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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep. Animals (Basel) 2022; 12:ani12111346. [PMID: 35681809 PMCID: PMC9179888 DOI: 10.3390/ani12111346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
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Affiliation(s)
- Mária Mészárosová
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180 Vienna, Austria;
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
- Correspondence:
| | - Ivan Pavlík
- Research Institute of Animal Production—NPPC Slovakia, Hlohovecká 2, 95141 Nitra—Lužianky, Slovakia;
| | - Milan Margetín
- Faculty of Agrobiology and Food Resources, Institute of Animal Science, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
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3
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Werry N, Russell SJ, Gillis DJ, Miller S, Hickey K, Larmer S, Lohuis M, Librach C, LaMarre J. Characteristics of miRNAs Present in Bovine Sperm and Associations With Differences in Fertility. Front Endocrinol (Lausanne) 2022; 13:874371. [PMID: 35663333 PMCID: PMC9160602 DOI: 10.3389/fendo.2022.874371] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/14/2022] [Indexed: 12/23/2022] Open
Abstract
Small non-coding RNAs have been linked to different phenotypes in bovine sperm, however attempts to identify sperm-borne molecular biomarkers of male fertility have thus far failed to identify a robust profile of expressed miRNAs related to fertility. We hypothesized that some differences in bull fertility may be reflected in the levels of different miRNAs in sperm. To explore such differences in fertility that are not due to differences in visible metrics of sperm quality, we employed Next Generation Sequencing to compare the miRNA populations in Bos taurus sperm from bulls with comparable motility and morphology but varying Sire Conception Rates. We identified the most abundant miRNAs in both populations (miRs -34b-3p; -100-5p; -191-5p; -30d-4p; -21-5p) and evaluated differences in the overall levels and specific patterns of isomiR expression. We also explored correlations between specific pairs of miRNAs in each population and identified 10 distinct pairs of miRNAs that were positively correlated in bulls with higher fertility and negatively correlated in comparatively less fertile individuals. Furthermore, 8 additional miRNA pairs demonstrated the opposite trend; negatively correlated in high fertility animals and positively correlated in less fertile bulls. Finally, we performed pathway analysis to identify potential roles of miRNAs present in bull sperm in the regulation of specific genes that impact spermatogenesis and embryo development. Together, these results present a comprehensive picture of the bovine sperm miRNAome that suggests multiple potential roles in fertility.
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Affiliation(s)
- Nicholas Werry
- Department of Biomedical Sciences, The University of Guelph, Guelph, ON, Canada
| | | | - Daniel J. Gillis
- School of Computer Science, The University of Guelph, Guelph, ON, Canada
| | | | | | | | | | - Clifford Librach
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, The University of Guelph, Guelph, ON, Canada
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Crum TE, Schnabel RD, Decker JE, Taylor JF. Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds. Front Genet 2021; 12:758394. [PMID: 34733318 PMCID: PMC8558500 DOI: 10.3389/fgene.2021.758394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.
