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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [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: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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Kour A, Deb SM, Nayee N, Niranjan SK, Raina VS, Mukherjee A, Gupta ID, Patil CS. Novel insights into genome-wide associations in Bos indicus reveal genetic linkages between fertility and growth. Anim Biotechnol 2023; 34:39-55. [PMID: 34120566 DOI: 10.1080/10495398.2021.1932520] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bos indicus breed Sahiwal, famous for its optimum performance, has so far been genetically improved for performance traits based on phenotypic records and the genomic knowhow regarding genes, regions and biological processes underlying the complex quantitative traits is lacking. In this context, a Genome-wide Association Study was performed for fertility and growth traits in Sahiwal cattle to shed light on its genomic profile. A total of 46 SNPs were found associated with the traits at genome-wide suggestive threshold of P ≤ 10-4. USP32, LRPPRC, PLA2G10, RRN3 and ASAP1 were identified as putative candidate genes for body weight at different ages. However, several genes mapped for growth traits like GREB1, PLA2G10, RAD51C, BIRC6, TEX14 and PEBP4 had significant physiological underpinnings in determining fertility of the animals. Moreover, Quantitative trait loci (QTL) identification revealed potential overlaps with the already reported QTLs for both fertility and growth for most of the traits. Further, candidate SNP enrichment analysis revealed an enriched biological process for birth weight with a significant reproductive role. Based on the findings, genetic linkages underlying fertility and growth could be discerned in Sahiwal population and may be utilized for improving fertility traits in future.
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Affiliation(s)
- Aneet Kour
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | | | - Nilesh Nayee
- National Dairy Development Board, Anand, Gujarat, India
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Oviduct Transcriptomic Reveals the Regulation of mRNAs and lncRNAs Related to Goat Prolificacy in the Luteal Phase. Animals (Basel) 2022; 12:ani12202823. [PMID: 36290212 PMCID: PMC9597788 DOI: 10.3390/ani12202823] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The kidding number is an important reproductive trait in domestic goats. The oviduct, as one of the most major organs, is directly involved in the reproductive process, providing nutrition and a location for early embryonic development. The current study provides genome-wide expression profiles of mRNA and long noncoding RNAs (lncRNAs) expression in Yunshang black goat, a new breed of meat goat bred in China with a high kidding number. During the luteal phases, oviduct mRNAs and lncRNAs associated with high- and low-fecundity Yunshang black goats were identified, and their potential biological functions were predicted using GO, KEGG, and GSEA enrichment analysis. These findings shed light on the oviduct-based prolificacy mechanism in goats. Abstract The oviduct is associated with embryo development and transportation and regulates the pregnancy success of mammals. Previous studies have indicated a molecular mechanism of lncRNAs in gene regulation and reproduction. However, little is known about the function of lncRNAs in the oviduct in modulating goat kidding numbers. Therefore, we combined RNA sequencing (RNA-seq) to map the expression profiles of the oviduct at the luteal phase from high- and low-fecundity goats. The results showed that 2023 differentially expressed mRNAs (DEGs) and 377 differentially expressed lncRNAs (DELs) transcripts were screened, and 2109 regulated lncRNA-mRNA pairs were identified. Subsequently, the genes related to reproduction (IGF1, FGFRL1, and CREB1) and those associated with embryonic development and maturation (DHX34, LHX6) were identified. KEGG analysis of the DEGs revealed that the GnRH- and prolactin-signaling pathways, progesterone-mediated oocyte maturation, and oocyte meiosis were related to reproduction. GSEA and KEGG analyses of the target genes of DELs demonstrated that several biological processes and pathways might interact with oviduct functions and the prolificacy of goats. Furthermore, the co-expression network analysis showed that XLOC_029185, XLOC_040647, and XLOC_090025 were the cis-regulatory elements of the DEGs MUC1, PPP1R9A, and ALDOB, respectively; these factors might be associated with the success of pregnancy and glucolipid metabolism. In addition, the GATA4, LAMA2, SLC39A5, and S100G were trans-regulated by lncRNAs, predominantly mediating oviductal transport to the embryo and energy metabolism. Our findings could pave the way for a better understanding of the roles of mRNAs and lncRNAs in fecundity-related oviduct function in goats.
