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Nonneman DJ, Lents CA. Functional genomics of reproduction in pigs: Are we there yet? Mol Reprod Dev 2023; 90:436-444. [PMID: 35704517 DOI: 10.1002/mrd.23625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.
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Affiliation(s)
- Dan J Nonneman
- United States Department of Agriculture, Agriculture Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Clay A Lents
- United States Department of Agriculture, Agriculture Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
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Johnson RK, Trenhaile-Grannemann MD, Moreno R, Ciobanu DC, Miller PS. Effects of restricting energy during the gilt development period on growth and reproduction of lines differing in lean growth rate: Responses in reproductive performance and longevity. J Anim Sci 2021; 100:6444302. [PMID: 34849984 DOI: 10.1093/jas/skab352] [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] [Received: 09/28/2021] [Accepted: 11/23/2021] [Indexed: 11/12/2022] Open
Abstract
Longevity and reproductive performance are economically important traits in the swine industry that are largely influenced by nutrition and other environmental factors. Reproductive performance and longevity through 4 parities was assessed in gilts of 2 genetic lines developed on ad libitum access to feed or restricted to 75% of ad libitum intake. A total of 661 gilts were used in a 2 x 2 factorial with half of the gilts allocated to an ad libitum diet (AL; n = 330), while the other half were energy restricted by 25% (R; n = 331) from 123 to 235 d of age. All gilts were sired by an industry maternal line. Dams of the gilts were from either a Large White by Landrace industry maternal line or Nebraska Selection Line 45X, producing gilts designated as W x L (n = 355) and L45X (n = 306), respectively. Daily estrus detection began at 140 d of age to obtain age at puberty (AP). Gilts (n = 510) were mated on their second or later estrus, beginning at 240 d of age. Sow weight and backfat were recorded at 110 d of gestation and weaning of each parity. Number of live-born, stillborn, and mummified pigs per litter and piglet birth and weaning weights were recorded through 4 parities. More L45X than W x L and more AL than R gilts reached puberty by 230 d of age (P < 0.01). Dietary treatment did not affect probability to produce parities 1 to 4 or any litter trait analyzed. The L45X females tended to be more likely to produce parities 1 (P < 0.08) and 3 (P < 0.06), while W x L had heavier litters at birth (P < 0.01) and weaning (P = 0.01). Treatment by parity interactions (P < 0.01) existed for weight and backfat prior to farrowing and backfat at weaning, and weight at weaning exhibited a line by treatment by parity interaction (P = 0.04) as R sows had lower weights and backfats in earlier parities, but caught up to AL sows in later parities. A treatment by parity interaction (P < 0.01) was also present for backfat loss from farrowing to weaning as R gilts lost less backfat than AL in parities 1 and 2, but more in parities 3 and 4. No significant differences were detected between lines or treatments for lifetime production traits. The populations of pigs and data presented here provide a framework for a diverse array of further studies. Alternative approaches to restrict energy have been assessed in addition to methods of marker-assisted and genomic selection for improvement of litter size and sow longevity.
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Affiliation(s)
- R K Johnson
- Animal Science Department, University of Nebraska, Lincoln, NE 68583-0908, USA
| | | | - R Moreno
- Animal Science Department, University of Nebraska, Lincoln, NE 68583-0908, USA
| | - D C Ciobanu
- Animal Science Department, University of Nebraska, Lincoln, NE 68583-0908, USA
| | - P S Miller
- Animal Science Department, University of Nebraska, Lincoln, NE 68583-0908, USA
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Zamorano-Algandar R, Sánchez-Castro MA, Hernández-Cordero AI, Enns RM, Speidel SE, Thomas MG, Medrano JF, Rincón G, Leyva-Corona JC, Luna-Nevárez G, Reyna-Granados JR, Luna-Nevárez P. Molecular marker prediction for days open and pregnancy rate in Holstein cows managed in a warm climate. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Nonneman D, Lents CA, Rempel LA, Rohrer GA. Potential functional variants in AHR signaling pathways are associated with age at puberty in swine. Anim Genet 2021; 52:284-291. [PMID: 33667011 DOI: 10.1111/age.13051] [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: 02/05/2021] [Indexed: 12/31/2022]
Abstract
Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.
