeding coefficients in small populations by analyzing the correlation between them in the Holstein population of Mexico and to choose the best option in order to aid breeding programs to improve the productive traits of Holstein cattle in small-specialized populations. Abstract This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.
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13
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Hajihosseinlo A, Nejati-Javaremi A, Miraei-Ashtiani SR. Genetic structure analysis in several populations of cattle using SNP genotypes. Anim Biotechnol 2021; 34:288-300. [PMID: 34591729 DOI: 10.1080/10495398.2021.1960360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Parameters such as effective population size (Ne), runs of homozygosity (ROH), and inbreeding based on ROH (FROH) can give new insight into the level of genetic diversity for the population under selection. This research aimed to measure the extent of linkage disequilibrium (LD), effective population size (Ne), Haplotype Block Structure, and runs of homozygosity (ROHs) in several populations of cattle using SNP genotypes. In this study, that the average r2 decreased with the increasing distance of SNP pairs. A general decrease in Ne can be seen for all four populations, indicating a loss of genetic diversity. The Iranian Holstein had the lowest level of genomic inbreeding at an ROH of 1, 5, 10 Mb, while the French Holstein had the highest. The maximum number of ROH is seen at a distance of less than 1 Mb, and the lowest number of ROH is seen at a distance of 10 Mb. The number of ROH decreases with increasing distance due to the increased recombination rate. This is a concern as an increase in inbreeding leads to a reduction in the effective population size, which was also evident in the study populations.
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Affiliation(s)
- Abbas Hajihosseinlo
- Department of Animal Science, University of Tehran Aras International Campus, Jolfa, Iran
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14
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Polak G, Gurgul A, Jasielczuk I, Szmatoła T, Krupiński J, Bugno-Poniewierska M. Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs. Genes (Basel) 2021; 12:genes12030429. [PMID: 33802830 PMCID: PMC8002693 DOI: 10.3390/genes12030429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/21/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (FPED) and genomic inbreeding estimates was found for FROH (runs of homozygosity-based F coefficient) and FUNI (F coefficient based on the correlation between uniting gametes). FROH correlation with FPED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.
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Affiliation(s)
- Grażyna Polak
- Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
- Office of the Director for Scientific Affairs, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
- Correspondence:
| | - Artur Gurgul
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland; (A.G.); (I.J.); (T.S.)
| | - Igor Jasielczuk
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland; (A.G.); (I.J.); (T.S.)
| | - Tomasz Szmatoła
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland; (A.G.); (I.J.); (T.S.)
| | - Jędrzej Krupiński
- Department of Horse Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059 Kraków, Poland;
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15
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Nosrati M, Asadollahpour Nanaei H, Javanmard A, Esmailizadeh A. The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations. Genomics 2021; 113:1407-1415. [PMID: 33705888 DOI: 10.1016/j.ygeno.2021.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, PO BOX 19395-3697, Tehran, Iran.
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Arash Javanmard
- Departement of Animal Sceince, Faculty of Agriculture, University of Tabriz, PB 5166616471,Tabriz, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
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16
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Bizarria Dos Santos W, Pimenta Schettini G, Fonseca MG, Pereira GL, Loyola Chardulo LA, Rodrigues Machado Neto O, Baldassini WA, Nunes de Oliveira H, Abdallah Curi R. Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed. J Anim Breed Genet 2021; 138:161-173. [PMID: 32949478 DOI: 10.1111/jbg.12508] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022]
Abstract
With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array-670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH ) = 0.16; pedigree-based (FPED ) = 0.008; and a method based on excess homozygosity (FHOM ) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0-2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0-2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg2+ /Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.
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Affiliation(s)
| | - Gustavo Pimenta Schettini
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal, Brazil
| | | | - Guilherme Luis Pereira
- School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil
| | - Luis Artur Loyola Chardulo
- School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil
| | | | - Welder Angelo Baldassini
- School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil
| | - Henrique Nunes de Oliveira
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Rogério Abdallah Curi
- School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil
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17
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Sumreddee P, Toghiani S, Hay EH, Roberts A, Aggrey SE, Rekaya R. Runs of homozygosity and analysis of inbreeding depression. J Anim Sci 2021; 98:5979489. [PMID: 33180906 DOI: 10.1093/jas/skaa361] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/07/2020] [Indexed: 01/24/2023] Open
Abstract
Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.
