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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Moradi MH, Mahmodi R, Farahani AHK, Karimi MO. Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds. Sci Rep 2022; 12:14286. [PMID: 35996004 PMCID: PMC9395407 DOI: 10.1038/s41598-022-18571-4] [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: 02/09/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.
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Affiliation(s)
- Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran.
| | - Roqiah Mahmodi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran
| | | | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Herat University, Herat, Afghanistan
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Taghizadeh S, Gholizadeh M, Rahimi-Mianji G, Moradi MH, Costilla R, Moore S, Di Gerlando R. Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds. Sci Rep 2022; 12:8834. [PMID: 35614300 PMCID: PMC9132911 DOI: 10.1038/s41598-022-12778-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) are a type of genetic polymorphism which contribute to phenotypic variation in several species, including livestock. In this study, we used genomic data of 192 animals from 3 Iranian sheep breeds including 96 Baluchi sheep and 47 Lori-Bakhtiari sheep as fat-tailed breeds and 47 Zel sheep as thin-tailed sheep breed genotyped with Illumina OvineSNP50K Beadchip arrays. Also, for association test, 70 samples of Valle del Belice sheep were added to the association test as thin-tailed sheep breed. PennCNV and CNVRuler software were, respectively, used to study the copy number variation and genomic association analyses. We detected 573 and 242 CNVs in the fat and thin tailed breeds, respectively. In terms of CNV regions (CNVRs), these represented 328 and 187 CNVRs that were within or overlapping with 790 known Ovine genes. The CNVRs covered approximately 73.85 Mb of the sheep genome with average length 146.88 kb, and corresponded to 2.6% of the autosomal genome sequence. Five CNVRs were randomly chosen for validation, of which 4 were experimentally confirmed using Real time qPCR. Functional enrichment analysis showed that genes harbouring CNVs in thin-tailed sheep were involved in the adaptive immune response, regulation of reactive oxygen species biosynthetic process and response to starvation. In fat-tailed breeds these genes were involved in cellular protein modification process, regulation of heart rate, intestinal absorption, olfactory receptor activity and ATP binding. Association test identified one copy gained CNVR on chromosomes 6 harbouring two protein-coding genes HGFAC and LRPAP1. Our findings provide information about genomic structural changes and their association to the interested traits including fat deposition and environmental compatibility in sheep.
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Affiliation(s)
- Shadan Taghizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran.
| | - Ghodrat Rahimi-Mianji
- Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, P.O. Box - 578, Sari, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - Roy Costilla
- Ruakura Research Centre, AgResearch, Hamilton, New Zealand
| | - Stephen Moore
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Rosalia Di Gerlando
- Dipartimento Di Scienze Agrarie, Alimentari E Forestali, Università Degli Studi Di Palermo, Palermo, Italy
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4
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Identification of Copy Number Variations and Genetic Diversity in Italian Insular Sheep Breeds. Animals (Basel) 2022; 12:ani12020217. [PMID: 35049839 PMCID: PMC8773107 DOI: 10.3390/ani12020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
Copy number variants (CNVs) are one of the major contributors to genetic diversity and phenotypic variation in livestock. The aim of this work is to identify CNVs and perform, for the first time, a CNV-based population genetics analysis with five Italian sheep breeds (Barbaresca, Comisana, Pinzirita, Sarda, and Valle del Belìce). We identified 10,207 CNVs with an average length of 1.81 Mb. The breeds showed similar mean numbers of CNVs, ranging from 20 (Sarda) to 27 (Comisana). A total of 365 CNV regions (CNVRs) were determined. The length of the CNVRs varied among breeds from 2.4 Mb to 124.1 Mb. The highest number of shared CNVRs was between Comisana and Pinzirita, and only one CNVR was shared among all breeds. Our results indicated that segregating CNVs expresses a certain degree of diversity across all breeds. Despite the low/moderate genetic differentiation among breeds, the different approaches used to disclose the genetic relationship showed that the five breeds tend to cluster in distinct groups, similar to the previous studies based on single-nucleotide polymorphism markers. Gene enrichment was described for the 37 CNVRs selected, considering the top 10%. Out of 181 total genes, 67 were uncharacterized loci. Gene Ontology analysis showed that several of these genes are involved in lipid metabolism, immune response, and the olfactory pathway. Our results corroborated previous studies and showed that CNVs represent valuable molecular resources for providing useful information for separating the population and could be further used to explore the function and evolutionary aspect of sheep genome.
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Igoshin AV, Deniskova TE, Yurchenko AA, Yudin NS, Dotsev AV, Selionova MI, Zinovieva NA, Larkin DM. Copy number variants in genomes of local sheep breeds from Russia. Anim Genet 2021; 53:119-132. [PMID: 34904242 DOI: 10.1111/age.13163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2021] [Indexed: 01/21/2023]
Abstract
Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.
