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Mota LFM, Carvajal AB, Silva Neto JB, Díaz C, Carabaño MJ, Baldi F, Munari DP. Assessment of inbreeding coefficients and inbreeding depression on complex traits from genomic and pedigree data in Nelore cattle. BMC Genomics 2024; 25:944. [PMID: 39379819 PMCID: PMC11460123 DOI: 10.1186/s12864-024-10842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - FROH 1-2; 2-4 Mb FROH 2-4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). RESULTS The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1-2, r = 0.20 with FROH 2-4 and r = 0.28 with FROH 4-8). Meanwhile, the FPed had a moderate correlation with FSNP (r = 0.47) and high correlation with FROH >8 (r = 0.58) and FROH-genome (r = 0.60). The FROH-genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH-genome (r = 0.55) and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2-4 to 0.37 for FROH 1-2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for FPed, 0.19-0.59 for FGRM, 0.21-0.58 for FROH-genome, and 0.19-0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49-1.97% for FGRM, 0.34-2.2% for FROH-genome, and 0.50-1.62% for FSNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. CONCLUSIONS The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.
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Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil.
| | - Alejandro B Carvajal
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil
| | - João B Silva Neto
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil
| | - Clara Díaz
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-C SIC), Madrid, 28040, Spain
| | - Maria J Carabaño
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-C SIC), Madrid, 28040, Spain
| | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil
- National Association of Breeders and Researchers, Rua João Godoy 463, Ribeirão Preto, 14020-230, SP, Brazil
| | - Danísio P Munari
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil
- National Council for Science and Technological Development (CNPq), Brasilia, 71605-001, DF, Brazil
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Mekonnen KT, Lee DH, Cho YG, Son AY, Seo KS. Genomic and Conventional Inbreeding Coefficient Estimation Using Different Estimator Models in Korean Duroc, Landrace, and Yorkshire Breeds Using 70K Porcine SNP BeadChip. Animals (Basel) 2024; 14:2621. [PMID: 39272406 PMCID: PMC11394220 DOI: 10.3390/ani14172621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
The purpose of this study was to estimate the homozygosity distribution and compute genomic and conventional inbreeding coefficients in three genetically diverse pig breed populations. The genomic and pedigree data of Duroc (1586), Landrace (2256), and Yorkshire (3646) were analyzed. We estimated and compared various genomic and pedigree inbreeding coefficients using different models and approaches. A total of 709,384 ROH segments in Duroc, 816,898 in Landrace, and 1,401,781 in Yorkshire, with average lengths of 53.59 Mb, 56.21 Mb, and 53.46 Mb, respectively, were identified. Relatively, the Yorkshire breed had the shortest ROH segments, whereas the Landrace breed had the longest mean ROH segments. Sus scrofa chromosome 1 (SSC1) had the highest chromosomal coverage by ROH across all breeds. Across breeds, an absolute correlation (1.0) was seen between FROH total and FROH1-2Mb, showing that short ROH were the primary contributors to overall FROH values. The overall association between genomic and conventional inbreeding was weak, with values ranging from 0.058 to 0.140. In contrast, total genomic inbreeding (FROH) and ROH classes showed a strong association, ranging from 0.663 to 1.00, across the genotypes. The results of genomic and conventional inbreeding estimates improve our understanding of the genetic diversity among genotypes.
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Affiliation(s)
- Kefala Taye Mekonnen
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea
- Department of Animal Science, College of Agriculture and Environmental Science, Arsi University, Asella P.O. Box 193, Ethiopia
| | - Dong-Hui Lee
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Young-Gyu Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Ah-Yeong Son
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Kang-Seok Seo
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Republic of Korea
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Marcuzzi O, Calcaterra F, Loza Vega A, Ortega Masagué MF, Armstrong E, Pereira Rico JA, Jara E, Olivera LH, Peral García P, Giovambattista G. Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America. Anim Genet 2024; 55:527-539. [PMID: 38716584 DOI: 10.1111/age.13435] [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: 03/25/2024] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 07/04/2024]
Abstract
The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.
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Affiliation(s)
- O Marcuzzi
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - F Calcaterra
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - A Loza Vega
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - M F Ortega Masagué
- Instituto de Investigación Animal del Chaco Semiárido, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Leales, Tucumán, Argentina
| | - E Armstrong
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - J A Pereira Rico
- Facultad de Ciencias Veterinarias, Universidad Autónoma Gabriel René Moreno, Santa Cruz de la Sierra, Bolivia
| | - E Jara
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - L H Olivera
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - P Peral García
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria 'Ing. Fernando N. Dulout' (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias UNLP, La Plata, Argentina
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Bem RD, Benfica LF, Silva DA, Carrara ER, Brito LF, Mulim HA, Borges MS, Cyrillo JNSG, Canesin RC, Bonilha SFM, Mercadante MEZ. Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population. BMC Genomics 2024; 25:738. [PMID: 39080557 PMCID: PMC11290228 DOI: 10.1186/s12864-024-10641-3] [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: 04/05/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. RESULTS The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. CONCLUSIONS Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.
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Affiliation(s)
- Ricardo D Bem
- Institute of Animal Science, Sertãozinho, SP, Brazil.
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Lorena F Benfica
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Delvan A Silva
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Eula R Carrara
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Henrique A Mulim
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907, USA
| | - Marcelo S Borges
- Department of Pathology, Reproduction and One Health, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
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Li X, Lan F, Chen X, Yan Y, Li G, Wu G, Sun C, Yang N. Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding. BMC Genomics 2024; 25:638. [PMID: 38926812 PMCID: PMC11210043 DOI: 10.1186/s12864-024-10551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding. RESULTS In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight. CONCLUSIONS In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.