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Affiliation(s)
| | - Sajjad Toghiani
- Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD
| | - El Hamidi Hay
- Fort Keogh Livestock and Range Research Laboratory, USDA Agricultural Research Service, Miles City, MT
| | - Andrew Roberts
- Fort Keogh Livestock and Range Research Laboratory, USDA Agricultural Research Service, Miles City, MT
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA.,Department of Statistics, University of Georgia, Athens, GA
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18
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Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data. Animals (Basel) 2020; 10:E2285. [PMID: 33287320 PMCID: PMC7761732 DOI: 10.3390/ani10122285] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals' pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.
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Affiliation(s)
- Filippo Biscarini
- CNR-IBBA (National Research Council, Institute of Agricultural Biology and Biotechnology), 20133 Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Gennaro Catillo
- CREA Research Centre for Animal Production and Acquaculture, CREA, 00015 Monterotondo, Italy;
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy;
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie—Università di Pisa, 56124 Pisa, Italy;
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19
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Estimates of Autozygosity Through Runs of Homozygosity in Farmed Coho Salmon. Genes (Basel) 2020; 11:genes11050490. [PMID: 32365758 PMCID: PMC7290985 DOI: 10.3390/genes11050490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 11/17/2022] Open
Abstract
The characterization of runs of homozygosity (ROH), using high-density single nucleotide polymorphisms (SNPs) allows inferences to be made about the past demographic history of animal populations and the genomic ROH has become a common approach to characterize the inbreeding. We aimed to analyze and characterize ROH patterns and compare different genomic and pedigree-based methods to estimate the inbreeding coefficient in two pure lines (POP A and B) and one recently admixed line (POP C) of coho salmon (Oncorhynchus kisutch) breeding nuclei, genotyped using a 200 K Affymetrix Axiom® myDesign Custom SNP Array. A large number and greater mean length of ROH were found for the two “pure” lines and the recently admixed line (POP C) showed the lowest number and smaller mean length of ROH. The ROH analysis for different length classes suggests that all three coho salmon lines the genome is largely composed of a high number of short segments (<4 Mb), and for POP C no segment >16 Mb was found. A high variable number of ROH, mean length and inbreeding values across chromosomes; positively the consequence of artificial selection. Pedigree-based inbreeding values tended to underestimate genomic-based inbreeding levels, which in turn varied depending on the method used for estimation. The high positive correlations between different genomic-based inbreeding coefficients suggest that they are consistent and may be more accurate than pedigree-based methods, given that they capture information from past and more recent demographic events, even when there are no pedigree records available.
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20
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Szmatoła T, Gurgul A, Jasielczuk I, Fu W, Ropka-Molik K. A detailed characteristics of bias associated with long runs of homozygosity identification based on medium density SNP microarrays. J Genomics 2020; 8:43-48. [PMID: 32328205 PMCID: PMC7171384 DOI: 10.7150/jgen.39147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/18/2020] [Indexed: 01/18/2023] Open
Abstract
In the present study, runs of homozygosity (ROH) detected with the use of a standard bovine 54k single nucleotide polymorphism (SNP) genotyping assay and two different ROH detection approaches, based on 50 (M1) or 15 (M2) consecutive SNPs, were compared with results of whole genome sequencing. Both microarray-based methods accurately recognised medium-sized ROH, however, it was found that M2 method seemed to better than M1 identify short ROH, but highly overestimated their number, leading to numerous false positive calls. Moreover, long ROH identified with microarray data tended to break into shorter segments in sequencing data because of the presence of regions with high heterozygosity within the ROH sequences. This may indicate, that these long ROH are formed by closely positioned shorter homozygous segments that may be of older origin or may be created by two similar but not identical haplotypes, showing minor internal recombination signs. Such finding also suggests that at least some of the results of previous studies in regard to long ROH may be biased leading to inaccurate estimations of genomes autozygosity via ROH classification into length categories.