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Affiliation(s)
- Tamar E Crum
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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Chen Z, Brito LF, Luo H, Shi R, Chang Y, Liu L, Guo G, Wang Y. Genetic and Genomic Analyses of Service Sire Effect on Female Reproductive Traits in Holstein Cattle. Front Genet 2021; 12:713575. [PMID: 34539741 PMCID: PMC8446201 DOI: 10.3389/fgene.2021.713575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022] Open
Abstract
Fertility and reproductive performance are key drivers of dairy farm profitability. Hence, reproduction traits have been included in a large majority of worldwide dairy cattle selection indexes. The reproductive traits are lowly heritable but can be improved through direct genetic selection. However, most scientific studies and dairy cattle breeding programs have focused solely on the genetic effects of the dam (GED) on reproductive performance and, therefore, ignored the contribution of the service sire in the phenotypic outcomes. This study aimed to investigate the service sire effects on female reproductive traits in Holstein cattle from a genomic perspective. Genetic parameter estimation and genome-wide association studies (GWAS) were performed for the genetic effect of service sire (GESS) on conception rate (CR), 56-day non-return rate (NRR56), calving ease (CE), stillbirth (SB), and gestation length (GL). Our findings indicate that the additive genetic effects of both sire and dam contribute to the phenotypic variance of reproductive traits measured in females (0.0196 vs. 0.0109, 0.0237 vs. 0.0133, 0.0040 vs. 0.0289, 0.0782 vs. 0.0083, and 0.1024 vs. 0.1020 for GESS and GED heritability estimates for CR, NRR56, CE, SB, and GL, respectively), and these two genetic effects are positively correlated for SB (0.1394) and GL (0.7871). Interestingly, the breeding values for GESS on insemination success traits (CR and NRR56) are unfavorably and significantly correlated with some production, health, and type breeding values (ranging from -0.449 to 0.274), while the GESS values on calving traits (CE, SB, and GL) are usually favorably associated with those traits (ranging from -0.493 to 0.313). One hundred sixty-two significant single-nucleotide polymorphisms (SNPs) and their surrounding protein-coding genes were identified as significantly associated with GESS and GED, respectively. Six genes overlapped between GESS and GED for calving traits and 10 genes overlapped between GESS for success traits and calving traits. Our findings indicate the importance of considering the GESS when genetically evaluating the female reproductive traits in Holstein cattle.
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Affiliation(s)
- Ziwei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hanpeng Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Rui Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Chang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Company Limited, Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Ferreira CER, Campos GS, Schmidt PI, Sollero BP, Goularte KL, Corcini CD, Gasperin BG, Lucia T, Boligon AA, Cardoso FF. Genome-wide association and genomic prediction for scrotal circumference in Hereford and Braford bulls. Theriogenology 2021; 172:268-280. [PMID: 34303226 DOI: 10.1016/j.theriogenology.2021.07.007] [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: 08/14/2020] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/19/2022]
Abstract
Scrotal circumference (SC) is widely used as a selection criterion for bulls in breeding programs, since it is easily assessed and correlated with several desirable reproductive traits. The objectives of this study were: to perform a genome-wide association study (GWAS) to identify genomic regions associated with SC adjusted for age (SCa) and for both age and weight (SCaw); to select Tag SNPs from GWAS to construct low-density panel for genomic prediction; and to compare the prediction accuracy of the SC through different methods for Braford and Hereford bulls from the same genetic breeding program. Data of SC from 18,172 bulls (30.4 ± 3.7 cm) and of genotypes from 131 sires and 3,545 animals were used. From GWAS, the top 1% of 1-Mb windows were observed on chromosome (BTA) 2, 20, 7, 8, 15, 3, 16, 27, 6 and 8 for SCa and on BTA 8, 15, 16, 21, 19, 2, 6, 5 and 10 for SCaw, representing 17.4% and 18.8% of the additive genetic variance of SCa and SCaw, respectively. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene functions related to the SCa and SCaw. The genomic enhancement methods, especially single step GBLUP, that combined phenotype and pedigree data with direct genomic values generated gains in accuracy in relation to pedigree BLUP, suggesting that genomic predictions should be applied to improve genetic gain and to narrow the generation interval compared to traditional methods. The proposed Tag-SNP panels may be useful for lower-cost commercial genomic prediction applications in the future, when the number of bulls in the reference population increases for SC in Hereford and Braford breeds.
