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Reimer C, Rubin CJ, Sharifi AR, Ha NT, Weigend S, Waldmann KH, Distl O, Pant SD, Fredholm M, Schlather M, Simianer H. Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. BMC Genomics 2018; 19:687. [PMID: 30231878 PMCID: PMC6146782 DOI: 10.1186/s12864-018-5009-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/14/2018] [Indexed: 12/30/2022] Open
Abstract
Background Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in “SweepFinder”, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region. Electronic supplementary material The online version of this article (10.1186/s12864-018-5009-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany. .,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.
| | - C-J Rubin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala Biomedicinska centrum BMC, Husargatan 3, 75237, Uppsala, Sweden
| | - A R Sharifi
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - N-T Ha
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - S Weigend
- Institute of Farm Animal Genetics of the Friedrich-Loeffler-Institut, Höltystraße 10, 31535, Neustadt-Mariensee, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - K-H Waldmann
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine - Foundation, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - O Distl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine - Foundation, Bünteweg 17p, 30559, Hannover, Germany
| | - S D Pant
- Graham Centre for Agricultural Innovation, School of Animal & Veterinary Sciences, Charles Sturt University, Locked Bag 588, Boorooma St., Wagga Wagga, NSW, Australia
| | - M Fredholm
- Department of Veterinary- and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
| | - M Schlather
- School of Business Informatics and Mathematics, University of Mannheim, A5 6, 68131, Mannheim, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - H Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
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Fortes MRS, Lehnert SA, Bolormaa S, Reich C, Fordyce G, Corbet NJ, Whan V, Hawken RJ, Reverter A. Finding genes for economically important traits: Brahman cattle puberty. ANIMAL PRODUCTION SCIENCE 2012. [DOI: 10.1071/an11165] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Age at puberty is an important component of reproductive performance in beef cattle production systems. Brahman cattle are typically late-pubertal relative to Bos taurus cattle and so it is of economic relevance to select for early age at puberty. To assist selection and elucidate the genes underlying puberty, we performed a genome-wide association study (GWAS) using the BovineSNP50 chip (~54 000 polymorphisms) in Brahman bulls (n = 1105) and heifers (n = 843) and where the heifers were previously analysed in a different study. In a new attempt to generate unbiased estimates of single-nucleotide polymorphism (SNP) effects and proportion of variance explained by each SNP, the available data were halved on the basis of year and month of birth into a calibration and validation set. The traits that defined age at puberty were, in heifers, the age at which the first corpus luteum was detected (AGECL, h2 = 0.56 ± 0.11) and in bulls, the age at a scrotal circumference of 26 cm (AGE26, h2 = 0.78 ± 0.10). At puberty, heifers were on average older (751 ± 142 days) than bulls (555 ± 101 days), but AGECL and AGE26 were genetically correlated (r = 0.20 ± 0.10). There were 134 SNPs associated with AGECL and 146 SNPs associated with AGE26 (P < 0.0001). From these SNPs, 32 (~22%) were associated (P < 0.0001) with both traits. These top 32 SNPs were all located on Chromosome BTA 14, between 21.95 Mb and 28.4 Mb. These results suggest that the genes located in that region of BTA 14 play a role in pubertal development in Brahman cattle. There are many annotated genes underlying this region of BTA 14 and these are the subject of current research. Further, we identified a region on Chromosome X where markers were associated (P < 1.00E–8) with AGE26, but not with AGECL. Information about specific genes and markers add value to our understanding of puberty and potentially contribute to genomic selection. Therefore, identifying these genes contributing to genetic variation in AGECL and AGE26 can assist with the selection for early onset of puberty.
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Masopust M, Vykoukalová Z, Knoll A, Bartenschlager H, Mileham A, Deeb N, Rohrer GA, Cepica S. Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study. Mol Biol Rep 2010; 38:2611-7. [PMID: 21104145 DOI: 10.1007/s11033-010-0402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 11/08/2010] [Indexed: 01/28/2023]
Abstract
Using PCR and inverse PCR techniques we obtained a 4,498 bp nucleotide sequence FN424076 encompassing the complete coding sequence of the porcine insulin receptor substrate 4 (IRS4) gene and its proximal promoter. The 1,269 amino acid porcine protein deduced from the nucleotide sequence shares 92% identity with the human IRS4 and possesses the same domains and the same number of tyrosine phosphorylation motifs as the human protein. We detected substitution FN424076:g.96C<G in the promoter region that segregates in Meishan and a synonymous substitution FN424076:g.1829T<C in the coding sequence with allele C present only in Meishan. Linkage mapping placed the IRS4 gene at position 82 cM on the current USDA-USMARC linkage map of porcine chromosome X. Association analyses were performed on 555 animals of 12th-15th generation of the Meishan × Large White cross and showed that both SNPs were highly significantly associated with backfat depth (P=0.0005) and that the SNP FN424076:g1829T<C was also associated with loin depth (P=0.017). The Meishan alleles increased back fat depth and decreased loin depth. IRS4 can be considered a positional candidate gene for at least some of the QTL located at the centromeric region of porcine chromosome X.
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Affiliation(s)
- Martin Masopust
- Institute of Animal Physiology and Genetics AS CR, v.v.i., Liběchov, Czech Republic
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Cepica S, Bartenschlager H, Geldermann H. Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map. Anim Genet 2007; 38:634-8. [PMID: 17931399 DOI: 10.1111/j.1365-2052.2007.01661.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar x Meishan F2family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F-ratio values for all QTL. Maxima of F-ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.
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Affiliation(s)
- S Cepica
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic.
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Lin C, Tholen E, Jennen D, Ponsuksili S, Schellander K, Wimmers K. Evidence for Effects of Testis and Epididymis Expressed Genes on Sperm Quality and Boar Fertility Traits. Reprod Domest Anim 2006; 41:538-43. [PMID: 17107514 DOI: 10.1111/j.1439-0531.2006.00710.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Retinol-binding protein 4 (RBP4), androgen receptor (AR), relaxin (RLN), acrosin (ACR) and osteopontin (polymorphism in intron 6 named OPNin6; polymorphism in promoter region named OPNprom) were addressed as functional candidate genes for sperm quality and boar fertility and investigated for their association with sperm concentration, motility, semen volume per ejaculate, plasma droplets rate, abnormal spermatozoa rate as well as non-return rate and number of piglets born alive. Therefore 356 AI boars of the purebred Pietrain (PI) and crossbred Pietrain x Hampshire (PI x HA) were genotyped at these loci. Analysis of variance revealed significant associations of RBP4 (p < 0.05), ACR (p < 0.01), and OPNin6 (p < 0.05) with sperm motility. OPNin6 (p < 0.05) was also associated with number of piglets born alive. Moreover, AR (p < 0.05) and OPNprom (p < 0.05) were significantly associated with abnormal spermatozoa rate. For RLN (p < 0.01) there was evidence for effects on sperm volume and ACR significantly affected sperm concentration (p < 0.05) as well as non-return rate (p < 0.05). No significant effects of any locus on plasma droplets rate were observed.
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Affiliation(s)
- C Lin
- Animal Breeding and Husbandry group, Institute of Animal Science, University of Bonn, Bonn, Germany
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