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Affiliation(s)
- Tomasz Szmatoła
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland.,National Research Institute of Animal Production, Department of Animal Molecular Biology, Krakowska 1, 32-083 Balice, Poland
| | - Artur Gurgul
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland.,National Research Institute of Animal Production, Department of Animal Molecular Biology, Krakowska 1, 32-083 Balice, Poland
| | - Igor Jasielczuk
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland.,National Research Institute of Animal Production, Department of Animal Molecular Biology, Krakowska 1, 32-083 Balice, Poland
| | - Weiwei Fu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Katarzyna Ropka-Molik
- National Research Institute of Animal Production, Department of Animal Molecular Biology, Krakowska 1, 32-083 Balice, Poland
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21
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Ghoreishifar SM, Moradi-Shahrbabak H, Fallahi MH, Jalil Sarghale A, Moradi-Shahrbabak M, Abdollahi-Arpanahi R, Khansefid M. Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis. BMC Genet 2020; 21:16. [PMID: 32041535 PMCID: PMC7011551 DOI: 10.1186/s12863-020-0824-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/04/2020] [Indexed: 01/06/2023] Open
Abstract
Background Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.
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Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.
| | - Mohammad Hossein Fallahi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Ali Jalil Sarghale
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Mohammad Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Rostam Abdollahi-Arpanahi
- Departments of Animal and Poultry Science, College of Aburaihan, University of Tehran, Pakdasht, 33916-53755, Iran
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
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22
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Toro Ospina AM, Silva Faria RA, Vercesi Filho AE, Cyrillo JNDSG, Zerlotti Mercadante ME, Curi RA, Vasconcelos Silva JA. Genome‐wide identification of runs of homozygosity islands in the Gyr breed (
Bos indicus
). Reprod Domest Anim 2020; 55:333-342. [DOI: 10.1111/rda.13639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/29/2019] [Indexed: 01/19/2023]
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Inbreeding in a Population of Polish Holstein-Friesian Young Bulls Before and After Genomic Selection. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2019-0065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Inbreeding was analysed in a population of 14,144 Polish Black-and-White Holstein-Friesian (PBWHF) young bulls born between 1994 and 2017 and bred under both conventional and genomic breeding programmes. The inbreeding coefficients were computed using a model with genetic groups, according to the algorithm given by VanRaden. It was found that in the analysed population all bulls are inbred (100% of the population), with the mean coefficient of inbreeding ranging from 0.09% to 26.95%. Pedigree analysis also showed a relationship between the changing number of bulls over the years and the dynamics of population inbreeding. These trends are connected with changes in the breeding scheme, related to the implementation of genomic selection in the breeding programme for PBWHF cattle in 2014. The increasing number of weaned young bulls in Poland was paralleled by a fairly consistent increase in the mean inbreeding, but the inbreeding dynamics were relatively small. A reverse trend was observed in the group of young bulls born after 2013. As the number of bulls very rapidly decreased in successive birth years, the mean inbreeding for successive birth-year groups very rapidly increased. As a result, the estimated linear trend was equal to 0.02% inbreeding per year of birth in the group of bulls raised before genomic selection (~20 birth-year) whereas in the group of bulls raised after genomic selection (~4 birth-year) the trend was much higher and amounted to 0.56% inbreeding per year of birth. The high mean inbreeding found in the group of the genomically selected young bulls may translate into higher inbreeding in the whole population of PBWHF cattle, because these bulls are now intensively used as sires. The results of our study also show that the implementation of genomic selection in the breeding programme caused a very rapid increase in the inbreeding rate per birth-year in young bulls.
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Szmatoła T, Gurgul A, Jasielczuk I, Ząbek T, Ropka-Molik K, Litwińczuk Z, Bugno-Poniewierska M. A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types. Animals (Basel) 2019; 9:ani9121024. [PMID: 31775271 PMCID: PMC6941163 DOI: 10.3390/ani9121024] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Runs of homozygosity (ROH) regions are known to be common in the genomes of cattle and have become a subject of interest of various research in recent years. ROH can be used as a valuable tool to estimate inbreeding, which needs to be controlled in livestock populations. Moreover, analysis of ROH is considered to be an effective method of identifying genome regions that are a subject of selection pressure, which may help in understanding the genetic aspects of production traits under selection. In this study, we analyzed ROH characteristics of 11 cattle breeds, both commercial and native, maintained in Poland. We presented distinct differences in the length, quantity and frequency of ROH between the analyzed breeds as well as in the levels of genomic inbreeding. Higher levels of inbreeding were characteristic for commercial breeds, especially beef breeds. In addition, within ROH islands, we observed a number of genes with a confirmed influence on the level of production traits. The presented results and identified genes can be a basis for further research focused on the identification of genes and markers essential in the determination of the most important production traits in cattle. Abstract In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (FROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the FROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds.
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Affiliation(s)
- Tomasz Szmatoła
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland; (A.G.); (I.J.)
