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Kertz NC, Banerjee P, Dyce PW, Diniz WJS. Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle-A Review. Animals (Basel) 2023; 13:3284. [PMID: 37894009 PMCID: PMC10603720 DOI: 10.3390/ani13203284] [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: 09/07/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Female fertility is the foundation of the cow-calf industry, impacting both efficiency and profitability. Reproductive failure is the primary reason why beef cows are sold in the U.S. and the cause of an estimated annual gross loss of USD 2.8 billion. In this review, we discuss the status of the genomics, transcriptomics, and systems genomics approaches currently applied to female fertility and the tools available to cow-calf producers to maximize genetic progress. We highlight the opportunities and limitations associated with using genomic and transcriptomic approaches to discover genes and regulatory mechanisms related to beef fertility. Considering the complex nature of fertility, significant advances in precision breeding will rely on holistic, multidisciplinary approaches to further advance our ability to understand, predict, and improve reproductive performance. While these technologies have advanced our knowledge, the next step is to translate research findings from bench to on-farm applications.
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2
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Seabury CM, Smith JL, Wilson ML, Bhattarai E, Santos JEP, Chebel RC, Galvão KN, Schuenemann GM, Bicalho RC, Gilbert RO, Rodriguez-Zas SL, Rosa G, Thatcher WW, Pinedo PJ. Genome-wide association and genomic prediction for a reproductive index summarizing fertility outcomes in U.S. Holsteins. G3 (BETHESDA, MD.) 2023; 13:jkad043. [PMID: 36848195 PMCID: PMC10468724 DOI: 10.1093/g3journal/jkad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/18/2022] [Accepted: 12/20/2022] [Indexed: 03/01/2023]
Abstract
Subfertility represents one major challenge to enhancing dairy production and efficiency. Herein, we use a reproductive index (RI) expressing the predicted probability of pregnancy following artificial insemination (AI) with Illumina 778K genotypes to perform single and multi-locus genome-wide association analyses (GWAA) on 2,448 geographically diverse U.S. Holstein cows and produce genomic heritability estimates. Moreover, we use genomic best linear unbiased prediction (GBLUP) to investigate the potential utility of the RI by performing genomic predictions with cross validation. Notably, genomic heritability estimates for the U.S. Holstein RI were moderate (h2 = 0.1654 ± 0.0317-0.2550 ± 0.0348), while single and multi-locus GWAA revealed overlapping quantitative trait loci (QTL) on BTA6 and BTA29, including the known QTL for the daughter pregnancy rate (DPR) and cow conception rate (CCR). Multi-locus GWAA revealed seven additional QTL, including one on BTA7 (60 Mb) which is adjacent to a known heifer conception rate (HCR) QTL (59 Mb). Positional candidate genes for the detected QTL included male and female fertility loci (i.e. spermatogenesis and oogenesis), meiotic and mitotic regulators, and genes associated with immune response, milk yield, enhanced pregnancy rates, and the reproductive longevity pathway. Based on the proportion of the phenotypic variance explained (PVE), all detected QTL (n = 13; P ≤ 5e - 05) were estimated to have moderate (1.0% < PVE ≤ 2.0%) or small effects (PVE ≤ 1.0%) on the predicted probability of pregnancy. Genomic prediction using GBLUP with cross validation (k = 3) produced mean predictive abilities (0.1692-0.2301) and mean genomic prediction accuracies (0.4119-0.4557) that were similar to bovine health and production traits previously investigated.
