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Panigrahi M, Rajawat D, Nayak SS, Jain K, Vaidhya A, Prakash R, Sharma A, Parida S, Bhushan B, Dutt T. Genomic insights into key genes and QTLs involved in cattle reproduction. Gene 2024; 917:148465. [PMID: 38621496 DOI: 10.1016/j.gene.2024.148465] [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: 02/25/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
From an economic standpoint, reproductive characteristics are fundamental for sustainable production, particularly for monotocous livestock like cattle. A longer inter-calving interval is indicative of low reproductive capacity. This issue changes the dynamics of current and future lactations since it necessitates more inseminations, veterinary care, and hormone interventions. Various reproductive phenotypes, including ovulation, mating, fertility, pregnancy, embryonic growth, and calving-related traits, are observed in dairy cattle, and these traits have been associated with several QTLs. Calving ease, age at puberty, scrotal circumference, and inseminations per conception have been associated with 4437, 10623, 10498, and 2476 Quantitative Trait Loci (QTLs), respectively. This data offers valuable insights into enhancing and comprehending reproductive traits in livestock breeding. Studying QTLs associated with reproductive traits has far-reaching implications across various fields, from agriculture and animal husbandry to human health, evolutionary biology, and conservation. It provides the foundation for informed breeding practices, advances in biotechnology, and a deeper understanding of the genetic underpinnings of reproduction.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Ayushi Vaidhya
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Ravi Prakash
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Rocha RFB, Garcia AO, Dos Santos MG, Otto PI, da Silva MVB, Martins MF, Machado MA, Panetto JCC, Calus MPL, Guimarães SEF. Inheritance of genomic regions and genes associated with number of oocytes and embryos in Gir cattle through daughter design. J Dairy Sci 2024; 107:3794-3801. [PMID: 38310969 DOI: 10.3168/jds.2023-24111] [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: 08/22/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024]
Abstract
Over the past decades, daughter designs, including genotyped sires and their genotyped daughters, have been used as an approach to identify QTL related to economic traits. The aim of this study was to identify genomic regions inherited by Gir sire families and genes associated with number of viable oocytes (VO), total number of oocytes (TO), and number of embryos (EMBR) based on a daughter design approach. In total, 15 Gir sire families were selected. The number of daughters per family ranged from 26 to 395, which were genotyped with different SNP panels and imputed to the Illumina BovineHD BeadChip (777K) and had phenotypes for oocyte and embryo production. Daughters had phenotypic data for VO, TO, and EMBR. The search for QTL was performed through GWAS based on GBLUP. The QTL were found for each trait among and within families based on the top 10 genomic windows with the greatest genetic variance. For EMBR, genomic windows identified among families were located on BTA4, BTA5, BTA6, BTA7, BTA8, BTA13, BTA16, and BTA17, and they were most frequent on BTA7 within families. For VO, genomic windows were located on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA23, and BTA27 among families, being most frequent on BTA8 within families. For TO, the top 10 genomic windows were identified on BTA2, BTA4, BTA5, BTA7, BTA17, BTA21, BTA22, BTA26, and BTA27, being most frequent on BTA7 and BTA8 within families. Considering all results, the greatest number of genomic windows was found on BTA7, where the VCAN, XRCC4, TRNAC-ACA, HAPLN1, and EDIL3 genes were identified in the common regions. In conclusion, 15 Gir sire families with 26 to 395 daughters per family with phenotypes for oocyte and embryo production helped to identify the inheritance of several genomic regions, especially on BTA7, where the EDIL3, HAPLN1, and VCAN candidate genes were associated with number of oocytes and embryos in Gir cattle families.
