1
|
Sa P, Gòdia M, Lewis N, Lian Y, Clop A. Genomic, transcriptomic and epigenomic analysis towards the understanding of porcine semen quality traits. Past, current and future trends. Anim Reprod Sci 2024:107543. [PMID: 38981797 DOI: 10.1016/j.anireprosci.2024.107543] [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: 05/10/2024] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
The importance of boar reproductive traits, including semen quality, in the sustainability of pig production system is increasingly being acknowledged by academic and industrial sectors. Research is needed to understand the biology and genetic components underlying these traits so that they can be incorporated into selection schemes and managerial decisions. This article reviews our current understanding of genome biology and technologies for genome, transcriptome and epigenome analysis which now facilitate the identification of causal variants affecting phenotypes more than ever before. Genetic and transcriptomic analysis of candidate genes, Genome-Wide Association Studies, expression microarrays, RNA-Seq of coding and noncoding genes and epigenomic evaluations have been conducted to profile the molecular makeups of pig sperm. These studies have provided insightful information for a several semen-related parameters. Nonetheless, this research is still incipient. The spermatozoon harbors a reduced transcriptome and highly modified epigenome, and it is assumed to be transcriptionally silent for nuclear gene expression. For this reason, the extent to which the sperm's RNA and epigenome recapitulate sperm biology and function is unclear. Hence, we anticipate that single-cell level analyses of the testicle and other male reproductive organs, which can reveal active transcription and epigenomic profiles in cells influencing sperm quality, will gain popularity and markedly advance our understanding of sperm-related traits. Future research will delve deeper into sperm fertility, boar resilience to environmental changes or harsh conditions, especially in the context of global warming, and also in transgenerational inheritance and how the environment influences the sperm transcriptome and epigenome.
Collapse
Affiliation(s)
- Pedro Sa
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, the Netherlands
| | - Marta Gòdia
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, the Netherlands
| | - Nicole Lewis
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Yu Lian
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
| | - Alex Clop
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain; Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia, Spain.
| |
Collapse
|
2
|
Reyer H, Abou-Soliman I, Schulze M, Henne H, Reinsch N, Schoen J, Wimmers K. Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars. Genes (Basel) 2024; 15:382. [PMID: 38540441 PMCID: PMC10969825 DOI: 10.3390/genes15030382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/14/2024] Open
Abstract
Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches.
Collapse
Affiliation(s)
- Henry Reyer
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
| | - Ibrahim Abou-Soliman
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
- Department of Animal and Poultry Breeding, Desert Research Center, Cairo 11753, Egypt
| | - Martin Schulze
- Institute for Reproduction of Farm Animals Schönow, 16321 Bernau, Germany;
| | | | - Norbert Reinsch
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
| | - Jennifer Schoen
- Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
- Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (I.A.-S.); (N.R.); (K.W.)
- Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
| |
Collapse
|
3
|
Atrian-Afiani F, Berger B, Draxl C, Sölkner J, Mészáros G. Selective Sweeps in the Austrian Turopolje and Other Commercial Pig Populations. Animals (Basel) 2023; 13:3749. [PMID: 38136787 PMCID: PMC10741191 DOI: 10.3390/ani13243749] [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: 10/16/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection in the Turopolje breed. DPYD is associated with muscular development in pigs and other species and PTBP2 emerges as one of the potential genes linked to seminal characteristics. Furthermore, in the Large White breed, a number of genes were detected with the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In the Duroc breed, a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain, and other similar traits. Overall, our results have identified a number of genomic regions that are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds.
Collapse
Affiliation(s)
- Farzad Atrian-Afiani
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| | - Beate Berger
- Institut für Biologische Landwirtschaft und Biodiversität der Nutztiere, HBLFA Raumberg-Gumpenstein 2, 4600 Thalheim bei Wels, Austria;
| | - Christian Draxl
- Österreichische Schweineprüfanstalt GmbH, 2004 Streitdorf, Austria;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| | - Gábor Mészáros
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences, Vienna, 1180 Vienna, Austria; (F.A.-A.); (J.S.)
| |
Collapse
|
4
|
Fang X, Ye H, Zhang S, Guo L, Xu Y, Zhang D, Nie Q. Investigation of potential genetic factors for growth traits in yellow-feather broilers using weighted single-step genome-wide association study. Poult Sci 2023; 102:103034. [PMID: 37657249 PMCID: PMC10480639 DOI: 10.1016/j.psj.2023.103034] [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: 05/26/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/03/2023] Open
Abstract
Yellow-feather broilers take a large portion of poultry industry in China due to its meat characteristics. Improving the growth traits of yellow-feathered broilers will have great significance for the Chinese poultry market. The current study was designed to investigate the potential genetic factors using the weighted single-step genome-wide association study (wssGWAS) method, which takes consideration of more factors including pedigree, sex, environment and has more accuracy than traditional GWAS. The yellow-feather dwarf chickens from Wens Nanfang Poultry Breeding Co. Ltd. were revolved to recode 9 growth traits: Average daily gain (ADG), body weight (BW) at 45 d, 49 d, 56 d, 63 d, 70 d, 77 d, 84 d, 91 d for analysis. For the results, the region 4.63 to 5.03 Mb on chromosome 15, which was the QTL overlapped in BW45, BW49, BW56, BW63, BW84, might be the crucial genetic region for growth traits. Seven GO terms and 3 KEGG pathways, GO:0005200, GO:0005882, GO:0045111, GO:0099513, GO:0099081, GO:0099512, GO:0099080, KEGG:gga04020, KEGG:gga04540, KEGG:gga04210, were detected to relevant with growth traits. The genes enriched in these biological processes (NRAS, TUBB1, ADORA2B, NTRK3, NGF, TNNC2, F-KER, LOC429492, LOC431325, LOC431324, LOC396480) might have the function in growth of yellow-feather broilers.