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Affiliation(s)
- Christopher M Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Johanna L Smith
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Miranda L Wilson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Eric Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Jose E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Ricardo C Chebel
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Klibs N Galvão
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Gustavo M Schuenemann
- Department of Veterinary Preventative Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Rodrigo C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Rob O Gilbert
- Department of Clinical Sciences, School of Veterinary Medicine, Ross University, St. Kitts, West Indies, KN
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana-Champaign, IL 61801, USA
| | - Guilherme Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - William W Thatcher
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Pablo J Pinedo
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80521, USA
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3
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Kohil A, Chouliaras S, Alabduljabbar S, Lakshmanan AP, Ahmed SH, Awwad J, Terranegra A. Female infertility and diet, is there a role for a personalized nutritional approach in assisted reproductive technologies? A Narrative Review. Front Nutr 2022; 9:927972. [PMID: 35938101 PMCID: PMC9353397 DOI: 10.3389/fnut.2022.927972] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Female infertility is a major public health concern and a global challenge. It is a disorder of the reproductive system, defined as the inability to achieve a clinical pregnancy. Nutrition and other environmental factors are found to impact reproductive health in women as well as the outcome of assisted reproductive technologies (ART). Dietary factors, such as polyunsaturated fatty acids (PUFA), fiber as well as the intake of Mediterranean diet appear to exert beneficial effects on female reproductive outcomes. The exact mechanisms associating diet to female fertility are yet to be identified, although genomic, epigenomic, and microbial pathways may be implicated. This review aims to summarize the current knowledge on the impact of dietary components on female reproduction and ART outcomes, and to discuss the relevant interplay of diet with genome, epigenome and microbial composition.
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Affiliation(s)
- Amira Kohil
- Research Department, Sidra Medicine, Doha, Qatar
| | | | | | | | | | - Johnny Awwad
- Reproductive Medicine Unit, Sidra Medicine, Doha, Qatar
| | - Annalisa Terranegra
- Research Department, Sidra Medicine, Doha, Qatar
- *Correspondence: Annalisa Terranegra
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Ebenezer Samuel King JP, Kumaresan A, Talluri TR, Sinha MK, Raval K, Nag P, Karuthadurai T, Aranganathan V. Genom-wide analysis identifies single nucleotide polymorphism variations and altered pathways associated with poor semen quality in breeding bulls. Reprod Domest Anim 2022; 57:1143-1155. [PMID: 35702937 DOI: 10.1111/rda.14185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 12/20/2022]
Abstract
The reason for poor semen quality among the breeding bulls is not well understood. In the present study, we performed high-throughput RNAseq analysis of spermatozoa to identify the SNPs present in good and poor-quality semen-producing Holstein Friesian breeding bulls. A total of 21,360 and 44,650 SNPs were identified in good and poor-quality semen with a minimum read depth of 20, among which 4780 and 8710 novel variants were observed in good and poor-quality semen, respectively. Greater SNPs and indels variations were observed in poor compared to good-quality semen. In poor-quality semen, SNP variations were observed in ZNF280B, SLC26A2, DMXL1, OR52A1, MACROD2 and REV1 genes, which are associated with regulation of spermatogenesis, post-testicular maturation, Cl- channel activity, V-ATPase-mediated intracellular vesicle acidification, a mono-ADP-ribosyl hydrolase and ATR-Chk1 checkpoint activation. GO analysis of filtered genes with significant variations between good and poor-quality semen showed enrichment in important pathways related to semen quality such as MAPK signalling pathway, Akt signalling pathway, focal adhesion, cAMP signalling pathway, and Rap1 signalling pathway. Network analysis of filtered genes in poor-quality semen showed variations in pathways of purine metabolism, pyrimidine metabolism, prolactin signalling pathway and RNA cap-binding complex. It is inferred that SNP in genes involved in maintaining sperm functions could be the reason for poor-quality semen production in bulls, and the identified SNPs hold potential to be used as biomarkers for semen quality in bulls.