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Affiliation(s)
- Xiaochang Li
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Fangren Lan
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoman Chen
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yiyuan Yan
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guangqi Li
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Guiqin Wu
- Beijing Engineering Research Centre of Layer, Beijing, 101206, China
| | - Congjiao Sun
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Ning Yang
- State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding (MOE), and National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
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Sheriff O, Ahbara AM, Haile A, Alemayehu K, Han JL, Mwacharo JM. Whole-genome resequencing reveals genomic variation and dynamics in Ethiopian indigenous goats. Front Genet 2024; 15:1353026. [PMID: 38854428 PMCID: PMC11156998 DOI: 10.3389/fgene.2024.1353026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Ethiopia has about 52 million indigenous goats with marked phenotypic variability, which is the outcome of natural and artificial selection. Here, we obtained whole-genome sequence data of three Ethiopian indigenous goat populations (Arab, Fellata, and Oromo) from northwestern Ethiopia and analyzed their genome-wide genetic diversity, population structure, and signatures of selection. We included genotype data from four other Ethiopian goat populations (Abergelle, Keffa, Gumuz, and Woyto-Guji) and goats from Asia; Europe; and eastern, southern, western, and northern Africa to investigate the genetic predisposition of the three Ethiopian populations and performed comparative genomic analysis. Genetic diversity analysis showed that Fellata goats exhibited the lowest heterozygosity values (Ho = 0.288 ± 0.005 and He = 0.334 ± 0.0001). The highest values were observed in Arab goats (Ho = 0.310 ± 0.010 and He = 0.347 ± 4.35e-05). A higher inbreeding coefficient (FROH = 0.137 ± 0.016) was recorded for Fellata goats than the 0.105 ± 0.030 recorded for Arab and the 0.112 ± 0.034 recorded for Oromo goats. This indicates that the Fellata goat population should be prioritized in future conservation activities. The three goat populations showed the majority (∼63%) of runs of homozygosity in the shorter (100-150 Kb) length category, illustrating ancient inbreeding and/or small founder effects. Population relationship and structure analysis separated the Ethiopian indigenous goats into two distinct genetic clusters lacking phylogeographic structure. Arab, Fellata, Oromo, Abergelle, and Keffa represented one genetic cluster. Gumuz and Woyto-Guji formed a separate cluster and shared a common genetic background with the Kenyan Boran goat. Genome-wide selection signature analysis identified nine strongest regions spanning 163 genes influencing adaptation to arid and semi-arid environments (HOXC12, HOXC13, HOXC4, HOXC6, and HOXC9, MAPK8IP2), immune response (IL18, TYK2, ICAM3, ADGRG1, and ADGRG3), and production and reproduction (RARG and DNMT1). Our results provide insights into a thorough understanding of genetic architecture underlying selection signatures in Ethiopian indigenous goats in a semi-arid tropical environment and deliver valuable information for goat genetic improvement, conservation strategy, genome-wide association study, and marker-assisted breeding.
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Affiliation(s)
- Oumer Sheriff
- Department of Animal Science, Assosa University, Assosa, Ethiopia
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abulgasim M. Ahbara
- Department of Zoology, Faculty of Sciences, Misurata University, Misurata, Libya
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
| | - Aynalem Haile
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Kefyalew Alemayehu
- Department of Animal Production and Technology, Bahir Dar University, Bahir Dar, Ethiopia
- Biotechnology Research Institute, Bahir Dar University, Bahir Dar, Ethiopia
- Ethiopian Agricultural Transformation Institute, Amhara Agricultural Transformation Center, Bahir Dar, Ethiopia
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
| | - Joram M. Mwacharo
- Animal and Veterinary Sciences Scotland's Rural College (SRUC) and The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute Building, Edinburgh, United Kingdom
- Resilient Agricultural Livelihood Systems Program (RALSP), International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
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Xie K, Ning C, Yang A, Zhang Q, Wang D, Fan X. Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement. Genes (Basel) 2024; 15:433. [PMID: 38674368 PMCID: PMC11049387 DOI: 10.3390/genes15040433] [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: 02/21/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.
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Affiliation(s)
- Kerui Xie
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China;
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (C.N.); (Q.Z.)
| | - Aiguo Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (C.N.); (Q.Z.)
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (C.N.); (Q.Z.)
| | - Dan Wang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China
| | - Xinzhong Fan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, China;
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Santos MF, Silva MC, Freitas TMS, Dias JM, Moura MI, Juliano RS, Fioravanti CS, Carmo AS. Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds. Trop Anim Health Prod 2024; 56:92. [PMID: 38430430 DOI: 10.1007/s11250-024-03933-z] [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: 03/17/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024]
Abstract
This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.
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Affiliation(s)
- M F Santos
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - M C Silva
- Federal University of Grande Dourados, Grande Dourados, Dourados, MS, Brazil
| | - T M S Freitas
- Brasilia University Center of Goiás, São Luís dos Montes Belos, GO, Brazil
- Goiás State University - West Campus, São Luís de Montes Belos, GO, Brazil
| | - J M Dias
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - M I Moura
- Veterinary Medicine Department, Pontifical Catholic University of Goiás, Goiânia, GO, Brazil
| | - R S Juliano
- EMBRAPA - Brazilian Agricultural Research Corporation, Pantanal, MS, Brazil
| | - C S Fioravanti
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil
| | - A S Carmo
- School of Veterinary and Animal Science, Federal University of Goiás, Goiânia, GO, Brazil.
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Smaragdov MG. Identification of homozygosity-rich regions in the Holstein genome. Vavilovskii Zhurnal Genet Selektsii 2023; 27:471-479. [PMID: 37808215 PMCID: PMC10556852 DOI: 10.18699/vjgb-23-57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/03/2023] [Accepted: 02/27/2023] [Indexed: 10/10/2023] Open
Abstract
In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1-2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.
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Affiliation(s)
- M G Smaragdov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia
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10
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Schmidt PI, Mota LFM, Fonseca LFS, Dos Santos Silva DB, Frezarim GB, Arikawa LM, de Abreu Santos DJ, Magalhães AFB, Cole JB, Carvalheiro R, de Oliveira HN, Null DJ, VanRaden P, Ma L, de Albuquerque LG. Identification of candidate lethal haplotypes and genomic association with post-natal mortality and reproductive traits in Nellore cattle. Sci Rep 2023; 13:10399. [PMID: 37369809 DOI: 10.1038/s41598-023-37586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023] Open
Abstract
The wide use of genomic information has enabled the identification of lethal recessive alleles that are the major genetic causes of reduced conception rates, longer calving intervals, or lower survival for live-born animals. This study was carried out to screen the Nellore cattle genome for lethal recessive haplotypes based on deviation from the expected population homozygosity, and to test SNP markers surrounding the lethal haplotypes region for association with heifer rebreeding (HR), post-natal mortality (PNM) and stayability (STAY). This approach requires genotypes only from apparently normal individuals and not from affected embryos. A total of 62,022 animals were genotyped and imputed to a high-density panel (777,962 SNP markers). Expected numbers of homozygous individuals were calculated, and the probabilities of observing 0 homozygotes was obtained. Deregressed genomic breeding values [(G)EBVs] were used in a GWAS to identify candidate genes and biological mechanisms affecting HR, STAY and PNM. In the functional analyses, genes within 100 kb down and upstream of each significant SNP marker, were researched. Thirty haplotypes had high expected frequency, while no homozygotes were observed. Most of the alleles present in these haplotypes had a negative mean effect for PNM, HR and STAY. The GWAS revealed significant SNP markers involved in different physiological mechanisms, leading to harmful effect on the three traits. The functional analysis revealed 26 genes enriched for 19 GO terms. Most of the GO terms found for biological processes, molecular functions and pathways were related to tissue development and the immune system. More phenotypes underlying these putative regions in this population could be the subject of future investigation. Tests to find putative lethal haplotype carriers could help breeders to eliminate them from the population or manage matings in order to avoid homozygous.