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Affiliation(s)
- Carlos E R Ferreira
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
| | - Gabriel S Campos
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Patricia I Schmidt
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo, Jaboticabal, SP, Brazil
| | | | - Karina L Goularte
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carine D Corcini
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Bernardo G Gasperin
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Thomaz Lucia
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Arione A Boligon
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Fernando F Cardoso
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Embrapa Pecuária Sul, Bagé, RS, Brazil
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Hussain S, Alex R, Alyethodi RR, Sharma S, Verma N, Sirohi AS, Singh U, Kumar S, Chand N, Sengar GS, Sharma A, Tyagi R, Arya S, Tyagi S. Development of a RAPD marker-based classification criterion for quality semen production in Holstein crossbred bulls. Reprod Domest Anim 2021; 56:736-743. [PMID: 33559234 DOI: 10.1111/rda.13912] [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: 08/19/2020] [Revised: 11/19/2020] [Accepted: 02/04/2021] [Indexed: 11/30/2022]
Abstract
In cattle production systems, an intense selection pressure for production traits has resulted in the decline of fertility traits. To optimize an efficient reproduction system, the inclusion of both male and female fertility traits in the selection process is very much essential. RAPD (Random Amplified Polymorphic DNA) was developed as a molecular biology tool and has been extensively used, to study intra- and interspecific genetic diversity. The present study was undertaken to utilize RAPD primers to investigate the association between DNA markers and semen quality traits viz. Sperm concentration, total sperm count ejaculate and initial sperm motility and thereby to identify good/poor semen producers. DNA isolated from the blood samples of healthy bulls was subjected to RAPD-PCR. The multiple regression analysis followed by independent t test was carried out to identify suitable markers. Based on the results, only 12 bands were identified as marker suitable for any of the quality trait. This includes, OPA2 ~ 760, OPA2 ~ 700, OPA6 ~ 1,200, OPA9 ~ 400, OPA9 ~ 380, OPA12 ~ 970, OPA14 ~ 715, OPA14 ~ 605, OPA16 ~ 485, OPA17 ~ 860 and OPA18 ~ 480. Multiple regression analysis selected, OPA2 ~ 760 and OPA2 ~ 1,750 for sperm concentration and OPA2 ~ 760, OPA2 ~ 700, OPA9 ~ 620, OPA4 ~ 670 and OPA18 ~ 1,015 for total sperm count/ejaculate. But the t test revealed a significant association between OPA2 ~ 760 and total sperm count. Further, discriminant function analysis also identified this marker in the first step itself. The results of the present study can be exploited as a low-cost alternative strategy for identification of good /poor semen producers in crossbred bulls at an early age.
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Affiliation(s)
- Shaziya Hussain
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Rani Alex
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - Shalini Sharma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | - Nitika Verma
- Department of Biotechnology and Microbiology, MIET, Meerut, India
| | | | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Naimi Chand
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | | | - Ankur Sharma
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Rachna Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Sarmesh Arya
- ICAR-Central Institute for Research on Cattle, Meerut, India
| | - Srikant Tyagi
- ICAR-Central Institute for Research on Cattle, Meerut, India
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Long JA. The ‘omics’ revolution: Use of genomic, transcriptomic, proteomic and metabolomic tools to predict male reproductive traits that impact fertility in livestock and poultry. Anim Reprod Sci 2020; 220:106354. [DOI: 10.1016/j.anireprosci.2020.106354] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 12/17/2022]
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UPADHYAY ARPAN, CHAKRAVARTY ATISHKUMAR, DE SHACHINANDAN, SELVAN ASAKTHIVEL, SHIVAHRE PUSHPRAJ, GUPTA ASHOKKUMAR, SINGH AVTAR. Genetic polymorphism in MAP1B gene associated with conception rate in Holstein Friesian crossbred breeding bulls. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i4.104227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The microtubule associated protein 1 B (MAP1B) gene is one of the candidate genes which was found to be strongly associated with the sire conception rate. In the present study, identification of single nucleotide polymorphisms (SNPs) in the targeted region of MAP1B gene and their effect on conception rate (CR) in Karan Fries (KF) breeding bulls were sought. A tetra-primer ARMS PCR technique was adapted to genotype an SNP, g. 3,066A>G located on intron 1 of MAP1B gene. The relationship between the CR of KF breeding bulls and polymorphic locus of MAP1B gene was assessed. Genotyping of the targeted region revealed three kinds of genotype (AA, AG and GG) with respect to g. 3,066A>G SNP locus. The identified SNP had highly significant (P=0.0009) influence on CR. The KF bulls with AA and AG genotype had comparatively higher CR than the bulls with GG genotype. The identified SNP was significantly associated with CR, thus it may be utilized as a molecular marker for developing marker-assisted selection strategy to enhance the CR in KF cattle population.