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Affiliation(s)
- R F B Rocha
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil; Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, the Netherlands
| | - A O Garcia
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - M G Dos Santos
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - P I Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, RS, 97105-900, Brazil
| | - M V B da Silva
- EMBRAPA-Dairy Cattle, Juiz de Fora, MG, 36038-330, Brazil
| | - M F Martins
- EMBRAPA-Dairy Cattle, Juiz de Fora, MG, 36038-330, Brazil
| | - M A Machado
- EMBRAPA-Dairy Cattle, Juiz de Fora, MG, 36038-330, Brazil
| | - J C C Panetto
- EMBRAPA-Dairy Cattle, Juiz de Fora, MG, 36038-330, Brazil
| | - M P L Calus
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, the Netherlands
| | - S E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
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Contreras-Méndez LA, Medrano JF, Thomas MG, Enns RM, Speidel SE, Luna-Nevárez G, López-Castro PA, Rivera-Acuña F, Luna-Nevárez P. The Anti-Müllerian Hormone as Endocrine and Molecular Marker Associated with Reproductive Performance in Holstein Dairy Cows Exposed to Heat Stress. Animals (Basel) 2024; 14:213. [PMID: 38254382 PMCID: PMC10812537 DOI: 10.3390/ani14020213] [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: 11/14/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Anti-Müllerian hormone (AMH) is proposed as a biomarker for fertility in cattle, yet this associative relationship appears to be influenced by heat stress (HS). The objective was to test serum AMH and AMH-related single nucleotide polymorphisms (SNPs) as markers potentially predictive of reproductive traits in dairy cows experiencing HS. The study included 300 Holstein cows that were genotyped using BovineSNP50 (54,000 SNP). A genome-wide association study was then executed. Nine intragenic SNPs within the pathways that influence the AMH gene were found important with multiple comparisons adjustment tests (p < 1.09 × 10-6). A further validation study was performed in an independent Holstein cattle population, which was divided into moderate (MH; n = 152) and severe heat-stressed (SH; n = 128) groups and then subjected to a summer reproductive management program. Serum AMH was confirmed as a predictor of fertility measures (p < 0.05) in MH but not in the SH group. Cows were genotyped, which revealed four SNPs as predictive markers for serum AMH (p < 0.01), reproductive traits (p < 0.01), and additional physiological variables (p < 0.05). These SNPs were in the genes AMH, IGFBP1, LGR5, and TLR4. In conclusion, serum AMH concentrations and AMH polymorphisms are proposed as predictive markers that can be used in conjunction with genomic breeding value approaches to improve reproductive performance in Holstein cows exposed to summer HS conditions.
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Affiliation(s)
- Luis A. Contreras-Méndez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Juan F. Medrano
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | | | - R. Mark Enns
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Scott E. Speidel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pedro A. López-Castro
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Fernando Rivera-Acuña
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón 85000, Mexico
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Rocha RDFB, Garcia AO, Otto PI, Dos Santos MG, da Silva MVB, Martins MF, Machado MA, Panetto JCDC, Guimarães SEF. Single-step genome-wide association studies and post-GWAS analyses for the number of oocytes and embryos in Gir cattle. Mamm Genome 2023:10.1007/s00335-023-10009-0. [PMID: 37438444 DOI: 10.1007/s00335-023-10009-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/29/2023] [Indexed: 07/14/2023]
Abstract
Genome-Wide Association Studies (GWAS) are used for identification of quantitate trait loci (QTL) and genes associated with several traits. We aimed to identify genomic regions, genes, and biological processes associated with number of total and viable oocytes, and number of embryos in Gir dairy cattle. A dataset with 17,526 follicular aspirations, including the following traits: number of viable oocytes (VO), number of total oocytes (TO), and number of embryos (EMBR) from 1641 Gir donors was provided by five different stock farms. A genotype file with 2093 animals and 395,524 SNP markers was used to perform a single-step GWAS analysis for each trait. The top 10 windows with the highest percentage of additive genetic variance explained by 100 adjacent SNPs were selected. The genomic regions identified in our work were overlapped with QTLs from QTL database on chromosomes 1, 2, 5, 6, 7, 8, 9, 13, 17, 18, 20, 21, 22, 24, and 29. These QTLs were classified as External, Health, Meat and carcass, Production or Reproduction traits, and about 38% were related to Reproduction. In total, 117 genes were identified, of which 111 were protein-coding genes. Exclusively associations were observed for 42 genes with EMBR, and 1 with TO. Also, 42 genes were in common between VO and TO, 28 between VO and EMBR, and four genes were in common among all traits. In conclusion, great part of the identified genes plays a functional role in initial embryo development or general cell functions. The protein-coding genes ARNT, EGR1, HIF1A, AHR, and PAX2 are good markers for the production of oocytes and embryos in Gir cattle.