Collapse
Affiliation(s)
- Xiang Fang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Haoqiang Ye
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Siyu Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Lijin Guo
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Yibin Xu
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Dexiang Zhang
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, & Lingnan Guangdong Laboratory of Agriculture, South China Agricultural University, & Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China.
| |
Collapse
|
5
|
Krupa E, Krupová Z, Žáková E, Bauer J, Moravčíková N, Vrtková I. An Assessment of the Genetic Parameters of Boars' Reproductive Traits. Genes (Basel) 2023; 14:2003. [PMID: 38002946 PMCID: PMC10671126 DOI: 10.3390/genes14112003] [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: 09/20/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
The aim of this study was to estimate genetic parameters for the reproductive traits of boars based on single-nucleotide polymorphism data. A total of 109,836 semen samples from 2249 boars were collected between 2010 and 2022. Five basic traits were assessed: sperm volume, sperm concentration, motility, number of abnormal sperm, and, for the first time for the local population, libido. In addition, two derived traits were assessed: total sperm count and number of functional sperm. Genetic parameters were estimated using the single-step genomic best linear unbiased prediction method (ssGBLUP). Dam and sire breeds were evaluated separately. The five basic traits were evaluated using five-trait models, while the two derived traits were evaluated using single-trait models. The heritability coefficients had lower values for all sperm quality traits with both methods. For the basic traits, the heritability ranged from 0.099 to 0.342. The greatest difference between dam and sire breeds was observed for the heritability of the sperm concentration trait (0.099 and 0.271, respectively). The heritability of the libido trait was twice as high for boars of sire breeds as it was for boars of dam breeds. The genetic parameters estimated with ssGBLUP can be used in routine genetic evaluations to improve the pig breeding process.
Collapse
Affiliation(s)
- Emil Krupa
- Institute of Animal Science, 10400 Prague, Czech Republic; (Z.K.); (E.Ž.)
| | - Zuzana Krupová
- Institute of Animal Science, 10400 Prague, Czech Republic; (Z.K.); (E.Ž.)
| | - Eliška Žáková
- Institute of Animal Science, 10400 Prague, Czech Republic; (Z.K.); (E.Ž.)
| | - Jiří Bauer
- Czech-Moravian Breeders Association, 25209 Hradistko, Czech Republic;
| | - Nina Moravčíková
- Institute of Nutrition and Genomics, Slovak University of Agriculture, 94901 Nitra, Slovakia;
| | - Irena Vrtková
- Department of Morphology, Physiology and Animal Genetics, Mendel University, Zemedelska 1, 61300 Brno, Czech Republic;
| |
Collapse
|
6
|
Hodge MJ, de Las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. QTLs and Candidate Genes Associated with Semen Traits in Merino Sheep. Animals (Basel) 2023; 13:2286. [PMID: 37508063 PMCID: PMC10376747 DOI: 10.3390/ani13142286] [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: 06/03/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Ram semen traits play a significant role in conception outcomes, which in turn may influence reproductive efficiency and the overall productivity and profitability of sheep enterprises. Since hundreds of ewes may be inseminated from a single ejaculate, it is important to evaluate semen quality prior to use in sheep breeding programs. Given that semen traits have been found to be heritable, genetic variation likely contributes to the variability observed in these traits. Identifying such genetic variants could provide novel insights into the molecular mechanisms underlying variability in semen traits. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with semen traits in Merino sheep. A genome-wide association study (GWAS) was undertaken using 4506 semen collection records from 246 Merino rams collected between January 2002 and May 2021. The R package RepeatABEL was used to perform a GWAS for semen volume, gross motility, concentration, and percent post-thaw motility. A total of 35 QTLs, located on 16 Ovis aries autosomes (OARs), were significantly associated with either of the four semen traits in this study. A total of 89, 95, 33, and 73 candidate genes were identified, via modified Bonferroni, within the QTLs significantly associated with volume, gross motility, concentration, and percent post-thaw motility, respectively. Among the candidate genes identified, SORD, SH2B1, and NT5E have been previously described to significantly influence spermatogenesis, spermatozoal motility, and high percent post-thaw motility, respectively. Several candidate genes identified could potentially influence ram semen traits based on existing evidence in the literature. As such, validation of these putative candidates may offer the potential to develop future strategies to improve sheep reproductive efficiency. Furthermore, Merino ram semen traits are lowly heritable (0.071-0.139), and thus may be improved by selective breeding.
Collapse
Affiliation(s)
- Marnie J Hodge
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia
| | - Sara de Las Heras-Saldana
- Animal Genetics and Breeding Unit, a Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW 2351, Australia
| | | | - Cyril P Stephen
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Sameer D Pant
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| |
Collapse
|