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Rocha VCP, Alves JS, Costa RB, de Camargo GMF. Variability in the PRDM9 gene in Sindhi cattle. Mol Biol Rep 2023; 50:8839-8842. [PMID: 37658931 DOI: 10.1007/s11033-023-08778-7] [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: 08/04/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Sindhi is a dual-purpose breed adapted to tropical environments. However, this breed has the smallest total population among indicine breeds in Brazil and the smallest effective number. In addition, the inbreeding coefficient is higher than 6.25% in ~ 60% of the population. Therefore, alternatives to increase genetic diversity are important. Within this context, the PRDM9 gene is particularly interesting since it is involved in meiotic recombination events, consequently enhancing genetic variability in the population by increasing the number of circulating haplotypes. Each allele of the gene induces recombination at a different hotspot. The larger the number of circulating alleles, the higher the recombination rate and the greater the genetic variability. METHODS The aim of this study was to characterize alleles of the PRDM9 gene in Sindhi cattle. The region of the zinc finger domains of the gene was amplified by PCR, genotyped, and sequenced for allele identification in 50 Sindhi animals. RESULTS Three alleles (A-cattle1, B-cattle14, and C-cattle19) and six genotypes (AA, BB, CC, AB, AC, and BC) were identified. CONCLUSION The allele variation of the PRDM9 gene in the Sindhi breed enables to guide the mating of animals with different genotypes/alleles and to promote genetic variability by recombination if there is intralocus variability.
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Affiliation(s)
| | - Jackeline Santos Alves
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brasil
| | - Raphael Bermal Costa
- Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia, (UFBA), Salvador, BA, Brasil
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Wang X, Li Z, Feng T, Luo X, Xue L, Mao C, Cui K, Li H, Huang J, Huang K, Rehman SU, Shi D, Wu D, Ruan J, Liu Q. Chromosome-level genome and recombination map of the male buffalo. Gigascience 2022; 12:giad063. [PMID: 37589307 PMCID: PMC10433102 DOI: 10.1093/gigascience/giad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/20/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND The swamp buffalo (Bubalus bubalis carabanesis) is an economically important livestock supplying milk, meat, leather, and draft power. Several female buffalo genomes have been available, but the lack of high-quality male genomes hinders studies on chromosome evolution, especially Y, as well as meiotic recombination. RESULTS Here, a chromosome-level genome with a contig N50 of 72.2 Mb and a fine-scale recombination map of male buffalo were reported. We found that transposable elements (TEs) and structural variants (SVs) may contribute to buffalo evolution by influencing adjacent gene expression. We further found that the pseudoautosomal region (PAR) of the Y chromosome is subject to stronger purification selection. The meiotic recombination map showed that there were 2 obvious recombination hotspots on chromosome 8, and the genes around them were mainly related to tooth development, which may have helped to enhance the adaption of buffalo to inferior feed. Among several genomic features, TE density has the strongest correlation with recombination rates. Moreover, the TE subfamily, SINE/tRNA, is likely to play a role in driving recombination into SVs. CONCLUSIONS The male genome and sperm sequencing will facilitate the understanding of the buffalo genomic evolution and functional research.
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Affiliation(s)
- Xiaobo Wang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Lintao Xue
- Reproductive Medical and Genetic Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Chonghui Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Saif-ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
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AHLAWAT SONIKA, SHARMA REKHA, ARORA REENA, SHARMA HIMANI, SEHRAWAT RENUKA, SHARMA ANNU, SINGH KARANVEER, VIJH RAMESHKUMAR. Fertility of hybrids of dromedary and Bactrian camels: A possible role of conserved architecture of zinc finger domain of recombination regulator PRDM9. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i12.112968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recombination regulator, PRDM9, has been regarded as the most rapidly evolving gene in the genomes of many metazoans, in addition to being acknowledged as the sole speciation gene in vertebrates. It has become the focus of many scientific investigations because of exceptional numerical and sequence variability in its zinc finger (ZF) domain within and across species that contributes to reproductive isolation between species. This study is the maiden attempt to explore the architecture of PRDM9 ZF domain in two Camelid species (Camelus dromedarius and Camelus bactrianus). Sequence analysis revealed highly conserved domain architecture with presence of 3 and 4 ZFs in dromedary and Bactrian camels, respectively. Typical evolutionary features of PRDM9 ZF domain i.e. concerted evolution and positive selection were invariably absent in both the one-humped dromedary and the two-humped Bactrian camels. Fertility of hybrids of dromedary and Bactrian camels, despite being taxonomically distinct species can be attributed to the lack of sequence variability in PRDM9 in these species. Phylogenetic analysis underpinned clear demarcation of camels from other livestock species. The results of the present study defy what has been learnt so far about PRDM9 and add to the enigma surrounding the most intriguing gene in the genome.