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (T.Z.); (K.R.-M.)
- Correspondence: ; Tel.: +48-602-603-158
| | - Artur Gurgul
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland; (A.G.); (I.J.)
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (T.Z.); (K.R.-M.)
| | - Igor Jasielczuk
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland; (A.G.); (I.J.)
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (T.Z.); (K.R.-M.)
| | - Tomasz Ząbek
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (T.Z.); (K.R.-M.)
| | - Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (T.Z.); (K.R.-M.)
| | - Zygmunt Litwińczuk
- Sub-Department of Cattle Breeding and Genetic Resources Conservation, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland;
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059 Kraków, Poland;
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Szpiech ZA, Mak ACY, White MJ, Hu D, Eng C, Burchard EG, Hernandez RD. Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity. Am J Hum Genet 2019; 105:747-762. [PMID: 31543216 PMCID: PMC6817522 DOI: 10.1016/j.ajhg.2019.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations.
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Affiliation(s)
- Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Department of Biological Sciences, Auburn University, Auburn, AL 36842, USA.
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marquitta J White
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada; Genome Quebec Innovation Center, McGill University, Montreal, QC H3A 0G1, Canada.
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Gomez-Raya L, Rauw WM, Dunkelberger JR, Dekkers JCM. Autozygosity and Genetic Differentiation of Landrace and Large White Pigs as Revealed by the Genetic Analyses of Crossbreds. Front Genet 2019; 10:739. [PMID: 31543894 PMCID: PMC6739446 DOI: 10.3389/fgene.2019.00739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/15/2019] [Indexed: 11/17/2022] Open
Abstract
Genomic information from crossbreds is routinely generated for genomic evaluations. The objective of this study is to investigate autozygosity and genetic differentiation in Landrace by Large-White breeds by using the genotypic information of SNP arrays in 1,173 crossbreds. A maximum likelihood approach was developed to estimate the probability of autozygosity (FL). Regions of differentiation between breeds were investigated using FST and the difference in allele frequencies between the two parental breeds (릌Δ) at each single-nucleotide polymorphism (SNP) position. A maximum likelihood approach was proposed to estimate allele frequencies in the parental populations. The average length of runs of homozygosity (ROH) across the genome was 3.91, 2.3, and 0.7 Mb for segments with at least 25, 15, and 5 SNPs, respectively. Average age to coalesce was 46, 414, and 388 years for segments with at least 25, 15, and 5 SNPs, respectively. The probability of autozygosity was not uniform along the crossbred genome, being higher at the center for most chromosomes. The correlation between autozygosity and distance to the closest telomere was positive and significant in most chromosomes, which could be attributed to the higher recombination rate near telomeres. We also report a relatively high negative correlation between probability of recombination (from a published map) and probability of autozygosity. It supports that structural characteristics of the chromosomes related to recombination rate determine autozygosity at each chromosomal position of the pig genome. The average is Δ across the genome was 0.17 (SD = 0.16). After testing for differences in allele frequencies between the parental breeds, there were 4,184 SNPs with a likelihood ratio test, LRT ≥ 32.02. The average FST across the genome was 0.038 (SD = 0.059). There were 2,949 SNPs with FST > 0.125. The correlation between estimates of FL and estimates of FST across the genome was -0.10 (SE = 0.006). Analysis of the gene content of the genomic regions with the 2000 SNPs with highest LRT for FL and high FST showed overrepresentation of genes with a regulatory function. Genes with biological functions associated with production, such as tissue development, anatomical structure, and animal organ development, were also overrepresented in regions with a high FST.