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Shan S, Xu F, Bleyer M, Becker S, Melbaum T, Wemheuer W, Hirschfeld M, Wacker C, Zhao S, Schütz E, Brenig B. Association of α/β-Hydrolase D16B with Bovine Conception Rate and Sperm Plasma Membrane Lipid Composition. Int J Mol Sci 2020; 21:E627. [PMID: 31963602 PMCID: PMC7014312 DOI: 10.3390/ijms21020627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 02/01/2023] Open
Abstract
We have identified a Holstein sire named Tarantino who had been approved for artificial insemination that is based on normal semen characteristics (i.e., morphology, thermoresistance, motility, sperm concentration), but had no progeny after 412 first inseminations, resulting in a non-return rate (NRdev) of -29. Using whole genome association analysis and next generation sequencing, an associated nonsense variant in the α/β-hydrolase domain-containing 16B gene (ABHD16B) on bovine chromosome 13 was identified. The frequency of the mutant allele in the German Holstein population was determined to be 0.0018 in 222,645 investigated cattle specimens. The mutant allele was traced back to Whirlhill Kingpin (bornFeb. 13th, 1959) as potential founder. The expression of ABHD16B was detected by Western blotting and immunohistochemistry in testis and epididymis of control bulls. A lipidome comparison of the plasma membrane of fresh semen from carriers and controls showed significant differences in the concentration of phosphatidylcholine (PC), diacylglycerol (DAG), ceramide (Cer), sphingomyelin (SM), and phosphatidylcholine (-ether) (PC O-), indicating that ABHD16B plays a role in lipid biosynthesis. The altered lipid contents may explain the reduced fertilization ability of mutated sperms.
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Affiliation(s)
- Shuwen Shan
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Fangzheng Xu
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Martina Bleyer
- Pathology Unit, German Primate Center, Leibniz-Institute for Primate Research Goettingen, 37077 Goettingen, Germany
| | - Svenja Becker
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Torben Melbaum
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Wilhelm Wemheuer
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Marc Hirschfeld
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
- Department of Obstetrics and Gynecology, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Christin Wacker
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Shuhong Zhao
- Key Lab of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Goettingen, 37077 Goettingen, Germany
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Dechow C, Liu W, Idun J, Maness B. Short communication: Two dominant paternal lineages for North American Jersey artificial insemination sires. J Dairy Sci 2018; 101:2281-2284. [DOI: 10.3168/jds.2017-13694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/07/2017] [Indexed: 11/19/2022]
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12
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Nicolini P, Amorín R, Han Y, Peñagaricano F. Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle. BMC Genet 2018; 19:14. [PMID: 29486732 PMCID: PMC5830072 DOI: 10.1186/s12863-018-0600-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/21/2018] [Indexed: 01/04/2023] Open
Abstract
Background Service sire has a considerable impact on reproductive success in dairy cattle. Most gene mapping studies for bull fertility have focused on additive effects, while non-additive effects have been largely ignored. The main goal of this study was to assess the relevance of non-additive effects on Sire Conception Rate (SCR) in Holstein dairy cattle. The analysis included 7.5 k Holstein bulls with both SCR records and 57.8 k single nucleotide polymorphism (SNP) markers spanning the entire genome. Results The importance of non-additive effects was evaluated using an efficient two-step mixed model-based approach. Four genomic regions located on chromosomes BTA8, BTA9, BTA13 and BTA17 showed marked dominance and/or recessive effects. Most of these regions harbor genes, such as ADAM28, DNAJA1, TBC1D20, SPO11, PIWIL3 and TMEM119, that are directly implicated in testis development, male germ line maintenance, and sperm maturation. Conclusions This study provides further evidence for the relevance of non-additive effects in fitness-related traits, such as male fertility. In addition, these findings may point out new strategies for improving service sire fertility in dairy cattle via marker-assisted selection.