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Affiliation(s)
- Dan Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Clay A Lents
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Lea A Rempel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Gary A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
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Wijesena HR, Lents CA, Riethoven JJ, Trenhaile-Grannemann MD, Thorson JF, Keel BN, Miller PS, Spangler ML, Kachman SD, Ciobanu DC. GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows1,2. J Anim Sci 2017. [DOI: 10.2527/jas.2016.1334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- H. R. Wijesena
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - C. A. Lents
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933
| | - J.-J. Riethoven
- Center for Biotechnology, University of Nebraska, Lincoln 68583
| | | | - J. F. Thorson
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933
| | - B. N. Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933
| | - P. S. Miller
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - M. L. Spangler
- Department of Animal Science, University of Nebraska, Lincoln 68583
| | - S. D. Kachman
- Department of Statistics, University of Nebraska, Lincoln 68583
| | - D. C. Ciobanu
- Department of Animal Science, University of Nebraska, Lincoln 68583
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Panasiewicz G, Bieniek-Kobuszewska M, Lipka A, Majewska M, Jedryczko R, Szafranska B. Novel effects of identified SNPs within the porcine Pregnancy-Associated Glycoprotein gene family (pPAGs) on the major reproductive traits in Hirschmann hybrid-line sows. Res Vet Sci 2017; 114:123-130. [PMID: 28371694 DOI: 10.1016/j.rvsc.2017.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/18/2017] [Accepted: 03/27/2017] [Indexed: 02/07/2023]
Abstract
This is the first study describing identification of SNPs within the multiple and polymorphic Pregnancy-Associated Glycoprotein gene family (PAGs) in the genome of the domestic pig (pPAGs). We identified pPAG-like (pPAG-L) genotypes in primiparous and multiparous farmed hybrid-line JSR Hirschmann (Hrn) sows (N=159), in which various novel associations with their phenotypes for the major reproductive traits have been discovered. Genomic DNA templates were isolated from the blood and different pPAG-L primers were used to amplify various regions by PCR. Electrophoretically-separated amplicons were selected, purified and sequenced. All identified SNPs were verified for possible pPAG2-L genotype associations with the major reproductive traits. In total, 196 SNPs were identified within the entire structure of the pPAG2-Ls, encompassing 9 exons and 8 (A-H) introns, resembling all aspartic proteinases. It was discovered that among all SNPs, one diplotype localized in exon 6 (657C>T/749G>C; pPAG2 ORF cDNA numbering; L34361) caused amino acid substitutions (Asp220→Asn and Ser250→Thr) in the polypeptide precursors and was associated with an increase in the number of live-born piglets (P≤0.05) in Hrn sows. In turn, co-localized SNP (504g>a; KF537535 numbering) in the intron F of the pPAG2-Ls, but only in the homozygotic genotype (gg), was associated with an increased number of live-born (P≤0.01) and weaned (P≤0.05) piglets in the Hrn sows. These results qualify the pPAG2-Ls as candidate genes of the main QTLs. The novel pPAG SNP profiles provide the basis for a diagnostic genotyping test required for early pre-selection of female/male piglets, presumably mainly useful in various breeding herds.
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Affiliation(s)
- Grzegorz Panasiewicz
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719 Olsztyn-Kortowo, Poland.
| | - Martyna Bieniek-Kobuszewska
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719 Olsztyn-Kortowo, Poland; Department of Dermatology, Sexually Transmitted Diseases and Clinical Immunology, Faculty of Medical Sciences, University of Warmia and Mazury in Olsztyn, ul. Wojska Polskiego 30, 10-229 Olsztyn, Poland
| | - Aleksandra Lipka
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719 Olsztyn-Kortowo, Poland
| | - Marta Majewska
- Department of Human Physiology, Faculty of Medical Sciences, University of Warmia and Mazury in Olsztyn, ul. Warszawska 30, 10-082 Olsztyn, Poland
| | | | - Bozena Szafranska
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 1A, 10-719 Olsztyn-Kortowo, Poland
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Samorè AB, Fontanesi L. Genomic selection in pigs: state of the art and perspectives. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1080/1828051x.2016.1172034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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