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Kaur R, Ahlawat S, Choudhary V, Kumari A, Chhabra P, Arora R, Sharma R, Vijh RK. Comparative expression profiling of cytokine genes in Theileria annulata–infected and healthy cattle. Trop Anim Health Prod 2022; 54:383. [DOI: 10.1007/s11250-022-03381-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
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Leonard AS, Crysnanto D, Fang ZH, Heaton MP, Vander Ley BL, Herrera C, Bollwein H, Bickhart DM, Kuhn KL, Smith TPL, Rosen BD, Pausch H. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun 2022; 13:3012. [PMID: 35641504 PMCID: PMC9156671 DOI: 10.1038/s41467-022-30680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Michael P Heaton
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA.
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
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Damm E, Ullrich KK, Amos WB, Odenthal-Hesse L. Evolution of the recombination regulator PRDM9 in minke whales. BMC Genomics 2022; 23:212. [PMID: 35296233 PMCID: PMC8925151 DOI: 10.1186/s12864-022-08305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background PRDM9 is a key regulator of meiotic recombination in most metazoans, responsible for reshuffling parental genomes. During meiosis, the PRDM9 protein recognizes and binds specific target motifs via its array of C2H2 zinc-fingers encoded by a rapidly evolving minisatellite. The gene coding for PRDM9 is the only speciation gene identified in vertebrates to date and shows high variation, particularly in the DNA-recognizing positions of the zinc-finger array, within and between species. Across all vertebrate genomes studied for PRDM9 evolution, only one genome lacks variability between repeat types – that of the North Pacific minke whale. This study aims to understand the evolution and diversity of Prdm9 in minke whales, which display the most unusual genome reference allele of Prdm9 so far discovered in mammals. Results Minke whales possess all the features characteristic of PRDM9-directed recombination, including complete KRAB, SSXRD and SET domains and a rapidly evolving array of C2H2-type-Zincfingers (ZnF) with evidence of rapid evolution, particularly at DNA-recognizing positions that evolve under positive diversifying selection. Seventeen novel PRDM9 variants were identified within the Antarctic minke whale species, plus a single distinct PRDM9 variant in Common minke whales – shared across North Atlantic and North Pacific minke whale subspecies boundaries. Conclusion The PRDM9 ZnF array evolves rapidly, in minke whales, with at least one DNA-recognizing position under positive selection. Extensive PRDM9 diversity is observed, particularly in the Antarctic in minke whales. Common minke whales shared a specific Prdm9 allele across subspecies boundaries, suggesting incomplete speciation by the mechanisms associated with PRDM9 hybrid sterility. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08305-1.
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Affiliation(s)
- Elena Damm
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany
| | - Kristian K Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany
| | - William B Amos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany.
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Niayale R, Cui Y, Adzitey F. Male hybrid sterility in the cattle-yak and other bovines: a review. Biol Reprod 2020; 104:495-507. [PMID: 33185248 DOI: 10.1093/biolre/ioaa207] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/16/2020] [Accepted: 11/11/2020] [Indexed: 12/19/2022] Open
Abstract
Hybridization is important for both animal breeders attempting to fix new phenotypic traits and researchers trying to unravel the mechanism of reproductive barriers in hybrid species and the process of speciation. In interspecies animal hybrids, gains made in terms of adaptation to environmental conditions and hybrid vigor may be offset by reduced fertility or sterility. Bovine hybrids exhibit remarkable hybrid vigor compared to their parents. However, the F1 male hybrid exhibits sterility, whereas the female is fertile. This male-biased sterility is consistent with the Haldane rule where heterogametic sex is preferentially rare, absent, or sterile in the progeny of two different species. The obstacle of fixing favorable traits and passing them to subsequent generations due to the male sterility is a major setback in improving the reproductive potential of bovines through hybridization. Multiperspective approaches such as molecular genetics, proteomics, transcriptomics, physiology, and endocrinology have been used by several researchers over the past decade in an attempt to unravel the potential mechanisms underlying male hybrid sterility. However, the mechanism of sterility in the hybrid male is still not completely unravelled. This review seeks to provide an update of the mechanisms of the sterility in the cattle-yak and other bovines.