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Affiliation(s)
- Paula Nicolini
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,Polo de Desarrollo Universitario, Universidad de la República, Tacuarembó, Uruguay
| | - Rocío Amorín
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA
| | - Yi Han
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA. .,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
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Whiston R, Finlay EK, McCabe MS, Cormican P, Flynn P, Cromie A, Hansen PJ, Lyons A, Fair S, Lonergan P, O' Farrelly C, Meade KG. A dual targeted β-defensin and exome sequencing approach to identify, validate and functionally characterise genes associated with bull fertility. Sci Rep 2017; 7:12287. [PMID: 28947819 PMCID: PMC5613009 DOI: 10.1038/s41598-017-12498-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/11/2017] [Indexed: 12/30/2022] Open
Abstract
Bovine fertility remains a critical issue underpinning the sustainability of the agricultural sector. Phenotypic records collected on >7,000 bulls used in artificial insemination (AI) were used to identify 160 reliable and divergently fertile bulls for a dual strategy of targeted sequencing (TS) of fertility-related β-defensin genes and whole exome sequencing (WES). A haplotype spanning multiple β-defensin genes and containing 94 SNPs was significantly associated with fertility and functional analysis confirmed that sperm from bulls possessing the haplotype showed significantly enhanced binding to oviductal epithelium. WES of all exons in the genome in 24 bulls of high and low fertility identified 484 additional SNPs significantly associated with fertility. After validation, the most significantly associated SNP was located in the FOXJ3 gene, a transcription factor which regulates sperm function in mice. This study represents the first comprehensive characterisation of genetic variation in bovine β-defensin genes and functional analysis supports a role for β-defensins in regulating bull sperm function. This first application of WES in AI bulls with divergent fertility phenotypes has identified a novel role for the transcription factor FOXJ3 in the regulation of bull fertility. Validated genetic variants associated with bull fertility could prove useful for improving reproductive outcomes in cattle.
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Affiliation(s)
- Ronan Whiston
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Emma K Finlay
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Matthew S McCabe
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Paul Cormican
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland
| | - Paul Flynn
- Weatherbys Scientific, Johnstown, Naas, Co Kildare, Ireland
| | - Andrew Cromie
- Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - Peter J Hansen
- Department of Animal Sciences, University of Florida, Gainesville, Florida, USA
| | - Alan Lyons
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Sean Fair
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cliona O' Farrelly
- Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, Ireland
| | - Kieran G Meade
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
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14
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Jain V, Patel B, Umar FP, Ajithakumar HM, Gurjar SK, Gupta ID, Verma A. Identification of single nucleotide polymorphism in protein phosphatase 1 regulatory subunit 11 gene in Murrah bulls. Vet World 2017; 10:244-248. [PMID: 28344410 PMCID: PMC5352852 DOI: 10.14202/vetworld.2017.244-248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 01/23/2017] [Indexed: 11/19/2022] Open
Abstract
Aim: This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in protein phosphatase 1 regulatory subunit 11 (PPP1R11) gene in Murrah bulls. Materials and Methods: Genomic DNA was isolated by phenol–chloroform extraction method from the frozen semen samples of 65 Murrah bulls maintained at Artificial Breeding Research Centre, ICAR-National Dairy Research Institute, Karnal. The quality and concentration of DNA was checked by spectrophotometer reading and agarose gel electrophoresis. The target region of PPP1R11 gene was amplified using four sets of primer designed based on Bos taurus reference sequence. The amplified products were sequenced and aligned using Clustal Omega for identification of SNPs. Animals were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using EcoNI restriction enzyme. Results: The sequences in the NCBI accession number NW_005785016.1 for Bubalus bubalis were compared and aligned with the edited sequences of Murrah bulls with Clustal Omega software. A total of 10 SNPs were found, out of which 1 at 5’UTR, 3 at intron 1, and 6 at intron 2 region. PCR-RFLP using restriction enzyme EcoNI revealed only AA genotype indicating monomorphism in PPP1R11 gene of all Murrah animals included in the study. Conclusion: A total of 10 SNPs were found. PCR-RFLP revealed only AA genotype indicating monomorphism in PPP1R11 gene of all Murrah animals included in the study, due to which association analysis with conception rate was not feasible.