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Naji MM, Utsunomiya YT, Sölkner J, Rosen BD, Mészáros G. Assessing Bos taurus introgression in the UOA Bos indicus assembly. Genet Sel Evol 2021; 53:96. [PMID: 34922445 PMCID: PMC8684283 DOI: 10.1186/s12711-021-00688-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022] Open
Abstract
Background Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus—B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus—B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references. Results The alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. Conclusions We report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00688-1.
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Affiliation(s)
- Maulana M Naji
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Yuri T Utsunomiya
- AgroPartners Consulting, R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, São Paulo, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Johann Sölkner
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA, ARS, Beltsville, MD, USA.
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Zhong K, Chen D, Wu Z, Wang X, Pan B, Chen N, Zhong W. [Effect of small interfering RNA-mediated BIRC6 silencing on apoptosis and autophagy of renal cancer 786-O cells]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:1651-1655. [PMID: 33243730 DOI: 10.12122/j.issn.1673-4254.2020.11.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To study the expression of BIRC6 in renal cancer tissues and investigate the effect of BIRC6 silencing on apoptosis and autophagy of 786-O cells. METHODS Twenty surgical specimens of renal cancer tissues and adjacent renal tissues were collected from Meizhou People's Hospital between February, 2016 and December, 2018 for detection of BIRC6 protein expression using immunohistochemistry. Renal cancer 786-O cells were transfected with a control small interfering RNA (siRNA) or BIRC6 siRNA via lipofectamine 2000, and the changes in cell proliferation and apoptosis following 5-FU treatment were assessed using CCK8 assay and flow cytometry; the expressions of autophagy-related proteins Beclin and LC3A/B were detected by Western blotting. RESULTS The expression of BIRC6 protein was significantly higher in renal cancer tissues than in the adjacent renal tissues. Western blotting showed that siRNA-mediated silencing of BIRC6 significantly lowered the expression of BIRC6 in 786-O cells. In the cells with BIRC6 silencing, treatment with 12.5, 25, 50, 100 and 200 μg/mL 5-FU resulted in significantly higher proliferation inhibition rates than in the cells transfected with the control siRNA (P < 0.01). BIRC6 silencing also significantly increased the apoptosis rate of 786-O cells following 5-FU treatment (P < 0.01). The results of Western blotting showed that BIRC6 silencing significantly lowered the protein expressions of Beclin and LC3A/B in 786-O cells. CONCLUSIONS Interference of BIRC6 mediated by siRNA can inhibit autophagy and promote 5-FU-induced apoptosis to enhance the sensitivity of 786-O cells to 5-FU.
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Affiliation(s)
- Kaihua Zhong
- Department of Urology, Meizhou People's Hospital, Meizhou 514031, China
| | - Dong Chen
- Department of Urology, Sun Yat-sen Cancer Center, Guangzhou 510060, China
| | - Zhiming Wu
- Department of Urology, Sun Yat-sen Cancer Center, Guangzhou 510060, China
| | - Xiaohong Wang
- Department of Nephrology, Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China
| | - Bin Pan
- Department of Urology, First Affiliated Hospital of Jinan University, Guangzhou 510630, China
| | - Nanhui Chen
- Department of Urology, Meizhou People's Hospital, Meizhou 514031, China
| | - Weifeng Zhong
- Department of Urology, Meizhou People's Hospital, Meizhou 514031, China.,Department of Urology, Sun Yat-sen Cancer Center, Guangzhou 510060, China
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6
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Kinterova V, Kanka J, Petruskova V, Toralova T. Inhibition of Skp1-Cullin-F-box complexes during bovine oocyte maturation and preimplantation development leads to delayed development of embryos†. Biol Reprod 2020; 100:896-906. [PMID: 30535233 DOI: 10.1093/biolre/ioy254] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/17/2018] [Accepted: 12/06/2018] [Indexed: 11/12/2022] Open
Abstract
The mechanism of maternal protein degradation during preimplantation development has not been clarified yet. It is thought that a lot of maternal proteins are degraded by the ubiquitin-proteasome system. In this study, we focused on the role of the SCF (Skp1-Cullin-F-box) complexes during early bovine embryogenesis. We inhibited them using MLN4924, an inhibitor of SCF complex ligases controlled by neddylation. Oocytes maturated in MLN4924 could be fertilized, but we found no cumulus cell expansion and a high number of polyspermy after in vitro fertilization. We also found a statistically significant deterioration of development after MLN4924 treatment. After treatment with MLN4924 from the four-cell to late eight-cell stage, we found a statistically significant delay in their development; some of the treated embryos were, however, able to reach the blastocyst stage later. We found reduced levels of mRNA of EGA markers PAPOLA and U2AF1A, which can be related to this developmental delay. The cultivation with MLN4924 caused a significant increase in protein levels in MLN4924-treated oocytes and embryos; no such change was found in cumulus cells. To detect the proteins affected by MLN4924 treatment, we performed a Western blot analysis of selected proteins (SMAD4, ribosomal protein S6, centromeric protein E, P27, NFKB inhibitor alpha, RNA-binding motif protein 19). No statistically significant increase in protein levels was detected in either treated embryos or oocytes. In summary, our study shows that SCF ligases are necessary for the correct maturation of oocytes, cumulus cell expansion, fertilization, and early preimplantation development of cattle.