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Affiliation(s)
| | | | - Pamela Itajara Otto
- Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, RS, 97105-900, Brazil
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Al Kalaldeh M, Swaminathan M, Podtar V, Jadhav S, Dhanikachalam V, Joshi A, Gibson JP. Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows. Front Genet 2023; 13:1082802. [PMID: 36699459 PMCID: PMC9868639 DOI: 10.3389/fgene.2022.1082802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction: In India, crossbred cows incorporate the high production of B. taurus dairy breeds and the environmental adaptation of local B. indicus cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between B. indicus and B. taurus cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate B. indicus from B. taurus ancestry, as well as QTL that are segregating within the ancestral breeds. Methods: A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles. Results: At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of B. indicus versus B. taurus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98-49.44 Mbp) that differentiates B. indicus from B. taurus, with an estimated difference between homozygotes of approximately 10% of average yield, in favour of B. indicus origin. Discussion: Our results indicate that evolutionary differences between B. indicus and B. taurus cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.
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Affiliation(s)
- Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia,*Correspondence: Mohammad Al Kalaldeh, ; John P. Gibson,
| | - Marimuthu Swaminathan
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Vinod Podtar
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Santoshkumar Jadhav
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Velu Dhanikachalam
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Akshay Joshi
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - John P. Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia,*Correspondence: Mohammad Al Kalaldeh, ; John P. Gibson,
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Cortellari M, Bionda A, Negro A, Frattini S, Mastrangelo S, Somenzi E, Lasagna E, Sarti FM, Ciani E, Ciampolini R, Marletta D, Liotta L, Ajmone Marsan P, Pilla F, Colli L, Talenti A, Crepaldi P. Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems. Genet Sel Evol 2021; 53:92. [PMID: 34895134 PMCID: PMC8666052 DOI: 10.1186/s12711-021-00685-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00685-4.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Elisa Somenzi
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesca M Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Bari, Italy
| | | | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, Università degli Studi di Messina, Messina, Italy
| | - Paolo Ajmone Marsan
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti and BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy
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Zheng J, Deng T, Jiang E, Li J, Wijayanti D, Wang Y, Ding X, Lan X. Genetic variations of bovine PCOS-related DENND1A gene identified in GWAS significantly affect female reproductive traits. Gene 2021; 802:145867. [PMID: 34352299 DOI: 10.1016/j.gene.2021.145867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/13/2021] [Accepted: 07/30/2021] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have identified DENND1A as a potential candidate gene linked to the fertility-related phenotypes in dairy cows. However, to date, no studies have examined the association of the DENND1A insertion/deletions (indels) to bovine fertility on a large scale. Herein, two indel sites, including P4-del-26-bp and P8-ins-15-bp were identified in 1064 Holstein cows. The values of the minor allelic frequency (MAF) ranged between 0.471 (deletion) and 0.230 (deletion), respectively, and combined four different haplotypes by analyzing the haplotype combination. It is noteworthy that P4-del-26-bp is associated with the ovarian width (P = 0.0004) and corpus luteum diameter (P = 0.004). Meanwhile, P8-ins-15-bp was found to have a significant association with the ovarian width (P = 0.020), ovarian weight (P = 0.004), the number of mature follicles (P = 0.020), and diameter of the mature follicles (P = 0.016). Furthermore, the combinatorial analysis showed that the two indel combined-genotypes were significantly related to several reproductive traits (ovarian width, ovarian weight, etc.). Collectively, our findings indicated that these two novel indels and their combinations are correlated with the reproductive traits, and hence, they can serve in the marker-assisted selection (MAS) in cattle breeding. Nevertheless, further functional experiments are needed for understanding the mechanisms of these indels in cattle reproduction in a better way.