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Affiliation(s)
- Varsha Jain
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Brijesh Patel
- Livestock Production Management Section, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Farhat Paul Umar
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - H M Ajithakumar
- Division of Animal Physiology, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Suraj K Gurjar
- Division of Animal Physiology, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - I D Gupta
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Verma
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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15
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Nayeri S, Sargolzaei M, Abo-Ismail M, Miller S, Schenkel F, Moore S, Stothard P. Genome-wide association study for lactation persistency, female fertility, longevity, and lifetime profit index traits in Holstein dairy cattle. J Dairy Sci 2017; 100:1246-1258. [DOI: 10.3168/jds.2016-11770] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/13/2016] [Indexed: 12/12/2022]
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16
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Han Y, Peñagaricano F. Unravelling the genomic architecture of bull fertility in Holstein cattle. BMC Genet 2016; 17:143. [PMID: 27842509 PMCID: PMC5109745 DOI: 10.1186/s12863-016-0454-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fertility is considered an important economic trait in dairy cattle. Most studies have investigated cow fertility while bull fertility has received much less consideration. The main objective of this study was to perform a comprehensive genomic analysis in order to unravel the genomic architecture underlying sire fertility in Holstein dairy cattle. The analysis included the application of alternative genome-wide association mapping approaches and the subsequent use of diverse gene set enrichment tools. RESULTS The association analyses identified at least eight genomic regions strongly associated with bull fertility. Most of these regions harbor genes, such as KAT8, CKB, TDRD9 and IGF1R, with functions related to sperm biology, including sperm development, motility and sperm-egg interaction. Moreover, the gene set analyses revealed many significant functional terms, including fertilization, sperm motility, calcium channel regulation, and SNARE proteins. Most of these terms are directly implicated in sperm physiology and male fertility. CONCLUSIONS This study contributes to the identification of genetic variants and biological processes underlying sire fertility. These findings can provide opportunities for improving bull fertility via marker-assisted selection.
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Affiliation(s)
- Yi Han
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA. .,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
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Kropp J, Peñagaricano F, Salih S, Khatib H. Invited review: Genetic contributions underlying the development of preimplantation bovine embryos. J Dairy Sci 2014; 97:1187-201. [DOI: 10.3168/jds.2013-7244] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/08/2013] [Indexed: 01/09/2023]
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The Role of Genomics in Conservation and Reproductive Sciences. REPRODUCTIVE SCIENCES IN ANIMAL CONSERVATION 2014; 753:71-96. [DOI: 10.1007/978-1-4939-0820-2_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Peñagaricano F, Weigel KA, Rosa GJM, Khatib H. Inferring quantitative trait pathways associated with bull fertility from a genome-wide association study. Front Genet 2013; 3:307. [PMID: 23335935 PMCID: PMC3542705 DOI: 10.3389/fgene.2012.00307] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/11/2012] [Indexed: 11/13/2022] Open
Abstract
Whole-genome association studies typically focus on genetic markers with the strongest evidence of association. However, single markers often explain only a small component of the genetic variance and hence offer a limited understanding of the trait under study. As such, the objective of this study was to perform a pathway-based association analysis in Holstein dairy cattle in order to identify relevant pathways involved in bull fertility. The results of a single-marker association analysis, using 1,755 bulls with sire conception rate data and genotypes for 38,650 single nucleotide polymorphisms (SNPs), were used in this study. A total of 16,819 annotated genes, including 2,767 significantly associated with bull fertility, were used to interrogate a total of 662 Gene Ontology (GO) terms and 248 InterPro (IP) entries using a test of proportions based on the cumulative hypergeometric distribution. After multiple-testing correction, 20 GO categories and one IP entry showed significant overrepresentation of genes statistically associated with bull fertility. Several of these functional categories such as small GTPases mediated signal transduction, neurogenesis, calcium ion binding, and cytoskeleton are known to be involved in biological processes closely related to male fertility. These results could provide insight into the genetic architecture of this complex trait in dairy cattle. In addition, this study shows that quantitative trait pathways inferred from single-marker analyses could enhance our interpretations of the results of genome-wide association studies.
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