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Affiliation(s)
| | - Arumugam Kumaresan
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Thirumala Rao Talluri
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | | | - Kathan Raval
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Pradeep Nag
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
| | - Thirumalaisamy Karuthadurai
- Theriogenology Laboratory, Southern Regional Station of ICAR-National Dairy Research Institute, Bengaluru, India
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5
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Ross EM, Sanjana H, Nguyen LT, Cheng Y, Moore SS, Hayes BJ. Extensive Variation in Gene Expression is Revealed in 13 Fertility-Related Genes Using RNA-Seq, ISO-Seq, and CAGE-Seq From Brahman Cattle. Front Genet 2022; 13:784663. [PMID: 35401673 PMCID: PMC8990236 DOI: 10.3389/fgene.2022.784663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Fertility is a key driver of economic profitability in cattle production. A number of studies have identified genes associated with fertility using genome wide association studies and differential gene expression analysis; however, the genes themselves are poorly characterized in cattle. Here, we selected 13 genes from the literature which have previously been shown to have strong evidence for an association with fertility in Brahman cattle (Bos taurus indicus) or closely related breeds. We examine the expression variation of the 13 genes that are associated with cattle fertility using RNA-seq, CAGE-seq, and ISO-seq data from 11 different tissue samples from an adult Brahman cow and a Brahman fetus. Tissues examined include blood, liver, lung, kidney, muscle, spleen, ovary, and uterus from the cow and liver and lung from the fetus. The analysis revealed several novel isoforms, including seven from SERPINA7. The use of three expression characterization methodologies (5′ cap selected ISO-seq, CAGE-seq, and RNA-seq) allowed the identification of isoforms that varied in their length of 5′ and 3′ untranslated regions, variation otherwise undetectable (collapsed as degraded RNA) in generic isoform identification pipelines. The combinations of different sequencing technologies allowed us to overcome the limitations of relatively low sequence depth in the ISO-seq data. The lower sequence depth of the ISO-seq data was also reflected in the lack of observed expression of some genes that were observed in the CAGE-seq and RNA-seq data from the same tissue. We identified allele specific expression that was tissue-specific in AR, IGF1, SOX9, STAT3, and TAF9B. Finally, we characterized an exon of TAF9B as partially nested within the neighboring gene phosphoglycerate kinase 1. As this study only examined two animals, even more transcriptional variation may be present in a genetically diverse population. This analysis reveals the large amount of transcriptional variation within mammalian fertility genes and illuminates the fact that the transcriptional landscape cannot be fully characterized using a single technology alone.
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Affiliation(s)
- Elizabeth M. Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- *Correspondence: Elizabeth M. Ross,
| | - Hari Sanjana
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Loan T. Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - YuanYuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Stephen S. Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J. Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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6
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Vineeth MR, Gupta ID, Verma A, Kumari S. Identification of SNPs in coding sequence of PROP1 gene and their association with bull fertility in Sahiwal cattle. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1629092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- M. R. Vineeth
- Molecular Genetics Lab, Animal Genetics and Breeding Division, ICAR-NDRI, Karnal, India
| | - I. D. Gupta
- Molecular Genetics Lab, Animal Genetics and Breeding Division, ICAR-NDRI, Karnal, India
| | - Archana Verma
- Molecular Genetics Lab, Animal Genetics and Breeding Division, ICAR-NDRI, Karnal, India
| | - Santosh Kumari
- Molecular Genetics Lab, Animal Genetics and Breeding Division, ICAR-NDRI, Karnal, India
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Kiser JN, Clancey E, Moraes JGN, Dalton J, Burns GW, Spencer TE, Neibergs HL. Identification of loci associated with conception rate in primiparous Holstein cows. BMC Genomics 2019; 20:840. [PMID: 31718557 PMCID: PMC6852976 DOI: 10.1186/s12864-019-6203-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 10/21/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Subfertility is a major issue facing the dairy industry as the average US Holstein cow conception rate (CCR) is approximately 35%. The genetics underlying the physiological processes responsible for CCR, the proportion of cows able to conceive and maintain a pregnancy at each breeding, are not well characterized. The objectives of this study were to identify loci, positional candidate genes, and transcription factor binding sites (TFBS) associated with CCR and determine if there was a genetic correlation between CCR and milk production in primiparous Holstein cows. Cows were bred via artificial insemination (AI) at either observed estrus or timed AI and pregnancy status was determined at day 35 post-insemination. Additive, dominant, and recessive efficient mixed model association expedited (EMMAX) models were used in two genome-wide association analyses (GWAA). One GWAA focused on CCR at first service (CCR1) comparing cows that conceived and maintained pregnancy to day 35 after the first AI (n = 494) to those that were open after the first AI (n = 538). The second GWAA investigated loci associated with the number of times bred (TBRD) required for conception in cows that either conceived after the first AI (n = 494) or repeated services (n = 472). RESULTS The CCR1 GWAA identified 123, 198, and 76 loci associated (P < 5 × 10- 08) in additive, dominant, and recessive models, respectively. The TBRD GWAA identified 66, 95, and 33 loci associated (P < 5 × 10- 08) in additive, dominant, and recessive models, respectively. Four of the top five loci were shared in CCR1 and TBRD for each GWAA model. Many of the associated loci harbored positional candidate genes and TFBS with putative functional relevance to fertility. Thirty-six of the loci were validated in previous GWAA studies across multiple breeds. None of the CCR1 or TBRD associated loci were associated with milk production, nor was their significance with phenotypic and genetic correlations to 305-day milk production. CONCLUSIONS The identification and validation of loci, positional candidate genes, and TFBS associated with CCR1 and TBRD can be utilized to improve, and further characterize the processes involved in cattle fertility.