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Affiliation(s)
- Veronika Kinterova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic.,Department of Veterinary Sciences, Czech University of Life Sciences in Prague, Prague, Czech Republic
| | - Jiri Kanka
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic
| | - Veronika Petruskova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Tereza Toralova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic
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Pauletto M, Milan M, Huvet A, Corporeau C, Suquet M, Planas JV, Moreira R, Figueras A, Novoa B, Patarnello T, Bargelloni L. Transcriptomic features of Pecten maximus oocyte quality and maturation. PLoS One 2017; 12:e0172805. [PMID: 28253290 PMCID: PMC5333834 DOI: 10.1371/journal.pone.0172805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/09/2017] [Indexed: 11/19/2022] Open
Abstract
The king scallop Pecten maximus is a high valuable species of great interest in Europe for both fishery and aquaculture. Notably, there has been an increased investment to produce seed for enhancement programmes of wild scallop populations. However, hatchery production is a relatively new industry and it is still underdeveloped. Major hurdles are spawning control and gamete quality. In the present study, a total of 14 scallops were sampled in the bay of Brest (Brittany, France) to compare transcriptomic profiles of mature oocytes collected by spawning induction or by stripping. To reach such a goal, a microarray analysis was performed by using a custom 8x60K oligonucleotide microarray representing 45,488 unique scallop contigs. First we identified genes that were differentially expressed depending on oocyte quality, estimated as the potential to produce D-larvae. Secondly, we investigated the transcriptional features of both stripped and spawned oocytes. Genes coding for proteins involved in cytoskeletal dynamics, serine/threonine kinases signalling pathway, mRNA processing, response to DNA damage, apoptosis and cell-cycle appeared to be of crucial importance for both oocyte maturation and developmental competence. This study allowed us to dramatically increase the knowledge about transcriptional features of oocyte quality and maturation, as well as to propose for the first time putative molecular markers to solve a major bottleneck in scallop aquaculture.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Arnaud Huvet
- Ifremer, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des sciences de l’Environnement Marin (LEMAR), Plouzané, France
| | - Charlotte Corporeau
- Ifremer, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des sciences de l’Environnement Marin (LEMAR), Plouzané, France
| | - Marc Suquet
- Ifremer, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des sciences de l’Environnement Marin (LEMAR), Plouzané, France
| | - Josep V. Planas
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona i Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
| | - Rebeca Moreira
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
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8
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Rosse IC, Assis JG, Oliveira FS, Leite LR, Araujo F, Zerlotini A, Volpini A, Dominitini AJ, Lopes BC, Arbex WA, Machado MA, Peixoto MGCD, Verneque RS, Martins MF, Coimbra RS, Silva MVGB, Oliveira G, Carvalho MRS. Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance. Mamm Genome 2016; 28:66-80. [PMID: 27853861 DOI: 10.1007/s00335-016-9670-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/24/2016] [Indexed: 01/08/2023]
Abstract
In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.
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Affiliation(s)
- Izinara C Rosse
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil
| | - Juliana G Assis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.,Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Francislon S Oliveira
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.,Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Laura R Leite
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.,Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Flávio Araujo
- Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | - Angela Volpini
- Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Anderson J Dominitini
- Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | | | | | | | | | | | - Roney S Coimbra
- Neurogenômica, Centro de Pesquisa René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | - Guilherme Oliveira
- Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.,Vale Technology Institute, Belém, PA, Brazil
| | - Maria Raquel S Carvalho
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.