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Affiliation(s)
- Luis Gomez-Raya
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Wendy Mercedes Rauw
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | | | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Peripolli E, Stafuzza NB, Amorim ST, Lemos MVA, Grigoletto L, Kluska S, Ferraz JBS, Eler JP, Mattos EC, Baldi F. Genome‐wide scan for runs of homozygosity in the composite Montana Tropical
®
beef cattle. J Anim Breed Genet 2019; 137:155-165. [DOI: 10.1111/jbg.12428] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | | | - Sabrina Thaise Amorim
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Marcos Vinícius Antunes Lemos
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Laís Grigoletto
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Sabrina Kluska
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Joanir Pereira Eler
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Elisângela Chicaroni Mattos
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
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Kamiński S, Hering DM, Jaworski Z, Zabolewicz T, Ruść A. Assessment of genomic inbreeding in Polish Konik horses. Pol J Vet Sci 2019; 20:603-605. [PMID: 29166287 DOI: 10.1515/pjvs-2017-0074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to assess the inbreeding coefficient of Polish Konik horses based on runs of homozygosity (ROH). Ninety six horses kept in 6 herds located across Poland were genotyped with the use of EquineSNP60 BeadChip (Illumina). SNP markers with a Minor Allele Frequency lower than 0.01 and SNPs assigned to chromosome X or Y were excluded from the study. A total of 50 708 SNPs were included for statistical analysis (SVS software, Golden Helix). The analysis showed that the population is in genetic equilibrium, with He and Ho estimates both equal to 0.3086. Seven categories of Runs of Homozygozity (ROH) length were defined: >0.5, >1, >2, >4, >8, >16, >25 Mb. The genomic inbreeding coefficient derived from ROH (FROH) calculated for each ROH length ranged from 15.96% based on the shortest ROH (>0,5Mb) to 2.71% for the longest ROH (>25Mb). Among individual horses, the inbreeding coefficient ranged from 5.25% to 22.41% (for ROH >1Mb). Analysis of ROH in Polish Koniks allows for more effective management of their inbreeding in the future.
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Sumreddee P, Toghiani S, Hay EH, Roberts A, Agrrey SE, Rekaya R. Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information. J Anim Sci 2019; 97:1-18. [PMID: 30304409 DOI: 10.1093/jas/sky385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 11/14/2022] Open
Abstract
This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (FPED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix using estimated (FGRM) or fixed (FGRM0.5) minor allele frequencies or runs of homozygosity (ROH) (FROH). A pedigree containing 10,186 animals was used to calculate FPED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 SNP. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), ADG, and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The average inbreeding was 29.2%, 16.1%, 30.2%, and 22.9% for FPED, FGRM, FGRM0.5, and FROH, respectively. FROH provided the highest correlations with FPED (r = 0.66). Across paternal half-sib families, with minimal variation in FPED, there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that a 1% increase in an animal's FPED resulted in a decrease of 1.20 kg, 2.03 kg, and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 d for each 1% increase in FPED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (FROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half-sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected, which may be attributed to the purging of the deleterious alleles due to natural or artificial selection over time.
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Affiliation(s)
| | - Sajjad Toghiani
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT
| | - Andrew Roberts
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT
| | - Samuel E Agrrey
- Department of Poultry Science, The University of Georgia, Athens, GA.,Institute of Bioinformatics, The University of Georgia, Athens, GA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA.,Institute of Bioinformatics, The University of Georgia, Athens, GA.,Department of Statistics, The University of Georgia, Athens, GA
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Ben Jemaa S, Rahal O, Gaouar SBS, Mastrangelo S, Boussaha M, Ciani E. Genomic characterization of Algerian Guelmoise cattle and their genetic relationship with other North African populations inferred from SNP genotyping arrays. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Peripolli E, Metzger J, de Lemos MVA, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FLB, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CDU, Di Croce F, Osterstock J, Denise S, Pereira ASC, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018; 19:680. [PMID: 30223795 PMCID: PMC6142381 DOI: 10.1186/s12864-018-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Marcos Vinícius Antunes de Lemos
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Sabrina Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Bianca Ferreira Olivieri
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fabieli Louise Braga Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fernando Brito Lopes
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Raysildo Barbosa Lôbo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, 14020-230, Brazil
| | | | | | | | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
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32