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Affiliation(s)
- Robert Niayale
- Laboratory of Animal Anatomy & Tissue Embryology, Department of Basic Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu Province, China.,Faculty of Agriculture, Animal Science Department, University for Development Studies, Tamale, Ghana
| | - Yan Cui
- Laboratory of Animal Anatomy & Tissue Embryology, Department of Basic Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Fredrick Adzitey
- Faculty of Agriculture, Animal Science Department, University for Development Studies, Tamale, Ghana
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8
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Li YC, Wang GW, Xu SR, Zhang XN, Yang QE. The expression of histone methyltransferases and distribution of selected histone methylations in testes of yak and cattle-yak hybrid. Theriogenology 2020; 144:164-173. [PMID: 31972460 DOI: 10.1016/j.theriogenology.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 01/01/2020] [Accepted: 01/01/2020] [Indexed: 01/23/2023]
Abstract
Interspecies hybridization exists widely in nature and plays an important role in animal evolution and adaptation. It is commonly recognized that male offspring of interspecies hybrid are often sterile, which presents a crucial way of reproductive isolation. Currently, the mechanisms underlying interspecies hybrid male sterility are not well understood. Cattle-yak, progeny of yak (Bos grunniens) and cattle (Bos taurus) cross, is a unique animal model for investigating hybrid male sterility. Because histone modifications are vital for spermatogenesis, herein, we examined expressions of histone methyltransferases (HMTs) and distributions of histone methylations in the yak and cattle-yak testis. Histological examination of seminiferous tubules revealed that gonocytes and spermatocytes were established normally, however, spermatogenesis was arrested at the meiosis phase began at 10 months after birth in the hybrids. SUV420H1 was the only HMT examined showing a significant enrichment in cattle-yak testes at 3 months. Relative expressions of MLL5, SETDB1 and SUV420H1 were increased while SETDB2 and EZH2 were decreased in cattle-yak testes at 10 months. Relative concentrations of MLL5 and SUV420H1 were again increased while EHMT2 and PRDM9 expressions were decreased at 24 months. Immunofluorescent detection of selected histone methylations in cross-sections of testicular tissues or meiotic chromosomes demonstrated that depletion of H3K4me3 and significant enrichment of H3K27me3 and H4K20me3 were observed in Sertoli cells of cattle-yak. Levels and localizations of H3K4me3, H3K9me1, H3K9me3 and H4K20me3 were strikingly different in meiotic chromosomes of cattle-yak spermatocytes. These results highlighted the potential roles of histone methylations in spermatogenic failure and hybrid male sterility.
