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Sarakul M, Elzo MA, Koonawootrittriron S, Suwanasopee T, Jattawa D, Laodim T. A comparison of five sets of overlapping and non-overlapping sliding windows for semen production traits in the Thai multibreed dairy population. Anim Biosci 2024; 37:428-436. [PMID: 37946424 PMCID: PMC10915195 DOI: 10.5713/ab.23.0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/03/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population. METHODS The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows. RESULTS Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population. CONCLUSION This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.
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Affiliation(s)
- Mattaneeya Sarakul
- Department of Animal Science, Nakhon Phanom University, Nakhon Phanom, 48000,
Thailand
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611-0910,
USA
| | | | | | - Danai Jattawa
- Department of Animal Science, Kasetsart University, Bangkok 10900,
Thailand
| | - Thawee Laodim
- Department of Animal Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140,
Thailand
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Cesarani A, Corte Pause F, Hidalgo J, Garcia A, Degano L, Vicario D, Macciota NPP, Stradaioli G. Genetic background of semen parameters in Italian Simmental bulls. ITALIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1080/1828051x.2022.2160665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Francesca Corte Pause
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Andre Garcia
- Angus Genetics Inc. - American Angus Association, Saint Joseph, MO, USA
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | | | - Giuseppe Stradaioli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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EL Nagar AG, Salem MMI, Amin AMS, Khalil MH, Ashour AF, Hegazy MM, Abdel-Shafy H. A Single-Step Genome-Wide Association Study for Semen Traits of Egyptian Buffalo Bulls. Animals (Basel) 2023; 13:3758. [PMID: 38136796 PMCID: PMC10740893 DOI: 10.3390/ani13243758] [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: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom® Buffalo Genotyping 90 K array designed by the Affymetrix Expert Design Program. After conducting a quality assessment, we utilized 67,282 SNPs genotyped in 192 animals. We identified several genomic loci explaining high genetic variance by employing single-step genomic evaluation. The aforementioned regions were located on buffalo chromosomes no. 3, 4, 6, 7, 14, 16, 20, 22, and the X-chromosome. The X-chromosome exhibited substantial influence, accounting for 4.18, 4.59, 5.16, 5.19, and 4.31% of the genomic variance for ejaculate volume, mass motility, livability, abnormality, and concentration, respectively. In the examined genomic regions, we identified five novel candidate genes linked to male fertility and spermatogenesis, four in the X-chromosome and one in chromosome no. 16. Additional extensive research with larger sample sizes and datasets is imperative to validate these findings and evaluate their applicability for genomic selection.
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Affiliation(s)
- Ayman G. EL Nagar
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt;
| | - Mohamed M. I. Salem
- Department of Animal and Fish Production, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria 21545, Egypt;
| | - Amin M. S. Amin
- Animal Production Research Institute, Agricultural Research Center, Dokki, Giza 12619, Egypt; (A.M.S.A.); (A.F.A.); (M.M.H.)
| | - Maher H. Khalil
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt;
| | - Ayman F. Ashour
- Animal Production Research Institute, Agricultural Research Center, Dokki, Giza 12619, Egypt; (A.M.S.A.); (A.F.A.); (M.M.H.)
| | - Mohammed M. Hegazy
- Animal Production Research Institute, Agricultural Research Center, Dokki, Giza 12619, Egypt; (A.M.S.A.); (A.F.A.); (M.M.H.)
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, El-Gamma Street, Giza 12613, Egypt;
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Ramirez-Diaz J, Cenadelli S, Bornaghi V, Bongioni G, Montedoro SM, Achilli A, Capelli C, Rincon JC, Milanesi M, Passamonti MM, Colli L, Barbato M, Williams JL, Marsan PA. Identification of genomic regions associated with total and progressive sperm motility in Italian Holstein bulls. J Dairy Sci 2023; 106:407-420. [PMID: 36400619 DOI: 10.3168/jds.2021-21700] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/10/2022] [Indexed: 11/17/2022]
Abstract
Sperm motility is directly related to the ability of sperm to move through the female reproductive tract to reach the ovum. Sperm motility is a complex trait that is influenced by environmental and genetic factors and is associated with male fertility, oocyte penetration rate, and reproductive success of cattle. In this study we carried out a GWAS in Italian Holstein bulls to identify candidate regions and genes associated with variations in progressive and total motility (PM and TM, respectively). After quality control, the final data set consisted of 5,960 records from 949 bulls having semen collected in 10 artificial insemination stations and genotyped at 412,737 SNPs (call rate >95%; minor allele frequency >5%). (Co)variance components were estimated using single trait mixed models, and associations between SNPs and phenotypes were assessed using a genomic BLUP approach. Ten windows that explained the greatest percentage of genetic variance were located on Bos taurus autosomes 1, 2, 4, 6, 7, 23, and 26 for TM and Bos taurus autosomes 1, 2, 4, 6, 8, 16, 23, and 26 for PM. A total of 150 genes for TM and 72 genes for PM were identified within these genomic regions. Gene Ontology enrichment analyses identified significant Gene Ontology terms involved with energy homeostasis, membrane functions, sperm-egg interactions, protection against oxidative stress, olfactory receptors, and immune system. There was significant enrichment of quantitative trait loci for fertility, calving ease, immune response, feed intake, and carcass weight within the candidate windows. These results contribute to understanding the architecture of the genetic control of sperm motility and may aid in the development of strategies to identify subfertile bulls and improve reproductive success.