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Affiliation(s)
- Patrícia Iana Schmidt
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Danielly Beraldo Dos Santos Silva
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Leonardo Machestropa Arikawa
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Jordan de Abreu Santos
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - John Bruce Cole
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Roberto Carvalheiro
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Henrique Nunes de Oliveira
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Jacob Null
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Paul VanRaden
- Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, 20742, USA
| | - Lucia Galvão de Albuquerque
- Animal Science Department, School of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Via de Acesso Paulo Donato Castellane S/N, Departamento de Zootecnia, Jaboticabal, SP, 14884-900, Brazil.
- National Council for Scientific and Technological Development (CNPq), Brasília, Brazil.
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11
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Wang Q, Zhang J, Wang H, Wang Z, Li Q, Zhao G, Zheng M, Wen J. Estimates of genomic inbreeding and identification of candidate regions in Beijing-You chicken populations. Anim Genet 2023; 54:155-165. [PMID: 36541281 DOI: 10.1111/age.13286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (FROH ) was 0.1 in BY_P, whereas the lowest FROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (FROH = 0.0798) was higher than that of BY_R1 (FROH = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.
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Affiliation(s)
- Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jin Zhang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Hailong Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Zixuan Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Qinghe Li
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Guiping Zhao
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
| | - Jie Wen
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, State Key Laboratory of Animal Nutrition, Beijing, China
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12
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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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13
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Pedigree reconstruction and population structure using SNP markers in Gir cattle. J Appl Genet 2023; 64:329-340. [PMID: 36645582 DOI: 10.1007/s13353-023-00747-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Our objective was to establish a SNPs panel for pedigree reconstruction using microarrays of different densities and evaluate the genomic relationship coefficient of the inferred pedigree, in addition to analyzing the population structure based on genomic analyses in Gir cattle. For parentage analysis and genomic relationship, 16,205 genotyped Gir animals (14,458 females and 1747 males) and 1810 common markers to the four SNP microarrays were used. For population structure analyses, including linkage disequilibrium, effective population size, and runs of homozygosity (ROH), genotypes from 21,656 animals were imputed. Likelihood ratio (LR) approach was used to reconstruct the pedigree, deepening the pedigree and showing it is well established in terms of recent information. Coefficients for each relationship category of the inferred pedigree were adequate. Linkage disequilibrium showed rapid decay. We detected a decrease in the effective population size over the last 50 generations, with the average generation interval around 9.08 years. Higher ROH-based inbreeding coefficient in a class of short ROH segments, with moderate to high values, was also detected, suggesting bottlenecks in the Gir genome. Breeding strategies to minimize inbreeding and avoid massive use of few proven sires with high genetic value are suggested to maintain genetic variability in future generations. In addition, we recommend reducing the generation interval to maximize genetic progress and increase effective population size.
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14
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Wang H, Wang Q, Tan X, Wang J, Zhang J, Zheng M, Zhao G, Wen J. Estimation of genetic variability and identification of regions under selection based on runs of homozygosity in Beijing-You Chickens. Poult Sci 2022; 102:102342. [PMID: 36470032 PMCID: PMC9719870 DOI: 10.1016/j.psj.2022.102342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
The genetic composition of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. Runs of homozygosity (ROHs) are homozygous segments of the genome where the 2 haplotypes inherited from the parents are identical. The detection of ROH can be used to describe the genetic variability and quantify the level of inbreeding in an individual. Here, we investigated the occurrence and distribution of ROHs in 40 Beijing-You Chickens from the random breeding population (BJY_C) and 40 Beijing-You Chickens from the intramuscular fat (IMF) selection population (BJY_S). Principal component analysis (PCA) and maximum likelihood (ML) analyses showed that BJY_C was completely separated from the BJY_S. The nucleotide diversity of BJY_C was higher than that of BJY_S, and the decay rate of LD of BJY_C was faster. The ROHs were identified for a total of 7,101 in BJY_C and 9,273 in BJY_S, respectively. The ROH-based inbreeding estimate (FROH) of BJY_C was 0.079, which was significantly lower than that of BJY_S (FROH = 0.114). The results were the same as the estimates of the inbreeding coefficients calculated based on homozygosity (FHOM), the correlation between uniting gametes (FUNI), and the genomic relationship matrix (FGRM). Additionally, the distribution and number of ROH islands in chromosomes of BJY_C and BJY_S were significantly different. The ROH islands of BJY_S that included genes associated with lipid metabolism and fat deposition, such as CIDEA and S1PR1, were absent in BJY_C. However, GPR161 was detected in both populations, which is a candidate gene for the formation of the unique five-finger trait in Beijing-You chickens. Our findings contributed to the understanding of the genetic diversity of random or artificially selected populations, and allowed the accurate monitoring of population inbreeding using genomic information, as well as the detection of genomic regions that affect traits under selection.
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Affiliation(s)
- Hailong Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Qiao Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Xiaodong Tan
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jie Wang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jin Zhang
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Maiqing Zheng
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Guiping Zhao
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Jie Wen
- Chinese Academy of Agricultural Science, State Key Laboratory of Animal Nutrition, Beijing 100193, China.
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15
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Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China. PLoS One 2022; 17:e0271718. [PMID: 36006904 PMCID: PMC9409551 DOI: 10.1371/journal.pone.0271718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous segments from the common ancestor of parents. Evaluating ROH pattern can help to understand inbreeding level and genetic basis of important traits. In this study, three representative cattle populations including Leiqiong cattle (LQC), Lufeng cattle (LFC) and Hainan cattle (HNC) were genotyped using the Illumina BovineHD SNPs array (770K) to assess ROH pattern at genome wide level. Totally, we identified 26,537 ROH with an average of 153 ROH per individual. The sizes of ROH ranged from 0.5 to 53.26Mb, and the average length was 1.03Mb. The average of FROH ranged from 0.10 (LQC) to 0.15 (HNC). Moreover, we identified 34 ROH islands (with frequency > 0.5) across genome. Based on these regions, we observed several breed-specific candidate genes related to adaptive traits. Several common genes related to immunity (TMEM173, MZB1 and SIL1), and heat stress (DNAJC18) were identified in all three populations. Three genes related to immunity (UGP2), development (PURA) and reproduction (VPS54) were detected in both HNC and LQC. Notably, we identified several breed-specific genes related to sperm development (BRDT and SPAG6) and heat stress (TAF7) in HNC, and immunity (CDC23 and NME5) and development (WNT87) in LFC. Our findings provided valuable insights into understanding the genomic homozygosity pattern and promoting the conservation of genetic resources of Chinese indigenous cattle.
