1
|
Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection. Animals (Basel) 2022; 12:ani12111423. [PMID: 35681887 PMCID: PMC9179914 DOI: 10.3390/ani12111423] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Fatness-related traits are economically very important in sheep production and are associated with serious diseases in humans. Using a denser set of SNP markers and a variety of statistical approaches, our results were able to refine the regions associated with fat deposition and to suggest new insights into molecular aspects of fat tail selection. These results may provide a strong foundation for studying the regulation of fat deposition in sheep and do offer hope that the causal mutations and the mode of inheritance of this trait will soon be discovered by further investigation. Abstract The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (FST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR, EBP, CACNA1F, HSD17B10,SLC35A2, BMP15, WDR13, and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive assessment of how and where selection has affected the patterns of variation in candidate regions associated with fat deposition in thin and fat tail sheep breeds.
Collapse
|
2
|
Tan X, Liu R, Li W, Zheng M, Zhu D, Liu D, Feng F, Li Q, Liu L, Wen J, Zhao G. Assessment the effect of genomic selection and detection of selective signature in broilers. Poult Sci 2022; 101:101856. [PMID: 35413593 PMCID: PMC9018145 DOI: 10.1016/j.psj.2022.101856] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/01/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Due to high selection advances and shortened generation interval, genomic selection (GS) is now an effective animal breeding scheme. In broilers, many studies have compared the accuracy of different GS prediction methods, but few reports have demonstrated phenotypic or genetic changes using GS. In this study, the paternal chicken line B underwent continuous selection for 3 generations. The chicken 55 k SNP chip was used to estimate the genetic parameters and detect genomic response regions by selective sweep analysis. The heritability for body weight (BW), meat production, and abdominal fat traits were ranged from 0.12 to 0.38. A high genetic correlation was found between BW and meat production traits, while a low genetic correlation (<0.1) was found between meat production and abdominal fat traits. Selection resulted in an increase of about 516 g in BW and 140 g in breast muscle weight. Percentage of breast muscle and whole thigh were increased 0.8 to 1.5%. No change was observed in abdominal fat percentage. The genomic estimated breeding value advances was positive for BW and meat production (except whole thigh percentage), while negative for abdominal fat percentage. By selective sweep analysis, 39 common chromosomal regions and 102 protein coding genes were found to be influenced, including MYH1A, MYH1B, and MYH1D of the MYH gene family. Tight junction pathway as well as myosin complex related terms were enriched. This study demonstrates the effective use of GS for improvements in BW and meat production in chicken line B. Further, genomic regions, responsive to intensive genetic selection, were identified to contain genes of the MYH family.
Collapse
|
3
|
Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
Collapse
Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
4
|
Hume DA, Gutowska‐Ding MW, Garcia‐Morales C, Kebede A, Bamidele O, Trujillo AV, Gheyas AA, Smith J. Functional evolution of the colony‐stimulating factor 1 receptor (CSF1R) and its ligands in birds. J Leukoc Biol 2019; 107:237-250. [DOI: 10.1002/jlb.6ma0519-172r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/02/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Affiliation(s)
- David A. Hume
- Mater Research Institute‐University of Queensland Translational Research Institute Woolloongabba QLD 4102 Australia
| | | | - Carla Garcia‐Morales
- Department Biotecnologia Universidad Automona del Estado de Mexico Toluca Area Mexico
| | - Adebabay Kebede
- Department of Microbial, Cellular and Molecular Biology Addis Ababa University Addis Ababa Ethiopia
- Amhara Regional Agricultural Research Institute Bahir Dar Ethiopia
- International Livestock Research Institution (ILRI) Addis Ababa Ethiopia
| | - Oladeji Bamidele
- African Chicken Genetic Gains Project‐Nigeria The International Livestock Research Institute (ILRI) Addis Ababa Ethiopia
| | - Adriana Vallejo Trujillo
- Cells, Organisms and Molecular Genetics, School of Life Sciences University of Nottingham Nottingham United Kingdom
| | - Almas A. Gheyas
- The Roslin Institute University of Edinburgh Midlothian United Kingdom
- Centre for Tropical Livestock Genetics and Health University of Edinburgh Midlothian United Kingdom
| | - Jacqueline Smith
- The Roslin Institute University of Edinburgh Midlothian United Kingdom
- Centre for Tropical Livestock Genetics and Health University of Edinburgh Midlothian United Kingdom
| |
Collapse
|
5
|
Zhu C, Li M, Qin S, Zhao F, Fang S. Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:1378-1386. [PMID: 31480185 PMCID: PMC7468164 DOI: 10.5713/ajas.18.0661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/17/2019] [Indexed: 01/08/2023]
Abstract
Objective Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types. Methods In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays. Results In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system. Conclusion The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.