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Affiliation(s)
- Juanshan Zheng
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianyu Deng
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Enhui Jiang
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Li
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dwi Wijayanti
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongsheng Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
| | - Xianyong Lan
- Laboratory of Animal Genome and Gene Function, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle. Front Genet 2021; 12:699422. [PMID: 34306039 PMCID: PMC8299338 DOI: 10.3389/fgene.2021.699422] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Background In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip. Result De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent. Conclusion The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
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Affiliation(s)
- Satish Kumar Illa
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sabyasachi Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sapna Nath
- Artificial Breeding Research Center, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Anupama Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
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Jaton C, Schenkel FS, Chud TCS, Malchiodi F, Sargolzaei M, Price CA, Canovàs A, Baes C, Miglior F. Genetic and genomic analyses of embryo production in dairy cattle. Reprod Fertil Dev 2020; 32:50-55. [PMID: 32188557 DOI: 10.1071/rd19275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Canadian dairy industry has been using invivo and invitro assisted reproductive technologies to produce embryos. Technological improvements have helped increase the number and quality of embryos produced, but genetic and genomic tools for improving these traits have yet to be assessed for the Canadian Holstein population. Genetic parameters and a genome-wide association study were performed in Canadian Holstein for the total number of embryos (NE) and the number of viable embryos (VE). Results showed potential for genetic selection for both NE and VE, with heritability estimates (± s.e.) of approximately 0.15±0.01. Genetic correlations between the number of embryos produced using different procedures (invivo and invitro) suggested that a similar number of embryos should be expected from a donor regardless of the procedure used. A region on chromosome 11 of the bovine genome was found to be significantly associated with the number of embryos, indicating a potential regulatory role of this region on embryo production. Overall, these findings are of interest for the Canadian dairy industry because they provide useful information for breeders that are interested in producing embryos from the elite donors in their herds or in the population using assisted reproductive technologies.
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Affiliation(s)
- C Jaton
- The Semex Alliance, 5653 ON-6, Guelph, ON N1G 3Z2, Canada
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - T C S Chud
- Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - F Malchiodi
- The Semex Alliance, 5653 ON-6, Guelph, ON N1G 3Z2, Canada
| | - M Sargolzaei
- Select Sires Inc., 11740 US-42, Plain City, OH 43064, USA
| | - C A Price
- Université de Montréal, Faculté de médecine vétérinaire, 3200 Rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - A Canovàs
- Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - C Baes
- Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock (CGIL), University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada; and Ontario Genomics, 661 University Ave, Suite 490, Toronto, ON M5G 1M1, Canada; and Corresponding author.
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10
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Mikkola M, Hasler JF, Taponen J. Factors affecting embryo production in superovulated Bos taurus cattle. Reprod Fertil Dev 2020; 32:104-124. [PMID: 32188562 DOI: 10.1071/rd19279] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Despite a long history of bovine superovulation research, significant commercial applications did not start until the early 1970s. For some 20 years thereafter, superovulation represented the primary tool for the production of cattle embryos. In the early 1990s, commercial invitro production (IVP) was initiated in cattle. Although ovum pick-up and IVP are now commercially practiced on a wide scale, superovulation and embryo recovery by flushing remain a widespread and very effective approach to the production of cattle embryos. This review covers both the history and the effects of multiple factors on superovulation in Bos taurus cattle. There are three general protocols for suitable pre-FSH programming of donors so that gonadotrophin-responsive follicles are available. Superovulation protocols vary widely based on the FSH source, the diluent used, the number and timing of FSH injections and the timing and utilisation of various prostaglandins, controlled internal progesterone releasing devices, gonadotrophin-releasing hormone, and other means of controlling follicular development and ovulation. The number of oocytes that can be stimulated to grow and ovulate within any given donor can be estimated by either ultrasound-guided sonography or by measuring concentrations of anti-Müllerian hormone in the blood. Animal-related factors that can influence the efficacy of superovulation include cattle breed, age, parity, genetics, lactational status and reproductive history. In addition, nutrition, stress, season, climate, weather and several semen factors are discussed.