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16
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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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17
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Utsunomiya YT, Fortunato AAAD, Milanesi M, Trigo BB, Alves NF, Sonstegard TS, Garcia JF. Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle. Anim Genet 2021; 53:58-67. [PMID: 34921423 DOI: 10.1111/age.13164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
Brazil is the largest exporter of beef in the world, and most of that beef derives from Nellore cattle. Although considered a zebu breed (Bos indicus), the history of Nellore cattle in Brazil is marked by the importation of bulls from India, the use of a Creole taurine (Bos taurus) maternal lineage to quickly expand the herds and backcrossing to Nellore bulls to recover zebu ancestry. As a consequence, the current Brazilian Nellore population carries an average taurine ancestry of approximately 1%. Although that percentage seems small, some taurine variants deviate substantially from that average, with the better-known cases being the PLAG1-Q haplotype involved with body size variation and the Guarani (PG ) polled variant producing hornless animals. Here, we report taurine haplotypes in 9074 Nellore animals genotyped for 539 657 imputed SNP markers. Apart from PLAG1-Q and PG , our analysis further revealed common taurine haplotypes (>3%) spanning genes related to immunity, growth, reproduction and hair and skin phenotypes. Using data from 22 economically important traits, we showed that many of the major QTL previously reported in the breed are at least partially driven by taurine haplotypes. As B. taurus and B. indicus haplotypes are highly divergent, presenting widely different sets of functional variants, our results provide promising targets for future scrutiny in Nellore cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil
| | - A A A D Fortunato
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,Personal-PEC. R. Sebastião Lima, 1336 - Centro, Campo Grande, MS, 79004-600, Brazil
| | - M Milanesi
- AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems, Università Della Tuscia, Via S. Camillo de Lellis snc, Viterbo, 01100, Italy
| | - B B Trigo
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | - N F Alves
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | | | - J F Garcia
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
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18
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Selli A, Ventura RV, Fonseca PAS, Buzanskas ME, Andrietta LT, Balieiro JCC, Brito LF. Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations. Animals (Basel) 2021; 11:2696. [PMID: 34573664 PMCID: PMC8472390 DOI: 10.3390/ani11092696] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/25/2022] Open
Abstract
In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.
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Affiliation(s)
- Alana Selli
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Ricardo V. Ventura
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Pablo A. S. Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Marcos E. Buzanskas
- Department of Animal Science, Federal University of Paraíba, João Pessoa 58051-900, Paraiba, Brazil;
| | - Lucas T. Andrietta
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Júlio C. C. Balieiro
- Department of Nutrition and Animal Production, School of Veterinary Medicine and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, São Paulo, Brazil; (L.T.A.); (J.C.C.B.)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA;
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19
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Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
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Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
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20
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Nascimento AV, Romero ARS, Nawaz MY, Cardoso DF, Santos DJA, Gondro C, Tonhati H. An updated Axiom buffalo genotyping array map and mapping of cattle quantitative trait loci to the new water buffalo reference genome assembly. Anim Genet 2021; 52:505-508. [PMID: 34106478 DOI: 10.1111/age.13103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 11/30/2022]
Abstract
The objectives of this study were to provide the buffalo research community with an updated SNP map for the Axiom Buffalo Genotyping (ABG) array with genomic positions for SNP currently unmapped and to map all cattle QTL from the CattleQTLdb onto the buffalo reference assembly. To update the ABG array map, all SNP probe sequences from the ABG array were re-aligned against the UOA_WB_1 assembly. With the new map, the number of mapped markers increased by approximately 10% and went from 106 778 to 116 708, which reduced the average marker spacing by approximately 2 kb. A comparison of results between signatures of autozygosity study using the ABG and the new map showed that, when the additional markers were used there was an increase in the autozygosity peaks and additional peaks in BBU5 and BBU11 could be identified. After sequence alignment and quality control, 64 650 (UMD3.1) and 76 530 (ARS_UCD1.2) cattle QTL were mapped onto the buffalo genome. The mapping of the bovine QTL database onto the buffalo genome should be useful for genome-wide association studies in buffalo and, given the high homology between the two species, the positions of cattle QTL on the buffalo genome can serve as a stepping stone towards a water buffalo QTL database.
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Affiliation(s)
- A V Nascimento
- Department of Animal Science, São Paulo State University, Jaboticabal, 14884900, Brazil
| | - A R S Romero
- Department of Animal Science, São Paulo State University, Jaboticabal, 14884900, Brazil
| | - M Y Nawaz
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48823, USA
| | - D F Cardoso
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - D J A Santos
- Department of Animal Science, University of Maryland, College Park, MD, 20740, USA
| | - C Gondro
- Department of Animal Science, Michigan State University, East Lansing, MI, 48823, USA
| | - H Tonhati
- Department of Animal Science, São Paulo State University, Jaboticabal, 14884900, Brazil
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21
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Trigo BB, Utsunomiya ATH, Fortunato AAAD, Milanesi M, Torrecilha RBP, Lamb H, Nguyen L, Ross EM, Hayes B, Padula RCM, Sussai TS, Zavarez LB, Cipriano RS, Caminhas MMT, Lopes FL, Pelle C, Leeb T, Bannasch D, Bickhart D, Smith TPL, Sonstegard TS, Garcia JF, Utsunomiya YT. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genet Sel Evol 2021; 53:40. [PMID: 33910501 PMCID: PMC8082809 DOI: 10.1186/s12711-021-00633-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. RESULTS We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. CONCLUSIONS Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.
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Affiliation(s)
- Beatriz B Trigo
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | - Adam T H Utsunomiya
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Alvaro A A D Fortunato
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,Personal-PEC, R. Sebastião Lima, 1336-Centro, Campo Grande, MS, 79004-600, Brazil
| | - Marco Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Rafaela B P Torrecilha
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Harrison Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Loan Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Ben Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | - Thayla S Sussai
- Centro Universitário Católico Salesiano, Araçatuba, SP, Brazil
| | - Ludmilla B Zavarez
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | | | - Maria M T Caminhas
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | - Flavia L Lopes
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland
| | - Danika Bannasch
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Derek Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Timothy P L Smith
- US. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | | | - José F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.,School of Agriculture and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Yuri T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil. .,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.
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22
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Wu X, Zhou R, Zhang W, Cao B, Xia J, Caiyun W, Zhang X, Chu M, Yin Z, Ding Y. Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs. Anim Biosci 2021; 34:1895-1902. [PMID: 33705632 PMCID: PMC8563231 DOI: 10.5713/ab.20.0679] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/07/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.
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Affiliation(s)
- Xudong Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Ren Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Wei Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, P.R. China
| | - Bangji Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Jing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Wang Caiyun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Mingxing Chu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing,100193, P. R. China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
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23
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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: 24] [Impact Index Per Article: 8.0] [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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24
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Ouédraogo D, Ouédraogo-Koné S, Yougbaré B, Soudré A, Zoma-Traoré B, Mészáros G, Khayatzadeh N, Traoré A, Sanou M, Mwai OA, Wurzinger M, Burger PA, Sölkner J. Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso. J Anim Breed Genet 2021; 138:379-388. [PMID: 33609004 PMCID: PMC8248134 DOI: 10.1111/jbg.12529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/16/2020] [Accepted: 11/23/2020] [Indexed: 12/30/2022]
Abstract
High-throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well-structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on-farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community-based breeding programs in the South-West of Burkina Faso. The three populations were pure Baoulé (called Lobi locally) in sedentary production systems, Baoulé x Zebu crossbreds in sedentary systems and Zebu × Baoulé crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoulé group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent-offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoulé animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community-based breeding program will make use of genomic information about admixture levels.