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9
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Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus). Sci Rep 2016; 6:36372. [PMID: 27796358 PMCID: PMC5087083 DOI: 10.1038/srep36372] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/14/2016] [Indexed: 01/29/2023] Open
Abstract
Goats (Capra hircus) are one of the oldest livestock domesticated species, and have been used for their milk, meat, hair and skins over much of the world. Detection of selection footprints in genomic regions can provide potential insights for understanding the genetic mechanism of specific phenotypic traits and better guide in animal breeding. The study presented here has generated 192.747G raw data and identified more than 5.03 million single-nucleotide polymorphisms (SNPs) and 334,151 Indels (insertions and deletions). In addition, we identified 155 and 294 candidate regions harboring 86 and 97 genes based on allele frequency differences in Dazu black goats (DBG) and Inner Mongolia cashmere goats (IMCG), respectively. Populations differentiation reflected by Fst values detected 368 putative selective sweep regions including 164 genes. The top 1% regions of both low heterozygosity and high genetic differentiation contained 239 (135 genes) and 176 (106 genes) candidate regions in DBG and IMCG, respectively. These genes were related to reproductive and productive traits, such as "neurohypophyseal hormone activity" and "adipocytokine signaling pathway". These findings may be conducive to molecular breeding and the long-term preservation of the valuable genetic resources for this species.
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10
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Tang X, Tang J, Liu X, Zeng L, Cheng C, Luo Y, Li L, Qin SL, Sang Y, Deng LM, Lv XB. Downregulation of miR-129-2 by promoter hypermethylation regulates breast cancer cell proliferation and apoptosis. Oncol Rep 2016; 35:2963-9. [PMID: 26935022 DOI: 10.3892/or.2016.4647] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 12/29/2015] [Indexed: 11/06/2022] Open
Abstract
Aberrant expression of the miR-129 family has been found in several types of cancer, yet its expression and potential biologic role in breast cancer remain largely unknown. In the present study, we found that miR-129-2 was consistently downregulated in the breast cancer specimens and cell lines. Overexpression of miR-129-2-3p markedly suppressed breast cancer cell proliferation and induced its apoptosis. In addition, a luciferase reporter assay revealed that miR-129-2-3p suppressed BCL2L2 expression. Furthermore, BCL2L2 was able to reverse miR-129-2-3p-mediated cell apoptosis, indicating that BCL2L2 plays a crucial role in mediating the tumor-suppressive role of miR-129-2-3p. Moreover, bisulfite DNA sequencing PCR (BSP) analysis identified that promoter hypermethylation was responsible for the downregulation of miR-129-2 in breast cancer. Collectively, our findings indicate that miR-129-2 is downregulated in breast cancer cells by promoter hypermethylation. Moreover, downregulation of miR-129-2 results in BCL2L2 overexpression and disease progression in breast cancer patients.
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Affiliation(s)
- Xiaofeng Tang
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Jianjun Tang
- Department of Gastroenterology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, P.R. China
| | - Xia Liu
- Department of Oncology, Guangzhou First Municipal People's Hospital Affiliated to Guangzhou Medical College, Guangzhou, Guangdong 510180, P.R. China
| | - Lei Zeng
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi 330029, P.R. China
| | - Chun Cheng
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Yanqin Luo
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Liping Li
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Shu-Lan Qin
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Yi Sang
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
| | - Liang-Ming Deng
- Department of Medicine, Gaoming Heshui Hospital, Foshan, Guangdong 528500, P.R. China
| | - Xiao-Bin Lv
- Nanchang Key Laboratory of Cancer Pathogenesis and Translational Research, Center Laboratory, The Third Affiliated Hospital, Nanchang University, Nanchang, Jiangxi 330008, P.R. China
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11
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Benesova V, Kinterova V, Kanka J, Toralova T. Characterization of SCF-Complex during Bovine Preimplantation Development. PLoS One 2016; 11:e0147096. [PMID: 26824694 PMCID: PMC4732672 DOI: 10.1371/journal.pone.0147096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/30/2015] [Indexed: 12/28/2022] Open