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Affiliation(s)
- M Mikkola
- Geno SA, Store Ree AI Station, Ekebergveien 54, 2335 Stange, Norway; and University of Helsinki, Department of Production Animal Medicine, FIN-04920 Saarentaus, Finland; and Corresponding author.
| | - J F Hasler
- Vetoquinol USA, 4250N Sylvania Avenue, Fort Worth, TX 76137, USA
| | - J Taponen
- University of Helsinki, Department of Production Animal Medicine, FIN-04920 Saarentaus, Finland
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11
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Abstract
Assisted reproduction techniques (ARTs) provide access to early stage embryos whose analysis and assessment deliver valuable information. The handling of embryos, including the in vitro production of bovine embryos, is a rapidly evolving area which nonetheless exposes the embryos to unnatural conditions for a period of time. The Fallopian tube provides innumerable quantitative and qualitative factors, all of which guarantee the successful development of the embryo. It is well known that the Fallopian tube can be bypassed, using embryo transfer, resulting in successful implantation in the target recipient animal and the birth of calves. However, the question arises as to whether such circumvention has a negative impact on the embryo during this sensitive development period. First crosstalk between the embryo and its environment confirms mutual recognition activities and indicate bilateral effects. Nowadays, in vitro production of bovine embryos is a well-established technology. However, it is still evident that in vitro generated embryos are not qualitatively comparable to embryos obtained ex vivo. To counteract these differences, comparative studies between in vitro and ex vivo embryos are advantageous, as embryos grown in their physiological environment can provide a blueprint or gold standard against which to compare embryos produced in vitro. Attempts to harness the bovine oviduct were sometimes very invasive and did not result in wide acceptance and routine use. Long-term development and refinement of transvaginal endoscopy for accessing the bovine oviduct has meanwhile been routinely applied for research as well as in practice. Comparative studies combining in vitro development with development in the cattle oviduct revealed that the environmental conditions to which the embryo is exposed before activation of the embryonic genome can have detrimental and lasting effects on its further development. These effects are manifested as deviations in gene expression profiles and methylation signatures as well as frequency of whole chromosomal or segmental aberrations. Furthermore, it was shown that hormonal superstimulation (multiple ovulation and embryo transfer), varying progesterone concentrations as well as metabolic disorders caused by high milk production, markedly affected embryo development in the postpartum period. Assisted reproductive techniques that allow the production and handling of extra numbers of generated embryos promise to have a very high impact on scientific and practical application. Any influence on the early embryonic life, both in animals and in vitro, is accompanied by a sensitive change in embryonic activity and should be assessed in vivo on the basis of physiological conditions before being used for ART.