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Affiliation(s)
- Dominique Ouédraogo
- Institut du Développement Rural (IDR), Université Nazi Boni (UNB), Bobo-Dioulasso, Burkina Faso.,Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Salifou Ouédraogo-Koné
- Institut du Développement Rural (IDR), Université Nazi Boni (UNB), Bobo-Dioulasso, Burkina Faso
| | - Bernadette Yougbaré
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria.,Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Albert Soudré
- Unité de Formation et de Recherche en Sciences et Technologies (UFR/ST), Université Norbert Zongo, Koudougou, Burkina Faso
| | - Bienvenue Zoma-Traoré
- Institut du Développement Rural (IDR), Université Nazi Boni (UNB), Bobo-Dioulasso, Burkina Faso.,Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gábor Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Negar Khayatzadeh
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Amadou Traoré
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Moumouni Sanou
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Maria Wurzinger
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna
| | - Johann Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural System, University of Natural Resources and Life Sciences, Vienna, Austria
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25
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Kasarda R, Moravčíková N, Vostrý L, Krupová Z, Krupa E, Lehocká K, Olšanská B, Trakovická A, Nádaský R, Polák P, Židek R, Belej Ľ, Golian J. Fine-scale analysis of six beef cattle breeds revealed patterns of their genomic diversity. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1852894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Radovan Kasarda
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Nina Moravčíková
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Luboš Vostrý
- Katedra genetiky a šlechtění, Czech University of Life Sciences Prague, Praha, Czech Republic
- Institute of Animal Science, Praha-Uhříněves, Czech Republic
| | - Zuzana Krupová
- Institute of Animal Science, Praha-Uhříněves, Czech Republic
| | - Emil Krupa
- Institute of Animal Science, Praha-Uhříněves, Czech Republic
| | - Kristína Lehocká
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Barbora Olšanská
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Anna Trakovická
- Katedra genetiky a plemenárskej biológie, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Rudolf Nádaský
- Agricultural cooperation Špačince, Špačince, Slovak Republic
| | - Peter Polák
- Beef Breeders Association, Ivanka pri Nitre, Slovak Republic
| | - Radoslav Židek
- Katedra hygieny a bezpečnosti potravín, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Ľubomír Belej
- Katedra hygieny a bezpečnosti potravín, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Jozef Golian
- Katedra hygieny a bezpečnosti potravín, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
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Nascimento AV, Cardoso DF, Santos DJA, Romero ARS, Scalez DCB, Borquis RRA, Neto FRA, Gondro C, Tonhati H. Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo. J Dairy Sci 2020; 104:1917-1927. [PMID: 33272579 DOI: 10.3168/jds.2020-18397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/10/2020] [Indexed: 01/03/2023]
Abstract
Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.
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Affiliation(s)
- A V Nascimento
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D F Cardoso
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D J A Santos
- Department of Animal Science, University of Maryland, College Park 20742
| | - A R S Romero
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D C B Scalez
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - R R A Borquis
- College of Agricultural Sciences, Federal University of Grande Dourados (UFGD), Dourados, 79804970, Brazil
| | - F R A Neto
- Goiano Federal Institute, Campus Rio Verde, Rio Verde, 75909120, Brazil
| | - C Gondro
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - H Tonhati
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil.
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Fallahi MH, Shahrbabak HM, Shahrbabak MM, Arpanahi RA, Gholami S. Assessment of Genetic Diversity in Azerbaijani Buffalo Population in Iran Based on Runs of Homozygosity Stretches. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542010004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle. Animals (Basel) 2020; 10:ani10081425. [PMID: 32824035 PMCID: PMC7460448 DOI: 10.3390/ani10081425] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.
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Saravanan KA, Panigrahi M, Kumar H, Parida S, Bhushan B, Gaur GK, Kumar P, Dutt T, Mishra BP, Singh RK. Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India. Anim Biotechnol 2020; 33:297-311. [PMID: 32730141 DOI: 10.1080/10495398.2020.1796696] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (HO) and expected heterozygosity (HE) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by FROH, FHOM, FGRM and FUNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r2 was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Pushpendra Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - R K Singh
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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Zhan H, Zhang S, Zhang K, Peng X, Xie S, Li X, Zhao S, Ma Y. Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs. Genes (Basel) 2020; 11:genes11050577. [PMID: 32455573 PMCID: PMC7291003 DOI: 10.3390/genes11050577] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/11/2020] [Accepted: 05/11/2020] [Indexed: 01/06/2023] Open
Abstract
Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.
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Affiliation(s)
| | | | | | | | | | | | | | - Yunlong Ma
- Correspondence: ; Tel.: +86-027-87282091
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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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Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino. Animals (Basel) 2020; 10:ani10030524. [PMID: 32245132 PMCID: PMC7143548 DOI: 10.3390/ani10030524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Runs of homozygosity (ROH) are commonly used to estimate inbreeding coefficients and identify selection signatures in livestock population. The present study determined ROH patterns, estimated the inbreeding levels, and identified the genome regions with high ROH frequency (ROH hotspots) in Chinese Merino. Our results showed that the genome of Chinese Merino harbored lower ROH abundance. Moreover, the inbreeding levels were relatively low. Thirteen ROH hotspots consisting of 190 genes were identified. The ROH hotspots overlapped the selective signatures might be associated with body size, horn traits, immune traits and environment adaption. These findings could contribute to an optimum breeding program by identifying the candidate genes related to economically traits in Chinese Merino. Abstract In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.
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Dixit SP, Singh S, Ganguly I, Bhatia AK, Sharma A, Kumar NA, Dang AK, Jayakumar S. Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus. Front Genet 2020; 11:92. [PMID: 32153647 PMCID: PMC7046685 DOI: 10.3389/fgene.2020.00092] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 01/28/2020] [Indexed: 02/04/2023] Open
Abstract
Genome-wide runs of homozygosity (ROH) are suitable for understanding population history, calculating genomic inbreeding, deciphering genetic architecture of complex traits and diseases as well as identifying genes linked with agro-economic traits. Autozygosity and ROH islands, genomic regions with elevated ROH frequencies, were characterized in 112 animals of seven Indian native cattle breeds (B. indicus) using BovineHD BeadChip. In total, 4138 ROH were detected. The average number of ROH per animal was maximum in draft breed, Kangayam (63.62 ± 22.71) and minimum in dairy breed, Sahiwal (24.62 ± 11.03). The mean ROH length was maximum in Vechur (6.97 Mb) and minimum in Hariana (4.04 Mb). Kangayam revealed the highest ROH based inbreeding (FROH > 1Mb = 0.113 ± 0.059), whereas Hariana (FROH > 1Mb = 0.042 ± 0.031) and Sahiwal (FROH > 1Mb = 0.043 ± 0.048) showed the lowest. The high standard deviation observed in each breed highlights a considerable variability in autozygosity. Out of the total autozygous segments observed in each breed except Vechur, > 80% were of short length (< 8 Mb) and contributed almost 50% of the genome proportion under ROH. However, in Vechur cattle, long ROH contributed 75% of the genome proportion under ROH. ROH patterns revealed Hariana and Sahiwal breeds as less consanguineous, while recent inbreeding was apparent in Vechur. Maximum autozygosity observed in Kangayam is attributable to both recent and ancient inbreeding. The ROH islands were harbouring higher proportion of QTLs for production traits (20.68% vs. 14.64%; P≤ 0.05) but lower for reproductive traits (11.49% vs. 15.76%; P≤ 0.05) in dairy breeds compared to draft breed. In draft cattle, genes associated with resistant to diseases/higher immunity (LYZL1, SVIL, and GPX4) and stress tolerant (CCT4) were identified in ROH islands; while in dairy breeds, for milk production (PTGFR, CSN1S1, CSN2, CSN1S2, and CSN3). Significant difference in ROH islands among large and short statured breeds was observed at chromosome 3 and 5 involving genes like PTGFR and HMGA2 responsible for milk production and stature, respectively. PCA analysis on consensus ROH regions revealed distinct clustering of dairy, draft and short stature cattle breeds.