Abstract
The degradation of maternal proteins is one of the most important events during early development, and it is presumed to be essential for embryonic genome activation (EGA), but the precise mechanism is still not known. It is thought that a large proportion of the degradation of maternal proteins is mediated by the ubiquitin-proteolytic system. In this study we focused on the expression of the Skp1-Cullin1-F-box (SCF) complex, a modular RING-type E3 ubiquitin-ligase, during bovine preimplantation development. The complex consists of three invariable components—Cul1, Skp1, Rbx1 and F-box protein, which determines the substrate specificity. The protein level and mRNA expression of all three invariable members were determined. Cul1 and Skp1 mRNA synthesis was activated at early embryonic stages, at the 4c and early 8c stage, respectively, which suggests that these transcripts are necessary for preparing the embryo for EGA. CUL1 protein level increased from MII to the morula stage, with a significant difference between MII and L8c, and between MII and the morula. The CUL1 protein was localized primarily to nuclei and to a lesser extent to the cytoplasm, with a lower signal in the inner cell mass (ICM) compared to the trophectoderm (TE) at the blastocyst stage. The level of SKP1 protein significantly increased from MII oocytes to 4c embryos, but then significantly decreased again. The localization of the SKP1 protein was analysed throughout the cell and similarly to CUL1 at the blastocyst stage, the staining was less intensive in the ICM. There were no statistical differences in RBX1 protein level and localization. The active SCF-complex, which is determined by the interaction of Cul1 and Skp1, was found throughout the whole embryo during preimplantation development, but there was a difference at the blastocyst stage, which exhibits a much stronger signal in the TE than in the ICM. These results suggest that all these genes could play an important role during preimplantation development. This paper reveals comprehensive expression profile, the basic but important knowledge necessary for further studying.
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Affiliation(s)
- Veronika Benesova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
| | - Veronika Kinterova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic
- Department of Veterinary Sciences, Czech University of Life Sciences in Prague, Prague, Czech Republic
| | - Jiri Kanka
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic
| | - Tereza Toralova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics Academy of Science of Czech Republic, v.v.i., Libechov, Czech Republic
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12
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Zhang S, Tang W, Weng S, Liu X, Rao B, Gu J, Chen S, Wang Q, Shen X, Xue R, Dong L. Apollon modulates chemosensitivity in human esophageal squamous cell carcinoma. Oncotarget 2015; 5:7183-97. [PMID: 25216531 PMCID: PMC4196194 DOI: 10.18632/oncotarget.2293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Patients with esophageal squamous cell carcinoma (ESCC) are often diagnosed with advanced diseases that respond poorly to chemotherapy. Here we reported that Apollon, a membrane-associated inhibitor of apoptosis protein, was overexpressed in ESCC cell lines and clinical ESCC tissues, and Apollon overexpression clinically correlated with poor response to chemotherapy (P = 0.001), and short overall survival (P = 0.021). Apollon knockdown increased cisplatin/docetaxel-induced apoptosis, mitochondrial dysfunction and cytochrome c release in two ESCC cell lines. Apollon knockdown potentiated cisplatin/docetaxel-induced long-term cell growth inhibition, and enhanced chemosensitivity of ESCC cells to cisplatin/docetaxel in xenograft tumor models. Apollon knockdown also enhanced cisplatin/docetaxel-induced activation of caspase-8 (extrinsic pathway) and caspase-9 (intrinsic pathway) in ESCC cells and xenograft tumor models. Mechanism studies revealed that the effect of Apollon on chemosensitivity is mainly mediated by Smac. Apollon expression strongly and negatively correlated with Smac expression in clinical ESCC tissues (P = 0.001). Apollon targeted Smac for degradation in ESCC cells. The effect of Apollon on chemosensitivity was reversed by Smac knockdown in ESCC cells. Taken together, our data show association of Apollon expression with chemotherapeutic response in ESCC, and provide a strong rationale for combining Apollon antagonism with chemotherapy to treat ESCC.