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Affiliation(s)
- J Ramirez-Diaz
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122; Institute of Agricultural Biology and Biotechnology (IBBA), Consiglio Nazionale di Ricerca, Milano, Italy.
| | - S Cenadelli
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - V Bornaghi
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - G Bongioni
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - S M Montedoro
- Institute Lazzaro Spallanzani, Rivolta d'Adda (CR), Cremona, Italy
| | - A Achilli
- Department of Biology and Biotechnology, Università degli Studi di Pavia, Pavia, Italy
| | - C Capelli
- Department of Chemical, Life and Environmental Sustainability Sciences, Università degli Studi di Parma, Parma, Italy
| | - J C Rincon
- Department of Animal Science, Universidad Nacional de Colombia, Palmira, Valle del Cauca, Colombia
| | - M Milanesi
- Department for Innovation in Biological, Agri-food and Forestry Systems (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
| | - M M Passamonti
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - L Colli
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - M Barbato
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - J L Williams
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
| | - P Ajmone Marsan
- Department of Animal Sciences, Food and Nutrition (DIANA), Università Cattolica del Sacro Cuore, Piacenza, Italy 29122
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Duarte INH, Bessa AFDO, Rola LD, Genuíno MVH, Rocha IM, Marcondes CR, Regitano LCDA, Munari DP, Berry DP, Buzanskas ME. Cross-population selection signatures in Canchim composite beef cattle. PLoS One 2022; 17:e0264279. [PMID: 35363779 PMCID: PMC8975110 DOI: 10.1371/journal.pone.0264279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.
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Affiliation(s)
| | | | - Luciana Diniz Rola
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | - Iasmin Marques Rocha
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | | | - Danísio Prado Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Donagh Pearse Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy Co. Cork., Ireland
| | - Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- * E-mail:
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Candidate Genes in Bull Semen Production Traits: An Information Approach Review. Vet Sci 2022; 9:vetsci9040155. [PMID: 35448653 PMCID: PMC9028852 DOI: 10.3390/vetsci9040155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/05/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Semen quality plays a crucial role in the successful implementation of breeding programs, especially where artificial insemination (AI) is practiced. Bulls with good semen traits have good fertility and can produce a volume of high semen per ejaculation. The aim of this review is to use an information approach to highlight candidate genes and their relation to bull semen production traits. The use of genome-wide association studies (GWAS) has been demonstrated to be successful in identifying genomic regions and individual variations associated with production traits. Studies have reported over 40 genes associated with semen traits using Illumina BeadChip single-nucleotide polymorphism (SNPs).
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Vanvanhossou SFU, Scheper C, Dossa LH, Yin T, Brügemann K, König S. A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits. BMC Genomics 2020; 21:783. [PMID: 33176675 PMCID: PMC7656759 DOI: 10.1186/s12864-020-07170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. RESULTS SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). CONCLUSIONS Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.
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Affiliation(s)
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
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Paredes-Sánchez FA, Sifuentes-Rincón AM, Casas E, Arellano-Vera W, Parra-Bracamonte GM, Riley DG, Welsh TH, Randel RD. Novel genes involved in the genetic architecture of temperament in Brahman cattle. PLoS One 2020; 15:e0237825. [PMID: 32822435 PMCID: PMC7446865 DOI: 10.1371/journal.pone.0237825] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Cattle temperament is a complex and economically relevant trait. The objective of this study was to identify genomic regions and genes associated with cattle temperament. From a Brahman cattle population of 1,370 animals evaluated for temperament traits (Exit velocity-EV, Pen Score-PS, Temperament Score-TS), two groups of temperament-contrasting animals were identified based on their EV-average values ±1/2 standard deviation (SD). To be considered in the calm group, the EV of females ranged between 0.16–1.82 m/s (n = 50) and the EV of males ranged between 0.4–1.56 m/s (n = 48). Females were classified as temperamental if their EV ranged between 3.13–7.66 m/s (n = 46) and males were classified as temperamental if their EV ranged between 3.05–10.83 m/s (n = 45). Selected animals were genotyped using a total of 139,376 SNPs (GGP-HD-150K), evaluated for their association with EV. The Genome-Wide Association analysis (GWAS) identified fourteen SNPs: rs135340276, rs134895560, rs110190635, rs42949831, rs135982573, rs109393235, rs109531929, rs135087545, rs41839733, rs42486577, rs136661522, rs110882543, rs110864071, rs109722627, (P<8.1E-05), nine of them were located on intergenic regions, harboring seventeen genes, of which only ACER3, VRK2, FANCL and SLCO3A1 were considered candidate associated with bovine temperament due to their reported biological functions. Five SNPs were located at introns of the NRXN3, EXOC4, CACNG4 and SLC9A4 genes. The indicated candidate genes are implicated in a wide range of behavioural phenotypes and complex cognitive functions. The association of the fourteen SNPs on bovine temperament traits (EV, PS and TS) was evaluated; all these SNPs were significant for EV; only some were associated with PS and TS. Fourteen SNPs were associated with EV which allowed the identification of twenty-one candidate genes for Brahman temperament. From a functional point of view, the five intronic SNPs identified in this study, are candidates to address control of bovine temperament, further investigation will probe their role in expression of this trait.
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Affiliation(s)
| | | | - Eduardo Casas
- USDA, ARS, National Animal Disease Center, Ames, IA, United States of America
| | | | | | - David G. Riley
- Texas A&M University, College Station, TX, United States of America
| | - Thomas H. Welsh
- Texas A&M University, College Station, TX, United States of America
| | - Ronald D. Randel
- Texas A&M AgriLife Research, Overton, TX, United States of America
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