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Affiliation(s)
- Jennifer N. Kiser
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA United States
| | - Erin Clancey
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA United States
| | - Joao G. N. Moraes
- Division of Animal Sciences, University of Missouri, Columbia, MO United States
| | - Joseph Dalton
- Department of Animal and Veterinary Science, University of Idaho, Caldwell, ID United States
| | - Gregory W. Burns
- Division of Animal Sciences, University of Missouri, Columbia, MO United States
| | - Thomas E. Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO United States
| | - Holly L. Neibergs
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA United States
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Kiser JN, Keuter EM, Seabury CM, Neupane M, Moraes JGN, Dalton J, Burns GW, Spencer TE, Neibergs HL. Validation of 46 loci associated with female fertility traits in cattle. BMC Genomics 2019; 20:576. [PMID: 31299913 PMCID: PMC6624949 DOI: 10.1186/s12864-019-5935-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/25/2019] [Indexed: 12/25/2022] Open
Abstract
Background Subfertility is one challenge facing the dairy industry as the average Holstein heifer conception rate (HCR), the proportion of heifers that conceive and maintain a pregnancy per breeding, is estimated at 55–60%. Of the loci associated with HCR, few have been validated in an independent cattle population, limiting their usefulness for selection or furthering our understanding of the mechanisms involved in successful pregnancy. Therefore, the objectives here were to identify loci associated with HCR: 1) to the first artificial insemination (AI) service (HCR1), 2) to repeated AI services required for a heifer to conceive (TBRD) and 3) to validate loci previously associated with fertility. Breeding and health records from 3359 Holstein heifers were obtained after heifers were bred by AI at observed estrus, with pregnancy determined at day 35 via palpation. Heifer DNA was genotyped using the Illumina BovineHD BeadChip, and genome-wide association analyses (GWAA) were performed with additive, dominant and recessive models using the Efficient Mixed Model Association eXpedited (EMMAX) method with a relationship matrix for two phenotypes. The HCR1 GWAA compared heifers that were pregnant after the first AI service (n = 497) to heifers that were open following the first AI service (n = 405), which included those that never conceived. The TBRD GWAA compared only those heifers which did conceive, across variable numbers of AI service (n = 712). Comparison of loci previously associated with fertility, HCR1 or TBRD were considered the same locus for validation when in linkage disequilibrium (D’ > 0.7). Results The HCR1 GWAA identified 116, 187 and 28 loci associated (P < 5 × 10− 8) in additive, dominant and recessive models, respectively. The TBRD GWAA identified 235, 362, and 69 QTL associated (P < 5 × 10− 8) with additive, dominant and recessive models, respectively. Loci previously associated with fertility were in linkage disequilibrium with 22 loci shared with HCR1 and TBRD, 5 HCR1 and 19 TBRD loci. Conclusions Loci associated with HCR1 and TBRD that have been identified and validated can be used to improve HCR through genomic selection, and to better understand possible mechanisms associated with subfertility. Electronic supplementary material The online version of this article (10.1186/s12864-019-5935-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer N Kiser
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Elizabeth M Keuter
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Christopher M Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Mahesh Neupane
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Joao G N Moraes
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Joseph Dalton
- Department of Animal and Veterinary Sciences, University of Idaho, Caldwell, ID, USA
| | - Gregory W Burns
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Holly L Neibergs
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
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Polymorphisms within the prolactin and growth hormone/insulin-like growth factor-1 functional pathways associated with fertility traits in Holstein cows raised in a hot-humid climate. Trop Anim Health Prod 2018; 50:1913-1920. [DOI: 10.1007/s11250-018-1645-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/12/2018] [Indexed: 12/25/2022]
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10