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Affiliation(s)
- Yong-Chang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guo-Wen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang-Rong Xu
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, Qinghai, 810008, China
| | - Xiao-Na Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810001, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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Seroussi E, Shirak A, Gershoni M, Ezra E, de Abreu Santos DJ, Ma L, Liu GE. Bos taurus-indicus hybridization correlates with intralocus sexual-conflict effects of PRDM9 on male and female fertility in Holstein cattle. BMC Genet 2019; 20:71. [PMID: 31462216 PMCID: PMC6714232 DOI: 10.1186/s12863-019-0773-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Crossover localization during meiotic recombination is mediated by the fast-evolving zinc-finger (ZnF) domain of gene PRDM9. To study its impact on dairy cattle performance, we compared its genetic variation between the relatively small Israeli (IL) Holsteins and the North American (US) Holsteins that count millions. RESULTS Initially, we analyzed the major BTA1 haplotypes present in IL Holsteins based on the 10 most telomeric SNPs of the BovineSNP50 BeadChip. Sequencing of representative haplotype carriers indicated that for all frequent haplotypes (> 6%), the variable PRDM9 ZnF array consisted of seven tandem ZnF repeats. Two rare haplotypes (frequency < 4%) carried an indicine PRDM9, whereas all others were variants of the taurine type. These two haplotypes included the minor SNP allele, which was perfectly linked with a previously described PRDM9 allele known to induce unique localization of recombination hotspots. One of them had a significant (p = 0.03) negative effect on IL sire fertility. This haplotype combined the rare minor alleles of the only SNPs with significant (p < 0.05) negative substitution effects on US sire fertility (SCR). Analysis of telomeric SNPs indicated general agreement of allele frequencies (R = 0.95) and of the substitution effects on sire fertility (SCR, R = 0.6) between the US and IL samples. Surprisingly, the alleles that had a negative impact on male fertility had the most positive substitution effects on female fertility traits (DPR, CCR and HCR). CONCLUSIONS A negative genetic correlation between male and female fertility is encoded within the BTA1 telomere. Cloning the taurine PRDM9 gene, which is the common form carried by Holsteins, we encountered the infiltration of an indicine PRDM9 variant into this population. During meiosis, in heterozygous males, the indicine PRDM9 variant may induce incompatibility of recombination hotspots and male infertility. However, this variant is associated with favorable female fertility, which would explain its survival and the general negative correlation (R = - 0.3) observed between male and female fertility in US Holsteins. Further research is needed to explain the mechanism underlying this positive effect and to devise a methodology to unlink it from the negative effect on male fertility during breeding.
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Affiliation(s)
- Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel.
| | - Andrey Shirak
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Moran Gershoni
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Ephraim Ezra
- Israel Cattle Breeders Association, Caesarea, Israel
| | | | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
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AHLAWAT SONIKA, SAROVA NEHA, SHARMA REKHA, ARORA REENA, TANTIA MS. Promoter DNA methylation and expression analysis of PIWIL1 gene in purebred and crossbred cattle bulls. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i7.92014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Major credit for India being the largest producer of milk in the world, goes to crossbred cows produced by inseminating low-producing indigenous cattle with semen from high producing exotic bulls. However, over the years, the policy of crossbreeding has been confronted with a major problem of subfertility in crossbred male progenies, culminating into disposal of a major fraction of mature bulls. Many studies have demonstrated relationship between epigenetic alterations and male fertility across different species. PIWIL1 is an important candidate gene for spermatogenesis and germ line development. Negative correlation between DNA methylation and expression of this gene has been highlighted in inter species hybrids of cattle and yaks. The present study envisaged elucidating promoter methylation status and expression profile of PIWIL1 gene in exotic Holstein Friesian cattle, indigenous Sahiwal cattle and their crossbreds with varying semen motility parameters. Semen samples were collected from bulls for isolation of DNA and RNA from spermatozoa. Bisulfite converted DNA was used to amplify promoter of PIWIL1 gene using methylation specific primers. The amplified products were sequenced after cloning in pTZ57R/ T vector. The degree of methylation of the PIWIL1 promoter region was significantly higher in poor motility crossbred bulls (7.17%) as compared to good motility crossbreds (1.02%), Sahiwal (1.02%) and Holstein Friesian bulls (0.77%). PIWIL1 expression was 1.75, 1.71 and 1.59 folds higher in HF, Sahiwal and good motility crossbreds, respectively as compared to poor motility crossbreds.