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12
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Butty AM, Chud TCS, Miglior F, Schenkel FS, Kommadath A, Krivushin K, Grant JR, Häfliger IM, Drögemüller C, Cánovas A, Stothard P, Baes CF. High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. Sci Rep 2020; 10:8044. [PMID: 32415111 PMCID: PMC7229195 DOI: 10.1038/s41598-020-64680-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/15/2020] [Indexed: 12/15/2022] Open
Abstract
Multiple methods to detect copy number variants (CNV) relying on different types of data have been developed and CNV have been shown to have an impact on phenotypes of numerous traits of economic importance in cattle, such as reproduction and immunity. Further improvements in CNV detection are still needed in regard to the trade-off between high-true and low-false positive variant identification rates. Instead of improving single CNV detection methods, variants can be identified in silico with high confidence when multiple methods and datasets are combined. Here, CNV were identified from whole-genome sequences (WGS) and genotype array (GEN) data on 96 Holstein animals. After CNV detection, two sets of high confidence CNV regions (CNVR) were created that contained variants found in both WGS and GEN data following an animal-based (n = 52) and a population-based (n = 36) pipeline. Furthermore, the change in false positive CNV identification rates using different GEN marker densities was evaluated. The population-based approach characterized CNVR, which were more often shared among animals (average 40% more samples per CNVR) and were more often linked to putative functions (48 vs 56% of CNVR) than CNV identified with the animal-based approach. Moreover, false positive identification rates up to 22% were estimated on GEN information. Further research using larger datasets should use a population-wide approach to identify high confidence CNVR.
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Affiliation(s)
- Adrien M Butty
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Tatiane C S Chud
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Arun Kommadath
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Kirill Krivushin
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jason R Grant
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, BE, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, BE, Switzerland
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada. .,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, BE, Switzerland.
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13
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AMH: Could It Be Used as A Biomarker for Fertility and Superovulation in Domestic Animals? Genes (Basel) 2019; 10:genes10121009. [PMID: 31817280 PMCID: PMC6947652 DOI: 10.3390/genes10121009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022] Open
Abstract
Anti-Müllerian hormone (AMH) is a reliable and easily detectable reproductive marker for the fertility competence of many farm animal species. AMH is also a good predictor of superovulation in cattle, sheep, and mares. In this review, we have summarized the recent findings related to AMH and its predictive reliability related to fertility and superovulation in domestic animals, especially in cattle. We focused on: (1) the dynamics of AMH level from infancy to prepubescence as well as during puberty and adulthood; (2) AMH as a predictor of fertility; (3) the association between antral follicle count (AFC) and plasma AMH level; (4) AMH as a predictor of superovulation; and (5) factors affecting AMH levels in domestic animals, especially cattle. Many factors affect the circulatory levels of AMH when considering the plasma, like nutrition, activity of granulosa cells, disease state and endocrine disruptions during fetal life. Briefly, we concluded that AMH concentrations are static within individuals, and collection of a single dose of blood has become more popular in the field of assisted reproductive technologies (ART). It may act as a potential predictor of fertility, superovulation, and ovarian disorders in domestic animals. However, due to the limited research in domestic animals, this potential of AMH remains underutilized.
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14
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Gobikrushanth M, Purfield DC, Canadas ER, Herlihy MM, Kenneally J, Murray M, Kearney FJ, Colazo MG, Ambrose DJ, Butler ST. Anti-Müllerian hormone in grazing dairy cows: Identification of factors affecting plasma concentration, relationship with phenotypic fertility, and genome-wide associations. J Dairy Sci 2019; 102:11622-11635. [PMID: 31521342 DOI: 10.3168/jds.2019-16979] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/19/2019] [Indexed: 11/19/2022]
Abstract