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Stafuzza NB, Silva RMDO, Peripolli E, Bezerra LAF, Lôbo RB, Magnabosco CDU, Di Croce FA, Osterstock JB, Munari DP, Lourenco DAL, Baldi F. Genome-wide association study provides insights into genes related with horn development in Nelore beef cattle. PLoS One 2018; 13:e0202978. [PMID: 30161212 PMCID: PMC6116989 DOI: 10.1371/journal.pone.0202978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 08/13/2018] [Indexed: 11/28/2022] Open
Abstract
The causal mutation for polledness in Nelore (Bos taurus indicus) breed seems to have appeared first in Brazil in 1957. The expression of the polled trait is known to be ruled by a few groups of alleles in taurine breeds; however, the genetic basis of this trait in indicine cattle is still unclear. The aim of this study was to identify genomic regions associated with the hornless trait in a commercial Nelore population. A total of 107,294 animals had phenotypes recorded and 2,238 were genotyped/imputed for 777k SNP. The weighted single-step approach for genome-wide association study (WssGWAS) was used to estimate the SNP effects and variances accounted for by 1 Mb sliding SNP windows. A centromeric region of chromosome 1 with 3.11 Mb size (BTA1: 878,631–3,987,104 bp) was found to be associated with hornless in the studied population. A total of 28 protein-coding genes are mapped in this region, including the taurine Polled locus and the IFNAR1, IFNAR2, IFNGR2, KRTAP11-1, MIS18A, OLIG1, OLIG2, and SOD1 genes, which expression can be related to the horn formation as described in literature. The functional enrichment analysis by DAVID tool revealed cytokine-cytokine receptor interaction, JAK-STAT signaling, natural killer cell mediated cytotoxicity, and osteoclast differentiation pathways as significant (P < 0.05). In addition, a runs of homozygosity (ROH) analysis identified a ROH island in polled animals with 2.47 Mb inside the region identified by WssGWAS. Polledness in Nelore cattle is associated with one region in the genome with 3.1 Mb size in chromosome 1. Several genes are harbored in this region, and they may act together in the determination of the polled/horned phenotype. Fine mapping the locus responsible for polled trait in Nelore breed and the identification of the molecular mechanisms regulating the horn growth deserve further investigation.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Departamento de Ciencias Exatas, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
- National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Leetown, West Virginia, United States of America
| | - Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Luiz Antônio Framartino Bezerra
- Departamento de Genetica, Faculdade de Medicina de Ribeirao Preto (FMRP), Universidade de Sao Paulo (USP), Ribeirao Preto, Sao Paulo, Brazil
| | - Raysildo Barbosa Lôbo
- Associaçao Nacional dos Criadores e Pesquisadores (ANCP), Ribeirao Preto, Sao Paulo, Brazil
| | | | | | | | - Danísio Prado Munari
- Departamento de Ciencias Exatas, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Daniela A. Lino Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, Georgia, United States of America
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciencias Agrarias e Veterinarias (FCAV), Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Jaboticabal, Sao Paulo, Brazil
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Goszczynski D, Molina A, Terán E, Morales-Durand H, Ross P, Cheng H, Giovambattista G, Demyda-Peyrás S. Runs of homozygosity in a selected cattle population with extremely inbred bulls: Descriptive and functional analyses revealed highly variable patterns. PLoS One 2018; 13:e0200069. [PMID: 29985951 PMCID: PMC6037354 DOI: 10.1371/journal.pone.0200069] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
The analysis of runs of homozygosity (ROH), using high throughput genomic data, has become a valuable and frequently used methodology to characterize the genomic and inbreeding variation of livestock and wildlife animal populations. However, this methodology has been scarcely used in highly inbred domestic animals. Here, we analyzed and characterized the occurrence of ROH fragments in highly inbred (HI; average pedigree-based inbreeding coefficient FPED = 0.164; 0.103 to 0.306) and outbred Retinta bulls (LI; average FPED = 0.008; 0 to 0.025). We studied the length of the fragments, their abundance, and genome distribution using high-density microarray data. The number of ROH was significantly higher in the HI group, especially for long fragments (>8Mb). In the LI group, the number of ROH continuously decreased with fragment length. Genome-wide distribution of ROH was highly variable between samples. Some chromosomes presented a larger number of fragments (BTA1, BTA19, BTA29), others had longer fragments (BTA4, BTA12, BTA17), while other ones showed an increased ROH accumulation over specific loci (BTA2, BTA7, BTA23, BTA29). Similar differences were observed in the analysis of 12 individuals produced by a similar inbred event (FPED3 = 0.125). The correlation between the fraction of the genome covered by ROH (FROH) and FPED was high (0.79), suggesting that ROH-based estimations are indicative of inbreeding levels. On the other hand, the correlation between FPED and the microsatellite-based inbreeding coefficient (FMIC) was only moderate (r = 0.44), suggesting that STR-based inbreeding estimations should be avoided. Similarly, we found a very low correlation (r = -0.0132) between recombination rate and ROH abundance across the genome. Finally, we performed functional annotation analyses of genome regions with significantly enriched ROH abundance. Results revealed gene clusters related to pregnancy-associated proteins and immune reaction. The same analysis performed for regions enriched with recently formed ROH (> 8 Mb) showed gene clusters related to flagellum assembly. In both cases, the processes were related to male and female reproductive functions, which may partially explain the reduced fertility associated with inbred populations.