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Affiliation(s)
- Si Zhang
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China. These authors contributed equally to this work
| | - Wenqing Tang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, Shanghai, China. These authors contributed equally to this work
| | - Shuqiang Weng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, Shanghai, China
| | - Xijun Liu
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Benqiang Rao
- Department of Gastrointestinal Anal Surgery and Institute of Gastroenterology, the Third Affiliated Hospital, Nanchang University, Nanchang, China
| | - Jianxin Gu
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - She Chen
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, Shanghai, China
| | - Ruyi Xue
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, Shanghai, China
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, Shanghai, China
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13
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Moussa M, Shu J, Zhang X, Zeng F. Maternal control of oocyte quality in cattle “a review”. Anim Reprod Sci 2015; 155:11-27. [DOI: 10.1016/j.anireprosci.2015.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 11/20/2014] [Accepted: 01/15/2015] [Indexed: 02/09/2023]
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14
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Salilew-Wondim D, Tesfaye D, Hossain M, Held E, Rings F, Tholen E, Looft C, Cinar U, Schellander K, Hoelker M. Aberrant placenta gene expression pattern in bovine pregnancies established after transfer of cloned or in vitro produced embryos. Physiol Genomics 2012; 45:28-46. [PMID: 23092953 DOI: 10.1152/physiolgenomics.00076.2012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In the present study, we used the global transcriptome profile approach to identify dysregulated genes, molecular pathways, and molecular functional alterations in bovine placentas derived from somatic cell nuclear transfer (SCNT) and in vitro embryo production (IVP) pregnancies compared with their artificial insemination (AI) counterparts at day 50 of gestation. For this, day 7 blastocysts derived from AI, IVP, or SCNT were transferred to oestrus-synchronized cows. The pregnant animals were slaughtered at day 50 of gestation, and the placentas were then recovered and used for transcriptome analysis using Affymetrix GeneChip bovine genome array. Results showed the SCNT placenta to be different from its AI counterpart in the expression of 1,196 transcripts. These genes were found to be associated with alterations in key biological processes and molecular pathways in SCNT placenta, and the dysregulation of 9% (n = 110) of these genes was due to transcriptional reprogramming error. IVP placenta also displayed alterations in the expression of 72 genes, of which 58 were common to SCNT placenta. Gene enrichment analysis revealed that the expression of genes involved in organ development, blood vessel development, extracellular matrix organization, and the immune system was affected in both SCNT and IVP placentas. However, 96% of the affected genes in SCNT were not significantly altered in IVP groups. Thus, the higher transcriptome dysregulation in SCNT placenta followed by IVP would reflect the degree of placental abnormality in SCNT and IVP pregnancies at day 50 of the gestation, which may have a profound effect on subsequent fetal development and health of the offspring.
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Affiliation(s)
- Dessie Salilew-Wondim
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Bonn, Germany
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15
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Toralová T, Benešová V, Kepková KV, Vodička P, Šušor A, Kaňka J. Bovine preimplantation embryos with silenced nucleophosmin mRNA are able to develop until the blastocyst stage. Reproduction 2012; 144:349-59. [DOI: 10.1530/rep-12-0033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study was conducted to investigate the effect of silencing nucleophosmin in the development of in vitro-produced bovine embryos. Nucleophosmin is an abundant multifunctional nucleolar phosphoprotein that participates, for example, in ribosome biogenesis or centrosome duplication control. We showed that although the transcription of embryonic nucleophosmin started already at late eight-cell stage, maternal protein was stored throughout the whole preimplantation development and was sufficient for the progression to the blastocyst stage. At the beginning of embryogenesis, translation occurs on maternally derived ribosomes, the functionally active nucleoli emerge during the fourth cell cycle in bovines. We found that nucleophosmin localisation reflected the nucleolar formation during bovine preimplantation development. The protein was detectable from the beginning of embryonic development. Before embryonic genome activation, it was dispersed throughout the nucleoplasm. The typical nucleolar localisation emerged with the formation of active nucleoli. At the blastocyst stage, nucleophosmin tended to localise especially to the trophectoderm. To see for how long is maternal nucleophosmin preserved, we silenced the nucleophosmin mRNA using RNA interference approach. Although a large portion of nucleophosmin was degraded in embryos with silenced nucleophosmin mRNA, an amount sufficient for normal development was preserved and we detected only a temporal delay in nucleophosmin relocalisation to nucleoli. Moreover, we observed no defects in nuclear shape or cytoskeleton previously found in somatic cells and only a non-significant decrease in embryonic developmental competence. Thus, our results show that the preserved amount of maternal nucleophosmin is sufficient for preimplantation development of bovine embryo.
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