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Affiliation(s)
- S P Dixit
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sanjeev Singh
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Indrajit Ganguly
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Avnish Kumar Bhatia
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Anurodh Sharma
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - N Anand Kumar
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Ajay Kumar Dang
- Animal Physiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Jayakumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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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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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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Ventura RV, Brito LF, Oliveira GA, Daetwyler HD, Schenkel FS, Sargolzaei M, Vandervoort G, Fonseca e Silva F, Miller SP, Carvalho ME, Santana MHA, Mattos EC, Fonseca P, Eler JP, Ferraz JBS. A comprehensive comparison of high-density SNP panels and an alternative ultra-high-density panel for genomic analyses in Nellore cattle. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an18305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
There is evidence that some genotyping platforms might not work very well for Zebu cattle when compared with Taurine breeds. In addition, the availability of panels with low to moderate number of overlapping markers is a limitation for combining datasets for genomic evaluations, especially when animals are genotyped using different SNP panels. In the present study, we compared the performance of medium- and high-density (HD) commercially available panels and investigated the feasibility of developing an ultra-HD panel (SP) containing markers from an Illumina (HD_I) and an Affymetrix (HD_A) panels. The SP panel contained 1123442 SNPs. After performing SNP pruning on the basis of linkage disequilibrium, HD_A, HD_I and SP contained 429624, 365225 and 658770 markers distributed across the whole genome. The overall mean proportion of markers pruned out per chromosome for HD_A, HD_I and SP was 15.17%, 43.18%, 38.63% respectively. The HD_I panel presented the highest mean number of runs-of-homozygosity segments per animal (45.48%, an increment of 5.11% compared with SP) and longer segments, on average (3057.95 kb per segment), than did both HD_A and SP. HD_I also showed the highest mean number of SNPs per run-of-homozygosity segment. Consequently, the majority of animals presented the highest genomic inbreeding levels when genotyped using HD_I. The visual examination of marker distribution along the genome illustrated uncovered regions among the different panels. Haplotype-block comparison among panels and the average haplotype size constructed on the basis of HD_A were smaller than those from HD_I. The average number of SNPs per haplotype was different between HD_A and HD_I. Both HD_A and HD_I panels achieved high imputation accuracies when used as the lower-density panels for imputing to SP. However, imputation accuracy from HD_A to SP was greater than was imputation from HD_I to SP. Imputation from one HD panel to the other is also feasible. Low- and medium-density panels, composed of markers that are subsets of both HD_A and HD_I panels, should be developed to achieve better imputation accuracies to both HD levels. Therefore, the genomic analyses performed in the present study showed significant differences among the SNP panels used.
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Xu Z, Sun H, Zhang Z, Zhao Q, Olasege BS, Li Q, Yue Y, Ma P, Zhang X, Wang Q, Pan Y. Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data. Front Genet 2019; 10:274. [PMID: 30984245 PMCID: PMC6448551 DOI: 10.3389/fgene.2019.00274] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/12/2019] [Indexed: 12/21/2022] Open
Abstract
Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1-5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.
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Affiliation(s)
- Zhong Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingbo Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Babatunde Shittu Olasege
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiumeng Li
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Yue
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangzhe Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qishan Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuchun Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
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Aguiar TS, Torrecilha RBP, Milanesi M, Utsunomiya ATH, Trigo BB, Tijjani A, Musa HH, Lopes FL, Ajmone-Marsan P, Carvalheiro R, Neves HHDR, do Carmo AS, Hanotte O, Sonstegard TS, Garcia JF, Utsunomiya YT. Association of Copy Number Variation at Intron 3 of HMGA2 With Navel Length in Bos indicus. Front Genet 2018; 9:627. [PMID: 30581455 PMCID: PMC6292862 DOI: 10.3389/fgene.2018.00627] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/23/2018] [Indexed: 01/07/2023] Open
Abstract
Navel injuries caused by friction against the pasture can promote infection, reproductive problems and costly treatments in beef cattle raised in extensive systems. A haplotype-based genome-wide association study (GWAS) was performed for visual scores of navel length at yearling in Nellore cattle (Bos indicus) using data from 2,016 animals and 503,088 single nucleotide polymorphism (SNP) markers. The strongest signal (p = 1.01 × 10-9) was found on chromosome 5 spanning positions 47.9-48.2 Mbp. This region contains introns 3 and 4 and exons 4 and 5 of the high mobility group AT-hook 2 gene (HMGA2). Further inspection of the region with whole genome sequence data of 21 Nellore bulls revealed correlations between counts of the significant haplotype and copy number gains of a ∼6.2 kbp segment of intron 3 of HMGA2. Analysis of genome sequences from five African B. indicus and four European Bos taurus breeds revealed that the copy number variant (CNV) is indicine-specific. This intronic CNV was then validated through quantitative polymerase chain reaction (qPCR) using Angus animals as copy neutral controls. Importantly, the CNV was not detectable by means of conventional SNP-based GWAS or SNP probe intensity analyses. Given that HMGA2 affects the expression of the insulin-like growth factor 2 gene (IGF2) together with the pleomorphic adenoma gene 1 (PLAG1), and that the latter has been repeatedly shown to be associated with quantitative traits of economic importance in cattle, these findings highlight the emerging role of variants impacting the insulin-like growth factor pathway to cattle breeding.