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Affiliation(s)
- Daniel Goszczynski
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
| | - Ester Terán
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Hernán Morales-Durand
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
| | - Guillermo Giovambattista
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Sebastián Demyda-Peyrás
- IGEVET–Instituto de Genética Veterinaria "Ing. Fernando N. Dulout” (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
- Departamento de Genética, Universidad de Córdoba, Córdoba, España
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail:
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Peripolli E, Stafuzza NB, Munari DP, Lima ALF, Irgang R, Machado MA, Panetto JCDC, Ventura RV, Baldi F, da Silva MVGB. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics 2018; 19:34. [PMID: 29316879 PMCID: PMC5759835 DOI: 10.1186/s12864-017-4365-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (FROH), genomic relationship matrix approach (FGRM) and based on the observed versus expected number of homozygous genotypes (FHOM), and from pedigree-based coefficient (FPED). Results ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH1–2 Mb) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of FROH, FGRM, FHOM, and FPED approaches. FPED estimates ranged from 0.00 to 0.327 and FROH from 0.001 to 0.201. Low to moderate correlations were observed between FPED-FROH and FGRM-FROH, with values ranging from −0.11 to 0.51. Low to high correlations were observed between FROH-FHOM and moderate between FPED-FHOM and FGRM-FHOM. Correlations between FROH from different lengths and FPED gradually increased with ROH length. Conclusions Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low FPED-FROH correlations for small segments indicate that FPED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. Electronic supplementary material The online version of this article (10.1186/s12864-017-4365-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
| | - André Luís Ferreira Lima
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Renato Irgang
- Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil
| | - Marco Antonio Machado
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.,Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil
| | | | - Ricardo Vieira Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, 13635-900, Brazil.,Beef Improvement Opportunities, Elora, ON, N0B 1S0, Canada.,University of Guelph, Centre for Genetic Improvement of Livestock, ABScBG, Guelph, N1G 2W1, Canada
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil
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Solé M, Gori AS, Faux P, Bertrand A, Farnir F, Gautier M, Druet T. Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle. Genet Sel Evol 2017; 49:92. [PMID: 29273000 PMCID: PMC5741860 DOI: 10.1186/s12711-017-0370-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/13/2017] [Indexed: 11/21/2022] Open
Abstract
Background
Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods.
Results When using 600 K single nucleotide polymorphisms (SNPs), the inbreeding coefficient (probability of sampling an HBD locus in an individual) was on average 0.303 (ranging from 0.258 to 0.375). HBD-classes associated to historical ancestors (with small segments ≤ 200 kb) accounted for 21.6% of the genome length (71.4% of the total length of the genome in HBD segments), whereas classes associated to more recent ancestors accounted for only 22.6% of the total length of the genome in HBD segments. However, these recent classes presented more individual variation than more ancient classes. Although inbreeding coefficients obtained with low SNP densities (7 and 32 K) were much lower (0.060 and 0.093), they were highly correlated with those obtained at higher density (r = 0.934 and 0.975, respectively), indicating that they captured most of the individual variation. At higher SNP density, smaller HBD segments are identified and, thus, more past generations can be explored. We observed very high correlations between our estimates and those based on homozygosity (r = 0.95) or on runs-of-homozygosity (r = 0.95). As expected, pedigree-based estimates were mainly correlated with recent HBD-classes (r = 0.56). Conclusions Although we observed high levels of autozygosity associated with small HBD segments in BBB cattle, recent inbreeding accounted for most of the individual variation. Recent autozygosity can be captured efficiently with low-density SNP arrays and relatively simple models (e.g., two HBD classes). The HMM framework provides local HBD probabilities that are still useful at lower SNP densities. Electronic supplementary material The online version of this article (10.1186/s12711-017-0370-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Solé
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, B34 (+1) Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Ann-Stephan Gori
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, B34 (+1) Avenue de l'Hôpital 1, 4000, Liège, Belgium.,Awé Coopérative (Association Wallonne de l'Élevage) - Recherche et Développement, Rue des Champs Elysées 4, 5590, Ciney, Belgium
| | - Pierre Faux
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, B34 (+1) Avenue de l'Hôpital 1, 4000, Liège, Belgium
| | - Amandine Bertrand
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, B34 (+1) Avenue de l'Hôpital 1, 4000, Liège, Belgium
| | - Frédéric Farnir
- BBASV, FARAH-PAD & Faculty of Veterinary Medicine, University of Liège, Quartier Vallée 2, Avenue de Cureghem, (B43 +3), 4000, Liège, Belgium
| | - Mathieu Gautier
