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Jiang W, Yang X, Zhu L, Yang Y, Liu C, Du Y, Wang Y, Niu L, Zhao Y, Liu Y, Gan M, Shen L, Zhu L. Genome-Wide Association Studies of Hair Whorl in Pigs. Genes (Basel) 2024; 15:1249. [PMID: 39457372 PMCID: PMC11506845 DOI: 10.3390/genes15101249] [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: 08/31/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/28/2024] Open
Abstract
BACKGROUND In pigs, a hair whorl refers to hairs that form a ring of growth around the direction of the hair follicle at the dorsal hip. In China, a hair whorl is considered a negative trait that affects marketing, and no studies have been conducted to demonstrate whether hair whorl affects pig performance and provide an explanation for its genetic basis. METHODS Performance-measured traits and slaughter-measured traits of hair whorl and non-hair whorl pigs were differentially analyzed, followed by genome-wide association analysis (GWAS) and copy number variation (CNV) methods to investigate the genetic basis of hair whorl in pigs. RESULTS Differential analysis of 2625 pigs (171 hair whorl and 2454 non-hair whorl) for performance measures showed that hair whorl and non-hair whorl pigs differed significantly (p < 0.05) in traits such as live births, total litter size, and healthy litter size (p < 0.05), while differential analysis of carcass and meat quality traits showed a significant difference only in the 45 min pH (p = 0.0265). GWAS identified 4 SNP loci significantly associated with the hair whorl trait, 2 of which reached genome-significant levels, and 23 candidate genes were obtained by annotation with the Ensembl database. KEGG and GO enrichment analyses showed that these genes were mainly enriched in the ErbB signaling, endothelial apoptosis regulation, and cell proliferation pathways. In addition, CNV analysis identified 652 differential genes between hair whorl and non-hair whorl pigs, which were mainly involved in the signal transduction, transcription factor activity, and nuclear and cytoplasmic-related pathways. CONCLUSIONS The candidate genes and copy number variation differences identified in this study provide a new theoretical basis for pig breeding efforts.
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Affiliation(s)
- Wenyu Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xidi Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Liangyu Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiting Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengming Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yong Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yihui Liu
- Sichuan Province General Station of Animal Husbandry, Chengdu 610066, China;
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (W.J.); (X.Y.); (L.Z.); (Y.Y.); (C.L.); (Y.D.); (Y.W.); (L.N.); (Y.Z.); (M.G.); (L.S.)
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Saif R, Mahmood T, Zia S, Henkel J, Ejaz A. Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat. Trop Anim Health Prod 2023; 55:331. [PMID: 37750990 DOI: 10.1007/s11250-023-03758-2] [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: 12/21/2022] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Population geneticists have long sought to comprehend various selection traces accumulated in the goat genome due to natural or human driven artificial selection through breeding practices, which led the wild animals to domestication, so understanding evolutionary process may helpful to utilize the full genetic potential of goat genome. METHODS AND RESULTS As a step forward to pinpoint the selection signals in Pakistani Dera-Din-Panah (DDP) goat, whole-genome pooled sequencing (n = 12) was performed, and 618,236,192 clean paired-end reads were mapped against ARS1 reference goat assembly. Five different selection signature statistics were applied using four site-frequency spectrum (SFS) methods (Tajima's D ([Formula: see text]), Fay and Wu's H ([Formula: see text]), Zeng's E ([Formula: see text]), [Formula: see text]) and one reduced local variability approach named pooled heterozygosity ([Formula: see text]). The under-selection regions were annotated with significant threshold values of [Formula: see text]≥4.7, [Formula: see text]≥6, [Formula: see text]≥2.5, Pool-HMM ≥ 12, and [Formula: see text]≥5 that resulted in accumulative 364 candidate gene hits. The highest genomic selection signals were observed on Chr. 4, 6, 10, 12, 15, 16, 18, 20, and 27 and harbor ADAMTS6, CWC27, RELN, MYCBP2, FGF14, STIM1, CFAP74, GNB1, CALML6, TMEM52, FAM149A, NADK, MMP23B, OPN3, FH, MFHAS1, KLKB1, RRM1, KMO, SPEF2, F11, KIT, KMO, ERI1, ATP8B4, and RHOG genes. Next, the validation of our captured genomic hits was also performed by more than one applied statistics which harbor meat production, immunity, and reproduction associated genes to strengthen our hypothesis of under-selection traits in this Pakistani goat breed. Furthermore, common candidate genes captured by more than one statistical method were subjected to gene ontology and KEGG pathway analysis to get insights of particular biological processes associated with this goat breed. CONCLUSION Current perception of genomic architecture of DDP goat provides a better understanding to improve its genetic potential and other economically important traits of medium to large body size, milk, and fiber production by updating the genomic insight driven breeding strategies to boost the livestock and agriculture-based economy of the country.