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Liu L, Yu S, Chen R, Lv X, Pan C. A novel synonymous SNP (A47A) of the <i>TMEM95</i> gene is significantly associated with the reproductive traits related to testis in male piglets. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-235-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Transmembrane protein 95 (TMEM95) is located on the acrosomal membrane of the sperm head involved in the acrosome reaction; thus, it is regarded as affecting spermatogenesis and reproduction traits. The aim of this study was to explore the novel single nucleotide polymorphisms (SNPs) within the pig TMEM95 gene as well as to evaluate their associations with the testicular sizes in male Landrace (LD) and Large White (LW) breeds. After pool sequencing and bioinformatics analysis, only one novel coding SNP was found in exon 1, namely NC_010454.3: g.341T > C, resulting in a synonymous mutation (A47A). This SNP could be genotyped using the StuI polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) assay. The minor allelic frequencies (MAFs) were 0.259 and 0.480 in the LD and LW breeds. Their polymorphism information content (PIC) values were 0.310 and 0.375. The LW population was at the Hardy–Weinberg equilibrium (HWE) (p > 0.05), whereas the LD population was not (p < 0.05). Association analyses demonstrated that a significant relationship was found between this A47A polymorphism and testis weight at 40 days of age in the LW population (p = 0.047), and the heterozygote individuals showed lower testis weight than those with other genotypes. Moreover, this SNP was significantly associated with three testis measurement traits at 15 days of age in the LW population (p < 0.05); the individuals with genotypes TT and TC showed consistently superior testis measurement traits than those with genotype CC. These findings demonstrate that the A47A polymorphism had a significant effect on testis measurement traits, suggesting that the TMEM95 gene could be a candidate gene associated with reproductive traits. These results could contribute to breeding and genetics programs in the pig industry via DNA marker-assisted selection (MAS).
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Chen R, Yu S, Ren F, Lv XY, Pan CY. Detection of one large insertion/deletion (indel) and two novel SNPs within the <i>SPEF2</i> gene and their associations with male piglet reproduction traits. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-275-2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.
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12
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Lan X, Peñagaricano F, DeJung L, Weigel K, Khatib H. Short communication: A missense mutation in the PROP1 (prophet of Pit 1) gene affects male fertility and milk production traits in the US Holstein population. J Dairy Sci 2013; 96:1255-7. [DOI: 10.3168/jds.2012-6019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/02/2012] [Indexed: 01/12/2023]
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Loor JJ, Bionaz M, Drackley JK. Systems Physiology in Dairy Cattle: Nutritional Genomics and Beyond. Annu Rev Anim Biosci 2013; 1:365-92. [DOI: 10.1146/annurev-animal-031412-103728] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juan J. Loor
- Department of Animal Sciences and
- Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, Illinois, 61801;
| | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, 97331;
| | - James K. Drackley
- Department of Animal Sciences and
- Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, Illinois, 61801;
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15
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Estrous behavior in dairy cows: identification of underlying mechanisms and gene functions. Animal 2012; 4:446-53. [PMID: 22443949 DOI: 10.1017/s1751731109991169] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Selection in dairy cattle for a higher milk yield has coincided with declined fertility. One of the factors is reduced expression of estrous behavior. Changes in systems that regulate the estrous behavior could be manifested by altered gene expression. This literature review describes the current knowledge on mechanisms and genes involved in the regulation of estrous behavior. The endocrinological regulation of the estrous cycle in dairy cows is well described. Estradiol (E2) is assumed to be the key regulator that synchronizes endocrine and behavioral events. Other pivotal hormones are, for example, progesterone, gonadotropin releasing hormone and insulin-like growth factor-1. Interactions between the latter and E2 may play a role in the unfavorable effects of milk yield-related metabolic stress on fertility in high milk-producing dairy cows. However, a clear understanding of how endocrine mechanisms are tied to estrous behavior in cows is only starting to emerge. Recent studies on gene expression and signaling pathways in rodents and other animals contribute to our understanding of genes and mechanisms involved in estrous behavior. Studies in rodents, for example, show that estrogen-induced gene expression in specific brain areas such as the hypothalamus play an important role. Through these estrogen-induced gene expressions, E2 alters the functioning of neuronal networks that underlie estrous behavior, by affecting dendritic connections between cells, receptor populations and neurotransmitter releases. To improve the understanding of complex biological networks, like estrus regulation, and to deal with the increasing amount of genomic information that becomes available, mathematical models can be helpful. Systems biology combines physiological and genomic data with mathematical modeling. Possible applications of systems biology approaches in the field of female fertility and estrous behavior are discussed.