The objectives of this study were to (1) characterize the distribution and variability of plasma anti-Müllerian hormone (AMH) concentration; (2) evaluate factors associated with phenotypic variation in plasma AMH; (3) examine the associations between categories of plasma AMH and reproductive outcomes [pregnancy to first artificial insemination (P/AI), and pregnancy rates within 21, 42, and 84 d after the mating start date (MSD)]; (4) estimate pedigree and genomic heritability for plasma AMH; and (5) identify and validate SNP associated with phenotypic variation in plasma AMH. Plasma AMH concentration (pg/mL) was determined from a blood sample collected (mean ± standard deviation) 10 ± 2 d after first insemination at detected estrus (IDE) in 2,628 first- and second-parity Irish dairy cows. Overall, plasma AMH had a positively skewed distribution with mean (± standard deviation), median, minimum, and maximum concentrations of 326 ± 231, 268, 15, and 2,863 pg/mL, respectively. Plasma AMH was greatest for Jersey, followed by Holstein × Jersey, Holstein × Norwegian Red, and Holstein cows (410, 332, 284, and 257 pg/mL, respectively). Second-parity cows had greater plasma AMH than first-parity cows (333 vs. 301 pg/mL, respectively). Samples collected at 7 and 8 d after first IDE had lesser plasma AMH than those collected on d 9, 10, 11, 12, and 13 after first IDE (291 and 297 vs. 317, 319, 331, 337, and 320 pg/mL). Plasma AMH was not associated with either body condition score at first IDE or the interval from calving to MSD. Cows were categorized into low (≤150 pg/mL; n = 526; lowest 20%), intermediate (>150 to ≤461 pg/mL; n = 1,576; intermediate 60%), and high AMH (>461 pg/mL; n = 526; highest 20%) groups based on plasma AMH, and associations with reproductive outcomes were tested. Cows with high and intermediate plasma AMH had 1.42- and 1.51-times-greater odds of becoming pregnant within 84 d after the MSD than those with low plasma AMH (90.3 and 90.8 vs. 86.8%, respectively); however, P/AI and pregnancy rate within 21 and 42 d after the MSD did not differ among AMH categories. Plasma AMH was moderately heritable (pedigree heritability of 0.40 ± 0.06 and genomic heritability of 0.45 ± 0.05), and 68 SNP across Bos taurus autosomes 7 and 11 were associated with phenotypic variation in plasma AMH. Out of 68 SNP, 42 were located in a single quantitative trait locus on Bos taurus autosome 11 that harbored 6 previously identified candidate genes (NR5A1, HSPA5, CRB2, DENND1A, NDUFA8, and PTGS) linked to fertility-related phenotypes in dairy cows.
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Affiliation(s)
- M Gobikrushanth
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G 2P5; Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland, P61 C996
| | - D C Purfield
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland, P61 C996
| | - E R Canadas
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland, P61 C996
| | - M M Herlihy
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland, P61 C996
| | - J Kenneally
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland, P61 C996
| | - M Murray
- Teagasc, Grange, Dunsany, Co. Meath, Ireland, C15 PW93
| | - F J Kearney
- Irish Cattle Breeding Association, Highfield House, Shinagh, Bandon, Co. Cork, Ireland, P72 X050
| | - M G Colazo
- Livestock Systems Section, Alberta Agriculture and Forestry, Edmonton, AB, Canada T6H 5T6
| | - D J Ambrose
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G 2P5; Livestock Systems Section, Alberta Agriculture and Forestry, Edmonton, AB, Canada T6H 5T6
| | - S T Butler
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland, P61 C996.
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15
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Mossa F, Ireland JJ. Physiology and endocrinology symposium: Anti-Müllerian hormone: a biomarker for the ovarian reserve, ovarian function, and fertility in dairy cows. J Anim Sci 2019; 97:1446-1455. [PMID: 30668706 DOI: 10.1093/jas/skz022] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/15/2019] [Indexed: 12/24/2022] Open
Abstract
This review summarizes studies we conducted to test the hypothesis that size of the ovarian reserve (number of healthy follicles and oocytes in ovaries) positively impacts ovarian function and fertility in cattle. Key results, primarily in Bos taurus dairy cattle, show that antral follicle count (AFC) during follicular waves is highly variable between individuals, but very highly repeatable within individuals. Cycling heifers with low (≤15 follicles ≥3 mm, ~20% of a herd) vs. a high AFC (≥25, ~20% of a herd) have a smaller ovarian reserve, higher FSH but lower anti-Müllerian hormone (AMH), androstenedione, estradiol, and progesterone concentrations. Moreover, cattle with low AFC have a thinner endometrium, decreased response of granulosal, thecal, or luteal cells to FSH or LH and a poorer response to superovulation compared to cattle with high AFC. Interestingly, cows with a very high AFC as heifers have reduced fertility, fewer lactations, and shorter herd longevity, whereas cows with a low vs. intermediate AFC have reduced fertility, fewer lactations, and shorter herd longevity. Anti-Müllerian hormone concentrations are static within individuals but highly positively correlated with AFC, but fertility is not correlated with circulating AMH concentration in heifers and dairy cows with low vs. a higher AMH as heifers have reduced fertility and a shorter herd longevity. Anti-Müllerian hormone concentrations in dairy heifers are a moderately heritable trait (36%), and negatively impacted by inadequate maternal nutrition during early pregnancy or high maternal somatic cell count. We conclude that genetic or environmental manipulations of AMH could enhance size of the ovarian reserve and ovarian function, thereby improving fertility, response to superovulation, and longevity in dairy cows.