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Affiliation(s)
- Rashid Saif
- Department of Biotechnology, Qarshi University, Lahore, Pakistan.
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan.
| | - Tania Mahmood
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
| | - Saeeda Zia
- Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Lahore, Pakistan
| | - Jan Henkel
- MGZ-Medical Genetics Center, Munich, Germany
| | - Aniqa Ejaz
- Decode Genomics, Punjab University Employees Housing Scheme, Lahore, Pakistan
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Encina A, Ligero M, Sánchez-Guerrero MJ, Rodríguez-Sainz de los Terreros A, Bartolomé E, Valera M. Phenotypic and Genetic Study of the Presence of Hair Whorls in Pura Raza Español Horses. Animals (Basel) 2023; 13:2943. [PMID: 37760344 PMCID: PMC10525084 DOI: 10.3390/ani13182943] [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: 06/15/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses with circular hair whorls than with linear whorls. The heritability ranges obtained were, in general, medium-high for both circular whorls (0.20 to 0.90) and linear whorls (0.44 to 0.84). High positive correlations were found on the between left and right positions, indicating a tendency to symmetry in certain locations. The laterality of hair whorls was also evidenced, with the biggest concentration on the left-hand side, particularly in gray horses, showing circular whorls below the central line of eyes, which has been associated in a previous paper with a calmer and more docile temperament.
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Affiliation(s)
- Ana Encina
- Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain;
| | - Manuel Ligero
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | - María José Sánchez-Guerrero
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | | | - Ester Bartolomé
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | - Mercedes Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
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Colpitts J, McLoughlin PD, Poissant J. Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds. BMC Genomics 2022; 23:501. [PMID: 35820826 PMCID: PMC9275264 DOI: 10.1186/s12864-022-08729-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood species like the horse could provide information on the genetic health of those populations and offer insight into how such metrics compare between managed and unmanaged populations. Here we characterized ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable Island, Canada, using ~41 000 SNPs and contrasted results with those from 33 domestic breeds to assess the impacts of isolation on ROH abundance, length, distribution, and ROH islands. RESULTS ROH number, length, and ROH-based inbreeding coefficients (FROH) in Sable Island horses were generally greater than in domestic breeds. Short runs, which typically coalesce many generations prior, were more abundant than long runs in all populations, but run length distributions indicated more recent population bottlenecks in Sable Island horses. Nine ROH islands were detected in Sable Island horses, exhibiting very little overlap with those found in domestic breeds. Gene ontology (GO) enrichment analysis for Sable Island ROH islands revealed enrichment for genes associated with 3 clusters of biological pathways largely associated with metabolism and immune function. CONCLUSIONS This study indicates that Sable Island horses tend to be more inbred than their domestic counterparts and that most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift and highlight the value of this population as a reservoir of equine genetic variation. This research illustrates how ROH analyses can be applied to gain insights into the population history, genetic health, and divergence of wild or feral populations of conservation concern.
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Affiliation(s)
- Julie Colpitts
- Department of Biology, University of Saskatchewan, Saskatchewan, Canada.
| | | | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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Araujo AC, Carneiro PLS, Alvarenga AB, Oliveira HR, Miller SP, Retallick K, Brito LF. Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle. Genes (Basel) 2021; 13:17. [PMID: 35052358 PMCID: PMC8775055 DOI: 10.3390/genes13010017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 01/23/2023] Open
Abstract
Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.
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Affiliation(s)
- Andre C. Araujo
- Graduate Program in Animal Sciences, State University of Southwestern Bahia, Itapetinga 45700-000, Brazil;
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| | - Paulo L. S. Carneiro
- Department of Biology, State University of Southwest Bahia, Jequié 45205-490, Brazil;
| | - Amanda B. Alvarenga
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| | - Hinayah R. Oliveira
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Stephen P. Miller
- American Angus Association, Angus Genetics Inc., 3201 Frederick Ave, St. Joseph, MO 64506, USA; (S.P.M.); (K.R.)
| | - Kelli Retallick
- American Angus Association, Angus Genetics Inc., 3201 Frederick Ave, St. Joseph, MO 64506, USA; (S.P.M.); (K.R.)
| | - Luiz F. Brito
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
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