Collapse
Affiliation(s)
- Caiye Zhu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Mingna Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shizhen Qin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fuping Zhao
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Suli Fang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| |
Collapse
|
6
|
Johnsson M. Integrating Selection Mapping With Genetic Mapping and Functional Genomics. Front Genet 2018; 9:603. [PMID: 30619447 PMCID: PMC6295561 DOI: 10.3389/fgene.2018.00603] [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: 04/02/2018] [Accepted: 11/19/2018] [Indexed: 01/23/2023] Open
Abstract
Genomic scans for signatures of selection allow us to, in principle, detect variants and genes that underlie recent adaptations. By combining selection mapping with genetic mapping of traits known to be relevant to adaptation, we can simultaneously investigate whether genes and variants show signals of recent selection and whether they impact traits that have likely been selected. There are three ways to integrate selection mapping with genetic mapping or functional genomics: (1) To use genetic mapping data from other populations as a form of genome annotation. (2) To perform experimental evolution or artificial selection to be able to study selected variants when they segregate, either by performing genetic mapping before selection or by crossing the selected individuals to some reference population. (3) To perform a comparative study of related populations facing different selection regimes. This short review discusses these different ways of integrating selection mapping with genetic mapping and functional genomics, with examples of how each has been done.
Collapse
Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
7
|
Drobik-Czwarno W, Wolc A, Fulton JE, Jankowski T, Arango J, O’Sullivan NP, Dekkers JCM. Genetic basis of resistance to avian influenza in different commercial varieties of layer chickens. Poult Sci 2018; 97:3421-3428. [DOI: 10.3382/ps/pey233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
|
8
|
Hudson NJ, Hawken RJ, Okimoto R, Sapp RL, Reverter A. Data compression can discriminate broilers by selection line, detect haplotypes, and estimate genetic potential for complex phenotypes. Poult Sci 2018. [PMID: 28633351 DOI: 10.3382/ps/pex151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers. Our approach is based on the concept of data compression from information theory. Using the real-world compressor gzip to estimate normalized compression distance (NCD) we have built compression-based relationship matrices (CRM) for 988 chickens from 4 commercial broiler lines-2 male and 2 female lines. For all pairs of individuals, we found a strong negative relationship between the commonly used genomic relationship matrix (GRM) and NCD. This reflects the fact that "similarity" is the inverse of "distance." The CRM explained more genetic variation than the corresponding GRM in 2 of 3 phenotypes, with corresponding improvements in accuracy of genomic-enabled predictions of breeding value. A sliding-window version of the analysis highlighted haplotype regions of the genome apparently under selection in a line-specific manner. In the male lines, we retrieved high population-specific scores for IGF-1 and a cognate receptor, INSR. For the female lines, we detected an extreme score for a region containing a reproductive hormone receptor (GNRHR). We conclude that our compression-based method is a valid approach to established relationships and identify regions under selective pressure in commercial lines of broiler chickens.
Collapse
Affiliation(s)
- N J Hudson
- School of Agriculture and Food Science, University of Queensland, Gatton Campus, Queensland 4343, Australia
| | - R J Hawken
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | - R Okimoto
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | - R L Sapp
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | - A Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Brisbane, Queensland 4067, Australia.
| |
Collapse
|
9
|
Boschiero C, Moreira GCM, Gheyas AA, Godoy TF, Gasparin G, Mariani PDSC, Paduan M, Cesar ASM, Ledur MC, Coutinho LL. Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines. BMC Genomics 2018; 19:83. [PMID: 29370772 PMCID: PMC5785814 DOI: 10.1186/s12864-018-4444-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 01/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. Results A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. Conclusions In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry. Electronic supplementary material The online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Clarissa Boschiero
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil. .,Noble Reserch Institute, 2510 Sam Noble Parkway, Ardmore, Oklahoma, 73401, USA.
| | - Gabriel Costa Monteiro Moreira
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Almas Ara Gheyas
- Department of Genetics and Genomics, The Roslin Institute and Royal School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Thaís Fernanda Godoy
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Gustavo Gasparin
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Pilar Drummond Sampaio Corrêa Mariani
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Marcela Paduan
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | - Aline Silva Mello Cesar
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| | | | - Luiz Lehmann Coutinho
- Animal Biotechnology Laboratory, Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, 13418-900, Brazil
| |
Collapse
|
10
|
Gutiérrez-Gil B, Esteban-Blanco C, Wiener P, Chitneedi PK, Suarez-Vega A, Arranz JJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds. Genet Sel Evol 2017; 49:81. [PMID: 29115919 PMCID: PMC5674817 DOI: 10.1186/s12711-017-0354-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/19/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. RESULTS Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. CONCLUSIONS Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.