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Affiliation(s)
- Tamíris Sayuri Aguiar
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, Brazil.,Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil
| | - Rafaela Beatriz Pintor Torrecilha
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, Brazil.,Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil
| | - Marco Milanesi
- Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil.,Department of Animal Science Food and Nutrition and Biodiversity and Ancient DNA Research Center - BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Adam Taiti Harth Utsunomiya
- Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
| | - Beatriz Batista Trigo
- Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
| | - Abdulfatai Tijjani
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Hassan Hussein Musa
- Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Flávia Lombardi Lopes
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
| | - Paolo Ajmone-Marsan
- Department of Animal Science Food and Nutrition and Biodiversity and Ancient DNA Research Center - BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, Brazil
| | | | | | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,LiveGene - CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
| | | | - José Fernando Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, Brazil.,Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
| | - Yuri Tani Utsunomiya
- Collaborating Centre on Animal Genomics and Bioinformatics, International Atomic Energy Agency, Araçatuba, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
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Zanella R, Lago LV, da Silva AN, Pértille F, de Carvalho NS, do Carmo Panetto JC, Zanella GC, Facioli FL, da Silva MVGB. Genetic Characterization of Indubrasil Cattle Breed Population. Vet Sci 2018; 5:vetsci5040098. [PMID: 30513897 PMCID: PMC6313910 DOI: 10.3390/vetsci5040098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/19/2018] [Accepted: 11/29/2018] [Indexed: 11/27/2022] Open
Abstract
The Indubrasil breed was developed in the Brazilian region called Triângulo Mineiro as a result of a cross between zebu cattle. Initially, it was used as a terminal cross and currently it represents approximately 4.45% of all the Brazilian zebu cattle. Studies were conducted to estimate genetic parameters in the Indubrasil using pedigree information, however, until now, no study has been developed using large-scale genomic markers in this breed. Pedigree information are widely used to investigate population parameters; however, they can neglect some estimates when compared to the use of genomic markers. Therefore, the objective of this study was to investigate the population structure and the genetic diversity of Indubrasil cattle using a high-density Single Nucleotide Polymorphism (SNP) panel (Illumina BovineHD BeadChip 700k). Levels of genomic homozygosity were evaluated using three different approaches: Runs of homozygosity (FROH), % of homozygosis (FSNP), and inbreeding coefficient (Fx). Further, Runs of Homozygosity (ROH) segments conserved among the animals were investigated to identify possible regions associated with the breed characteristics. Our results indicate that even the Indubrasil breed having a small effective population size, the levels of homozygosity (FROH = 0.046) are still small. This was possibly caused by the cross conducted among different breeds for its development. It suggests no immediate risks associated with loss of genetic variation. This information might be used in breeding programs, for the breed conservation and for the expansion of the Indubrasil breed.
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Affiliation(s)
- Ricardo Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
- Docente do programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Luísa V Lago
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Arthur N da Silva
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Fábio Pértille
- Laboratório de Biotecnologia Animal, Departamento de Ciência Animal e Pastagens, Universidade de São Paulo/Escola Superior de Agricultura Luiz de Queiroz, Av. Pádua Dias, 11, 13418-900 Piracicaba, SP, Brazil.
| | - Nathã S de Carvalho
- Mestrando do Curso de Zootecnia, Universidade Federal do Rio Grande do Sul/Faculdade de Agronomia, Av. Bento Gonçalves, 7712, 91540-000 Porto Alegre, RS, Brazil.
| | | | - Giovana C Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
| | - Fernanda L Facioli
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, BR 285, São José, 99052-900 Passo Fundo, RS, Brazil.
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Bertolini F, Cardoso TF, Marras G, Nicolazzi EL, Rothschild MF, Amills M. Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats. Genet Sel Evol 2018; 50:59. [PMID: 30449279 PMCID: PMC6241033 DOI: 10.1186/s12711-018-0424-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 10/15/2018] [Indexed: 01/15/2023] Open
Abstract
Background Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats. Results The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH (< 3 Mb) are the most frequent ones. Our data also indicate that ~ 60% of the breeds display low FROH coefficients (< 0.10), while ~ 30 and ~ 10% of the goat populations show moderate (0.10 < FROH < 0.20) or high (> 0.20) FROH values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection. Conclusions Patterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; FROH < 0.15) are similar in goats from different geographic areas. The increased homozygosity in local breeds is the consequence of their small population size and geographic isolation as well as of founder effects and recent inbreeding. The existence of three ROH hotspots that co-localize with signatures of selection demonstrates that selection has also played an important role in increasing the homozygosity of specific regions in the goat genome. Finally, most of the goat breeds analysed in this work display low levels of homozygosity, which is favourable for their genetic management and viability. Electronic supplementary material The online version of this article (10.1186/s12711-018-0424-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. .,National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark.
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Gabriele Marras
- Fondazione Parco Tecnologico Padano (PTP), 26900, Lodi, Italy
| | | | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus, Universitat Autonoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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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: 34] [Impact Index Per Article: 5.7] [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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Nandolo W, Utsunomiya YT, Mészáros G, Wurzinger M, Khayadzadeh N, Torrecilha RBP, Mulindwa HA, Gondwe TN, Waldmann P, Ferenčaković M, Garcia JF, Rosen BD, Bickhart D, van Tassell CP, Curik I, Sölkner J. Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances. Genet Sel Evol 2018; 50:43. [PMID: 30134820 PMCID: PMC6106898 DOI: 10.1186/s12711-018-0414-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 07/30/2018] [Indexed: 12/22/2022] Open
Abstract
Background Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. Methods ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. Results In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. Conclusions Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps. Electronic supplementary material The online version of this article (10.1186/s12711-018-0414-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wilson Nandolo
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, P. O. Box 219, Lilongwe, Malawi
| | - Yuri T Utsunomiya
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil
| | - Gábor Mészáros
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria.
| | - Maria Wurzinger
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
| | - Negar Khayadzadeh
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
| | - Rafaela B P Torrecilha
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil
| | - Henry A Mulindwa
- National Livestock Resources Research Institute, P.O Box 96, Tororo, Uganda
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, P. O. Box 219, Lilongwe, Malawi
| | - Patrik Waldmann
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - José F Garcia
- School of Agricultural and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), São Paulo, Brazil.,School of Veterinary Medicine, Araçatuba, Department of Support, Production and Animal Health, São Paulo State University (UNESP), São Paulo, Brazil
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Derek Bickhart
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Curt P van Tassell
- Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705-2350, USA
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Johann Sölkner
- Division of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Gregor-Mendel Strasse 33, 1180, Vienna, Austria
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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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Forutan M, Ansari Mahyari S, Baes C, Melzer N, Schenkel FS, Sargolzaei M. Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genomics 2018; 19:98. [PMID: 29374456 PMCID: PMC5787230 DOI: 10.1186/s12864-018-4453-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 01/15/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulation was performed and inbreeding estimates based on runs of homozygosity (ROH), pedigree, and the genomic relationship matrix were compared to true inbreeding. Inbreeding based on ROH was estimated using SNP1101, PLINK, and BCFtools software with different threshold parameters. The effects of different selection methods on ROH patterns were also compared. Furthermore, inbreeding coefficients were estimated in a sample of genotyped North American Holstein animals born from 1990 to 2016 using 50 k chip data and ROH patterns were assessed before and after genomic selection. RESULTS Using ROH with a minimum window size of 20 to 50 using SNP1101 provided the closest estimates to true inbreeding in simulation study. Pedigree inbreeding tended to underestimate true inbreeding, and results for genomic inbreeding varied depending on assumptions about base allele frequencies. Using an ROH approach also made it possible to assess the effect of population structure and selection on distribution of runs of autozygosity across the genome. In the simulation, the longest individual ROH and the largest average length of ROH were observed when selection was based on best linear unbiased prediction (BLUP), whereas genomic selection showed the largest number of small ROH compared to BLUP estimated breeding values (BLUP-EBV). In North American Holsteins, the average number of ROH segments of 1 Mb or more per individual increased from 57 in 1990 to 82 in 2016. The rate of increase in the last 5 years was almost double that of previous 5 year periods. Genomic selection results in less autozygosity per generation, but more per year given the reduced generation interval. CONCLUSIONS This study shows that existing software based on the measurement of ROH can accurately identify autozygosity across the genome, provided appropriate threshold parameters are used. Our results show how different selection strategies affect the distribution of ROH, and how the distribution of ROH has changed in the North American dairy cattle population over the last 25 years.