- INRA, UMR CBGP (Centre de Biologie pour la Gestion des Populations), Campus International de Baillarguet, 34988, Montferrier sur Lez, France.,IBD (Institut de Biologie Computationnelle), 34095, Montpellier, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, B34 (+1) Avenue de l'Hôpital 1, 4000, Liège, Belgium
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Blant A, Kwong M, Szpiech ZA, Pemberton TJ. Weighted likelihood inference of genomic autozygosity patterns in dense genotype data. BMC Genomics 2017; 18:928. [PMID: 29191164 PMCID: PMC5709839 DOI: 10.1186/s12864-017-4312-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/16/2017] [Indexed: 12/14/2022] Open
Abstract
Background Genomic regions of autozygosity (ROA) arise when an individual is homozygous for haplotypes inherited identical-by-descent from ancestors shared by both parents. Over the past decade, they have gained importance for understanding evolutionary history and the genetic basis of complex diseases and traits. However, methods to infer ROA in dense genotype data have not evolved in step with advances in genome technology that now enable us to rapidly create large high-resolution genotype datasets, limiting our ability to investigate their constituent ROA patterns. Methods We report a weighted likelihood approach for inferring ROA in dense genotype data that accounts for autocorrelation among genotyped positions and the possibilities of unobserved mutation and recombination events, and variability in the confidence of individual genotype calls in whole genome sequence (WGS) data. Results Forward-time genetic simulations under two demographic scenarios that reflect situations where inbreeding and its effect on fitness are of interest suggest this approach is better powered than existing state-of-the-art methods to infer ROA at marker densities consistent with WGS and popular microarray genotyping platforms used in human and non-human studies. Moreover, we present evidence that suggests this approach is able to distinguish ROA arising via consanguinity from ROA arising via endogamy. Using subsets of The 1000 Genomes Project Phase 3 data we show that, relative to WGS, intermediate and long ROA are captured robustly with popular microarray platforms, while detection of short ROA is more variable and improves with marker density. Worldwide ROA patterns inferred from WGS data are found to accord well with those previously reported on the basis of microarray genotype data. Finally, we highlight the potential of this approach to detect genomic regions enriched for autozygosity signals in one group relative to another based upon comparisons of per-individual autozygosity likelihoods instead of inferred ROA frequencies. Conclusions This weighted likelihood ROA inference approach can assist population- and disease-geneticists working with a wide variety of data types and species to explore ROA patterns and to identify genomic regions with differential ROA signals among groups, thereby advancing our understanding of evolutionary history and the role of recessive variation in phenotypic variation and disease. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4312-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Blant
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Michelle Kwong
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
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Signer-Hasler H, Burren A, Neuditschko M, Frischknecht M, Garrick D, Stricker C, Gredler B, Bapst B, Flury C. Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genet Sel Evol 2017; 49:83. [PMID: 29115934 PMCID: PMC5674839 DOI: 10.1186/s12711-017-0358-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 10/26/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). RESULTS The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH: 0.027), OB (F ROH: 0.029), and SI (F ROH: 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH: 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. CONCLUSIONS The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service results in more sires having progeny at each generation and thus this breeding practice is likely the major reason for the remarkable levels of genetic diversity retained within these populations. The fact that the EV population is regionally restricted and its small census size of herd-book cows explain its high level of genomic inbreeding.
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Affiliation(s)
- Heidi Signer-Hasler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Alexander Burren
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Mirjam Frischknecht
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
- Qualitas AG, Zug, Switzerland
| | | | | | | | | | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
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Wiener P, Sánchez-Molano E, Clements DN, Woolliams JA, Haskell MJ, Blott SC. Genomic data illuminates demography, genetic structure and selection of a popular dog breed. BMC Genomics 2017; 18:609. [PMID: 28806925 PMCID: PMC5557481 DOI: 10.1186/s12864-017-3933-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/09/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. RESULTS We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. CONCLUSIONS This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Enrique Sánchez-Molano
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Dylan N. Clements
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - John A. Woolliams
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
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Szmatoła T, Gurgul A, Ropka-Molik K, Jasielczuk I, Ząbek T, Bugno-Poniewierska M. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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