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Wyszyńska-Koko J, de Wit AAC, Beerda B, Veerkamp RF, te Pas MFW. Gene expression patterns in the ventral tegmental area relate to oestrus behaviour in high-producing dairy cows. J Anim Breed Genet 2011; 128:183-91. [PMID: 21554412 DOI: 10.1111/j.1439-0388.2010.00915.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Reduced oestrus behaviour expression or its absence (silent oestrus) results in subfertility in high-producing dairy cows. Insight into the genomic regulation of oestrus behaviour is likely to help alleviate reproduction problems. Here, gene expression was recorded in the ventral tegmental area (VTA) of high milk production dairy cows differing in the degree of showing oestrus behaviour (H - highly expressing versus L - lowly expressing), which was then analysed. Genes regulating cell morphology and adhesion or coding for immunoglobulin G (IgG) chains were differentially expressed in VTA between cows around day 0 and 12 of the oestrus cycle, but only in cows that earlier in life tended to show high levels of oestrus behaviour (H0 versus H12). The comparisons between H and L groups of cows also revealed differential expression of several genes (e.g. those of the IgG family or encoding for pro-melanin-concentrating hormone). However, any significant changes in VTA genes expression were detected in the comparison of L0 versus L12 cows. Altogether, the genes expression profile in VTA of cows highly expressing oestrus behaviour changes together with phases of the oestrus cycle, while in case of cows expressing oestrus behaviour lowly it remains stable. This supports the existence of genomic regulation by centrally expressed genes on the expression of oestrus behaviour in dairy cows.
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Affiliation(s)
- J Wyszyńska-Koko
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Wólka Kosowska, Poland.
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Wickramasinghe S, Rincon G, Medrano JF. Variants in the pregnancy-associated plasma protein-A2 gene on Bos taurus autosome 16 are associated with daughter calving ease and productive life in Holstein cattle. J Dairy Sci 2011; 94:1552-8. [PMID: 21338820 DOI: 10.3168/jds.2010-3237] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 11/15/2010] [Indexed: 01/29/2023]
Abstract
Reproductive disorders in dairy herds have a negative effect on farm profitability and sustainability of milk production. Given the substantial evidence of the role of the pregnancy-associated plasma protein (PAPP) gene family in the regulation of reproduction in humans and mice, its role in insulin-like growth factor metabolism, quantitative trait loci effects in the mouse, and location of a calving ease QTL on bovine chromosome 16, the PAPP-A2 gene was chosen as a candidate gene to perform an association study for reproductive health in cattle. Single nucleotide polymorphisms (SNP) were identified in coding and conserved noncoding regions of the PAPP-A2 gene in 3 dairy breeds. A total of 7 tag SNP were genotyped in 662 Holstein bulls (UCD-bulls) to perform marker trait association analysis. Three SNP (SNP 13, 15, and 16) were in strong linkage disequilibrium in Holsteins, showing significant positive associations with daughter calving ease, productive life, milk yield, and protein yield. These results were validated by genotyping SNP15 in a larger population of 992 bulls from the cooperative dairy DNA repository (CDDR-bulls). Our results demonstrate that the PAPP-A2 gene is associated with reproductive health in Holstein cattle and that the identified SNP can be used as genetic markers in dairy breeding due to their positive association with reproductive and productive traits. Functional studies need to be conducted to identify the mechanisms for the association of SNP with these traits.
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Affiliation(s)
- S Wickramasinghe
- Department of Animal Science, University of California, Davis, California 95616-8521, USA
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Khatib H, Monson R, Huang W, Khatib R, Schutzkus V, Khateeb H, Parrish J. Short communication: Validation of in vitro fertility genes in a Holstein bull population. J Dairy Sci 2010; 93:2244-9. [DOI: 10.3168/jds.2009-2805] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 01/25/2010] [Indexed: 11/19/2022]
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Gene expression patterns in anterior pituitary associated with quantitative measure of oestrous behaviour in dairy cows. Animal 2010; 4:1297-307. [PMID: 22444649 DOI: 10.1017/s1751731110000303] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Nutritional sub-fertility in the dairy cow: towards improved reproductive management through a better biological understanding. Animal 2010; 4:1197-213. [DOI: 10.1017/s1751731109991601] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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