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11
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Ahlawat S, Sharma R, Arora R, Kumari N, Mishra AK, Tantia MS. Promoter methylation and expression analysis of Bvh gene in bulls with varying semen motility parameters. Theriogenology 2018; 125:152-156. [PMID: 30447494 DOI: 10.1016/j.theriogenology.2018.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 10/09/2018] [Accepted: 11/04/2018] [Indexed: 12/18/2022]
Abstract
Crossbreds of low-producing indigenous cattle and high-producing exotic dairy bulls (Holstein Friesian and Jersey) have contributed in ensuring that India continues to be the world's top milk-producing country. However, subfertility observed in crossbred male progenies has been a major obstacle in exploitation of heterosis due to crossbreeding. There is sufficient scientific evidence in support of genetic and epigenetic regulation of key physiological processes including spermatogenesis. Bovine Vasa Homology (Bvh) is considered a molecular marker for the study of gametogenesis. Significant negative correlation between DNA methylation and gene expression has been reported in cattle-yaks hybrids and their parents. The present study analyzed promoter methylation status and expression profile of Bvh gene in spermatozoa from exotic Holstein Friesian cattle, indigenous Sahiwal cattle and their crossbreds with varying semen motility parameters. The degree of methylation of the Bvh promoter region was significantly higher in poor motility crossbred bulls (13.3%) as compared to good motility crossbreds (5.3%), Sahiwal (3%) and Holstein Friesian bulls (1%) (P < 0.05). Gene expression analysis revealed significantly higher mRNA abundance of Bvh in purebreds (Holstein Friesian and Sahiwal) as compared to crossbred counterparts (P < 0.001). Inverse correlation observed in this study between promoter methylation and gene expression of Bvh gene in spermatozoa from crossbred bulls with poor motility phenotype as compared to purebred parents provides an important insight into understanding the graded fertility of crossbred bulls.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Namita Kumari
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - A K Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Tiemann-Boege I, Schwarz T, Striedner Y, Heissl A. The consequences of sequence erosion in the evolution of recombination hotspots. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0462. [PMID: 29109225 PMCID: PMC5698624 DOI: 10.1098/rstb.2016.0462] [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] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans-acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro. Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
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Affiliation(s)
- Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Theresa Schwarz
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Angelika Heissl
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
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Sarova N, Ahlawat S, Grewal A, Sharma R, Arora R. Differential promoter methylation of DAZL gene in bulls with varying seminal parameters. Reprod Domest Anim 2018; 53:914-920. [PMID: 29604148 DOI: 10.1111/rda.13187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/03/2018] [Indexed: 12/19/2022]
Abstract
In India, cross-breeding of indigenous cattle with exotic cattle such as Holstein Friesian and Jersey has been going on since last four decades to improve milk production. Although it has led to increased milk yield, the subfertility in male cross-bred progeny has remained a significant problem. Epigenetic modifications (DNA methylation, histone modifications and chromatin remodelling) are regarded as key players influencing gene expression. DAZL gene plays an important role in germline development and gametogenesis. The methylation and mRNA expression level of this gene have been significantly negatively correlated in the testes of cattle-yak hybrids and their parents. This study analysed the methylation profile of DAZL gene promoter in bull spermatozoa in an attempt to speculate its role in cross-bred cattle subfertility. Semen samples from Sahiwal, Holstein Friesian and Frieswal bulls (Sahiwal X Holstein Friesian) with varying semen motility parameters were collected, and DNA was isolated. Methylation-specific primers were used to amplify part of promoter and exon 1 of DAZL gene using bisulphite-converted DNA. The amplified products were sequenced after cloning in pTZ57R/T vector. Sequence analysis revealed significantly higher DNA methylation of DAZL gene in Frieswal bulls with poor motility (28.26%) as compared to medium (15.21%) and high motility phenotype (6.52%). In pure-bred counterparts, Sahiwal and Holstein Friesian, epigenetic marks were more in the former (15.21%) than the latter (4.34%), but in both cases, the values were lower as compared to the poor motility Frieswal bulls. This suggests that differential hypermethylation of the CpG islands could possibly influence reproductive parameters in bovines.
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Affiliation(s)
- N Sarova
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - S Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - A Grewal
- University Institute of Engineering and Technology, Kurukshetra, India
| | - R Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - R Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Paigen K, Petkov PM. PRDM9 and Its Role in Genetic Recombination. Trends Genet 2018; 34:291-300. [PMID: 29366606 DOI: 10.1016/j.tig.2017.12.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022]
Abstract
PRDM9 is a zinc finger protein that binds DNA at specific locations in the genome where it trimethylates histone H3 at lysines 4 and 36 at surrounding nucleosomes. During meiosis in many species, including humans and mice where PRDM9 has been most intensely studied, these actions determine the location of recombination hotspots, where genetic recombination occurs. In addition, PRDM9 facilitates the association of hotspots with the chromosome axis, the site of the programmed DNA double-strand breaks (DSBs) that give rise to genetic exchange between chromosomes. In the absence of PRDM9 DSBs are not properly repaired. Collectively, these actions determine patterns of genetic linkage and the possibilities for chromosome reorganization over successive generations.
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