Collapse
Affiliation(s)
- Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
- Fundación Centro Supercomputación de Castilla y León, Campus de Vegazana, León, 24071 Spain
| | - Pamela Wiener
- Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG UK
| | - Praveen Krishna Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Aroa Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| | - Juan-Jose Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071 Spain
| |
Collapse
|
11
|
Wiener P, Sánchez-Molano E, Clements DN, Woolliams JA, Haskell MJ, Blott SC. Genomic data illuminates demography, genetic structure and selection of a popular dog breed. BMC Genomics 2017; 18:609. [PMID: 28806925 PMCID: PMC5557481 DOI: 10.1186/s12864-017-3933-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/09/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever. RESULTS We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient. CONCLUSIONS This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.
Collapse
Affiliation(s)
- Pamela Wiener
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Enrique Sánchez-Molano
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - Dylan N. Clements
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | - John A. Woolliams
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Scotland UK
| | | | | |
Collapse
|
12
|
Stainton JJ, Charlesworth B, Haley CS, Kranis A, Watson K, Wiener P. Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens. J Anim Breed Genet 2017; 134:87-97. [PMID: 27349343 PMCID: PMC5363361 DOI: 10.1111/jbg.12228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022]
Abstract
The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high-density SNP data from a broiler chicken line to detect low-diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these 'regression regions', including IGF1, GPD2 and MTNR1AI. The results suggest that the identification of zero-diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.
Collapse
Affiliation(s)
- J J Stainton
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - B Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - C S Haley
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - A Kranis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.,Aviagen Ltd, Edinburgh, UK
| | | | - P Wiener
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
13
|
Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
14
|
Fleming DS, Koltes JE, Markey AD, Schmidt CJ, Ashwell CM, Rothschild MF, Persia ME, Reecy JM, Lamont SJ. Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array. BMC Genomics 2016; 17:407. [PMID: 27230772 PMCID: PMC4882793 DOI: 10.1186/s12864-016-2711-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
Background Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study’s goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. Results Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. Conclusions The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2711-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - J E Koltes
- Iowa State University, Ames, IA, USA.,University of Arkansas, Fayetteville, AR, USA
| | | | | | - C M Ashwell
- North Carolina State University, Raleigh, NC, USA
| | | | - M E Persia
- Virginia Polytechnic University, Blacksburg, VA, USA
| | - J M Reecy
- Iowa State University, Ames, IA, USA
| | | |
Collapse
|
15
|
Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds. Int J Mol Sci 2015; 16:20360-74. [PMID: 26343642 PMCID: PMC4613208 DOI: 10.3390/ijms160920360] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 12/24/2022] Open
Abstract
Artificial selection has played a critical role in animal breeding. Detection of artificial selection footprints in genomic regions can provide insights for understanding the function of specific phenotypic traits and better guide animal breeding. To more fully understand the relationship between genomic composition and phenotypic diversity arising from breed development, a genome-wide scan was conducted using an OvineSNP50 BeadChip and integrated haplotype score and fixation index analyses to detect selection signatures on the X chromosome in three sheep breeds. We identified 49, 34, and 55 candidate selection regions with lengths of 27.49, 16.47, and 25.42 Mb in German Mutton, Dorper, and Sunit sheep, respectively. Bioinformatics analysis showed that some of the genes in these regions with selection signatures, such as BMP15, were relevant to reproduction. We also identified some selection regions harboring genes that had human orthologs, including BKT, CENPI, GUCY2F, MSN, PCDH11X, PLP1, VSIG4, PAK3, WAS, PCDH19, PDHA1, and SRPX2. The VSIG4 and PCDH11X genes are associated with the immune system and disease, PDHA1 is associated with biosynthetic related pathways, and PCDH19 is expressed in the nervous system and skin. These genes may be useful as candidate genes for molecular breeding.
Collapse
|