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Affiliation(s)
- A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - T E Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - M I Selionova
- Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, Moscow, 127550, Russia
| | - N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - D M Larkin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Royal Veterinary College, University of London, London, NW1 0TU, UK
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6
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Goyache F, Fernández I, Tapsoba ASR, Traoré A, Menéndez-Arias NA, Álvarez I. Functional characterization of Copy Number Variations regions in Djallonké sheep. J Anim Breed Genet 2021; 138:600-612. [PMID: 33682236 DOI: 10.1111/jbg.12542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/04/2021] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
A total of 184 Djallonké (West African Dwarf) sheep of Burkina Faso were analysed for Copy Number Variations (CNV) using Ovine 50 K SNP BeadChip genotyping data and two different CNV calling platforms: PennCNV and QuantiSNP. Analyses allowed to identify a total of 63 candidate Copy Number Variations Regions (CNVR) on 11 different ovine chromosomes covering about 82.5 Mb of the sheep genome. Gene-annotation enrichment analysis allowed to identify a total of 751 potential candidate ovine genes located in the candidate CNVR bounds. Functional annotation allowed to identify five statistically significant Functional Clusters (FC; enrichment factor > 1.3) involving 61 candidate genes. All genes forming significantly enriched FC were located on ovine chromosome (OAR) 21. FC1 (22 genes including PAG4 and PAG6) and FC5 (three genes: CTSC, CTSW and CTSF), coding proteases (peptidases and cathepsins, respectively), were involved in reproductive performance and modulation of gestation. Both FC3 and FC4 were involved in inflammatory and immunologic response through coding serum amyloid A and B-box-type zinc finger proteins, respectively. Finally, FC2 consisted of 27 genes (including OR10G6 and OR8B8) involved in olfactory receptor activity, key for animals adapting to new food resources. CNVR identified on at least 15% of individuals were considered CNVR hotspots and further overlapped with previously reported quantitative trait loci (QTL). CNVR hotspots spanning genes putatively involved with lipid metabolism (SKP1, TCF7, JADE2, UBE2B and SAR1B) and differential expression in mammary gland (SEC24A and CDKN2AIPNL) on OAR5 and dairy traits (CCDC198 and SLC35F4) on OAR7 overlapped with QTL associated with lipid metabolism, milk protein yield and milk fat percentage. Information obtained from local sheep populations naturally adapted to harsh environments contributes to increase our understanding of the genomic importance of CNV.
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Affiliation(s)
- Félix Goyache
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
| | - Iván Fernández
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
| | | | | | | | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA, Gijón, Spain
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Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations. Animals (Basel) 2020; 10:ani10061040. [PMID: 32560248 PMCID: PMC7341319 DOI: 10.3390/ani10061040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes and are known to be present in genomic regions that regulate important physiological functions. In this study, CNV detection was performed starting from genotypic data of 120 individuals, belonging to four Sicilian dairy goat breeds, genotyped with the Illumina GoatSNP50 BeadChip array. Using PennCNV software, a total of 702 CNVs were identified in 107 individuals. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair. Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs, which are involved in local adaptation, mild behaviour, immune response, reproduction, and olfactory receptors. This study provides insights into the genomic variations within these Italian goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits. Abstract Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits.
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Yao YF, Lyu S, Wang X, Zhang Z, Qu K, Xu J, Cai C, Li Z, Xie J, Ru B, Xu Z, Wang E, Lei C, Chen H, Huang B, Huang Y. The combination between NCSTN gene copy number variation and growth traits in Chinese cattle. Anim Biotechnol 2020; 32:683-687. [PMID: 32208881 DOI: 10.1080/10495398.2020.1741382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Copy number variation (CNV) has been used as an important source of phenotypic and genetic diversity in recent years. Nicastrin (NCSTN) gene is usually attached to human diseases such as Alzheimer's disease, and Acne inversa. However, there are no essays about the NCSTN gene combining with cattle breeds. In our study, we discovered different distributions of NCSTN gene copy number and associated it with phenotypic traits in four Chinese yellow cattle breeds (XN, PN, QC and YL). The result turned out that the CNV of the NCSTN gene was associated with several growth traits, such as cannon circumference, chest girth and rump length (p < 0.05). In general, we revealed the eminence over CNV of NCSTN gene and economic traits, suggesting that the CNV of the NCSTN gene can be considered to be a promising molecular breeding marker of Chinese beef cattle.
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Affiliation(s)
- Yu-Fei Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, People's Republic of China
| | - Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Cuicui Cai
- Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, People's Republic of China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Jianliang Xie
- Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Di Gerlando R, Sutera AM, Mastrangelo S, Tolone M, Portolano B, Sottile G, Bagnato A, Strillacci MG, Sardina MT. Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS One 2019; 14:e0215204. [PMID: 31013280 PMCID: PMC6478285 DOI: 10.1371/journal.pone.0215204] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 03/28/2019] [Indexed: 11/19/2022] Open
Abstract
Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
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Affiliation(s)
- Rosalia Di Gerlando
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Anna Maria Sutera
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Salvatore Mastrangelo
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Marco Tolone
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Baldassare Portolano
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
| | - Gianluca Sottile
- Università degli Studi di Palermo, Dipartimento di Scienze Economiche, Aziendali e Statistiche, Italy
| | - Alessandro Bagnato
- Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, Italy
| | | | - Maria Teresa Sardina
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie, Alimentari e Forestali, Italy
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Diversity of copy number variation in the worldwide goat population. Heredity (Edinb) 2018; 122:636-646. [PMID: 30401973 DOI: 10.1038/s41437-018-0150-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/09/2018] [Accepted: 09/18/2018] [Indexed: 11/08/2022] Open
Abstract
Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.
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