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Affiliation(s)
- Francesca Mossa
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - James J Ireland
- Molecular Reproductive Endocrinology Laboratory, Department of Animal Science, Michigan State University, East Lansing, MI
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16
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Nawaz MY, Jimenez-Krassel F, Steibel JP, Lu Y, Baktula A, Vukasinovic N, Neuder L, Ireland JLH, Ireland JJ, Tempelman RJ. Genomic heritability and genome-wide association analysis of anti-Müllerian hormone in Holstein dairy heifers. J Dairy Sci 2018; 101:8063-8075. [PMID: 30007805 DOI: 10.3168/jds.2018-14798] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/16/2018] [Indexed: 01/18/2023]
Abstract
Anti-Müllerian hormone (AMH) is an ovarian growth factor that plays an important role in regulation of ovarian follicle growth. The objectives of this study were to estimate the genomic heritability of AMH and identify genomic regions associated with AMH production in a genome-wide association (GWA) analysis. Concentrations of AMH were determined in 2,905 dairy Holstein heifers genotyped using the Zoetis medium density panel (Zoetis Inclusions, Kalamazoo, MI) with 54,519 single nucleotide polymorphism (SNP) markers remaining after standard genotype quality control edits. A linear mixed model was used to model the random effects of sampling day and genomics on the logarithm of AMH. The genomic heritability (± standard error of the mean) of AMH was estimated to be 0.36 ± 0.03. Our GWA analysis inferred significant associations between AMH and 11 SNP markers on chromosome 11 and 1 SNP marker on chromosome 20. Annotated genes with significant associations were identified using the Ensembl genome database (version 88) of the cow genome (version UMD 3.1; https://www.ensembl.org/biomart). Gene set enrichment analysis revealed that 2 gene ontology (GO) terms were significantly enriched in the list of candidate genes: G-protein coupled receptor signaling pathway (GO:0007186) and the detection of chemical stimulus involved in sensory perception (GO:0050907). The estimated high heritability and previously established associations between AMH and ovarian follicular reserve, fertility, longevity, and superovulatory response in cattle implies that AMH could be used as a biomarker for genetic improvement of reproductive potential.
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Affiliation(s)
- M Y Nawaz
- Department of Animal Science, Michigan State University, East Lansing 48823
| | - F Jimenez-Krassel
- Department of Animal Science, Michigan State University, East Lansing 48823
| | - J P Steibel
- Department of Animal Science, Michigan State University, East Lansing 48823
| | - Y Lu
- Department of Animal Science, Michigan State University, East Lansing 48823
| | - A Baktula
- Zoetis Inclusions, Kalamazoo, MI 49007
| | | | - L Neuder
- Green Meadow Dairy Farm, Elsie, MI 48831
| | - J L H Ireland
- Department of Animal Science, Michigan State University, East Lansing 48823
| | - J J Ireland
- Department of Animal Science, Michigan State University, East Lansing 48823
| | - R J Tempelman
- Department of Animal Science, Michigan State University, East Lansing 48823.
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