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Affiliation(s)
- Mehrnush Forutan
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Khomeyni Shahr, Iran
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Saeid Ansari Mahyari
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Khomeyni Shahr, Iran
| | - Christine Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Nina Melzer
- Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Flavio Schramm Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
- Semex Alliance, Guelph, Canada
- HiggsGene Solutions Inc., Guelph, Canada
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Lago LV, Nery da Silva A, Zanella EL, Groke Marques M, Peixoto JO, da Silva MVGB, Ledur MC, Zanella R. Identification of Genetic Regions Associated with Scrotal Hernias in a Commercial Swine Herd. Vet Sci 2018; 5:vetsci5010015. [PMID: 29382056 PMCID: PMC5876567 DOI: 10.3390/vetsci5010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 01/17/2023] Open
Abstract
In this paper, we have used two approaches to detect genetic associations with scrotal hernias in commercial pigs. Firstly, we have investigated the effects of runs of homozygosity (ROH) with the appearance of scrotal hernias, followed by a Genome Wide Association Study (GWAS). The phenotype classification was based on visual appearance of scrotal hernias. Each affected animal was matched to a healthy control from the same pen. In the total, 68 animals were genotyped using the Porcine SNP60 Beadchip, out of those, 41 animals had the presence of hernias and 27 were healthy animals. Fifteen animals were removed from the analysis due to differences in genetic background, leaving 18 healthy animals and 35 piglets with scrotal hernia. Further, the detection of extended haplotypes shared ROH were conducted for health (control) and affected (case) animals and a permutation test was used to test whether the ROH segments were more frequent in case/case pairs than non-case/case pairs. Using the ROH, we have identified an association (p = 0.019) on chromosome 2(SSC2) being segregated on animals with the presence of scrotal hernias. Using a GWAS, a region composed by 3 SNPs on the sexual chromosome X (SSCX) were associated with scrotal hernias (p < 1.6 × 10-5), this region harbors the Androgen Receptor Gene (AR).
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Affiliation(s)
- Luisa Vitória Lago
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | - Arthur Nery da Silva
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | - Eraldo L Zanella
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
- Docentes do Programa de Pós-Graduação em Bioexperimentação-UPF, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | | | - Jane O Peixoto
- Embrapa Suínos e Aves, Rodovia BR-153, Km110, Concórdia, SC 89715-899, Brazil.
| | - Marcos V G B da Silva
- Embrapa Gado de Leite, Rua Eugênio do Nascimento, 610, Juiz de Fora, MG 36038-330, Brazil.
| | - Mônica C Ledur
- Embrapa Suínos e Aves, Rodovia BR-153, Km110, Concórdia, SC 89715-899, Brazil.
| | - Ricardo Zanella
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
- Docentes do Programa de Pós-Graduação em Bioexperimentação-UPF, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
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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: 100] [Impact Index Per Article: 16.7] [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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A PLAG1 mutation contributed to stature recovery in modern cattle. Sci Rep 2017; 7:17140. [PMID: 29215042 PMCID: PMC5719367 DOI: 10.1038/s41598-017-17127-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/22/2017] [Indexed: 01/06/2023] Open
Abstract
The recent evolution of cattle is marked by fluctuations in body size. Height in the Bos taurus lineage was reduced by a factor of ~1.5 from the Neolithic to the Middle Ages, and increased again only during the Early Modern Ages. Using haplotype analysis, we found evidence that the bovine PLAG1 mutation (Q) with major effects on body size, weight and reproduction is a >1,000 years old derived allele that increased rapidly in frequency in Northwestern European B. taurus between the 16th and 18th centuries. Towards the 19th and 20th centuries, Q was introgressed into non-European B. taurus and Bos indicus breeds. These data implicate a major role of Q in recent changes in body size in modern cattle, and represent one of the first examples of a genomic sweep in livestock that was driven by selection on a complex trait.
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49
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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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50
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Mastrangelo S, Tolone M, Sardina MT, Sottile G, Sutera AM, Di Gerlando R, Portolano B. Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep. Genet Sel Evol 2017; 49:84. [PMID: 29137622 PMCID: PMC5684758 DOI: 10.1186/s12711-017-0360-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/07/2017] [Indexed: 11/23/2022] Open
Abstract
Background Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygosity has occurred and they offer new opportunities to improve the accuracy of inbreeding (\documentclass[12pt]{minimal}
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\begin{document}$$F$$\end{document}F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and distribution of ROH using a medium-dense SNP panel to characterize autozygosity in 516 Valle del Belice sheep and to identify the genomic regions with high ROH frequencies. Results We identified 11,629 ROH and all individuals displayed at least one ROH longer than 1 Mb. The mean value of \documentclass[12pt]{minimal}
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\begin{document}$$F$$\end{document}F estimated from ROH longer than1 Mb was 0.084 ± 0.061. ROH that were shorter than 10 Mb predominated. The highest and lowest coverages of Ovis aries chromosomes (OAR) by ROH were on OAR24 and OAR1, respectively. The number of ROH per chromosome length displayed a specific pattern, with higher values for the first three chromosomes. Both number of ROH and length of the genome covered by ROH varied considerably between animals. Two hundred and thirty-nine SNPs were considered as candidate markers that may be under directional selection and we identified 107 potential candidate genes. Six genomic regions located on six chromosomes, corresponding to ROH islands, are presented as hotspots of autozygosity, which frequently coincided with regions of medium recombination rate. According to the KEGG database, most of these genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. A genome scan revealed the presence of ROH islands in genomic regions that harbor candidate genes for selection in response to environmental stress and which underlie local adaptation. Conclusions These results suggest that natural selection has, at least partially, a role in shaping the genome of Valle del Belice sheep and that ROH in the ovine genome may help to detect genomic regions involved in the determinism of traits under selection. Electronic supplementary material The online version of this article (10.1186/s12711-017-0360-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy.
| | - Marco Tolone
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Maria T Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Gianluca Sottile
- Dipartimento di Scienze Economiche, Aziendali e Statistiche, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Anna M Sutera
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Rosalia Di Gerlando
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128, Palermo, Italy
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