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Pedenla Bomzan D, Sharma A, Lemos Cruz P, Carqueijeiro I, Bellenger L, Rai A, Thippesh AK, Chinnegowda VS, Parihar D, Ducos E, Courdavault V, Nagegowda DA. ROP GTPases with a geranylgeranylation motif modulate alkaloid biosynthesis in Catharanthus roseus. PLANT PHYSIOLOGY 2024; 195:2213-2233. [PMID: 38466200 DOI: 10.1093/plphys/kiae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 03/12/2024]
Abstract
Rho of Plant (ROP) GTPases function as molecular switches that control signaling processes essential for growth, development, and defense. However, their role in specialized metabolism is poorly understood. Previously, we demonstrated that inhibition of protein geranylgeranyl transferase (PGGT-I) negatively impacts the biosynthesis of monoterpene indole alkaloids (MIA) in Madagascar periwinkle (Catharanthus roseus), indicating the involvement of prenylated proteins in signaling. Here, we show through biochemical, molecular, and in planta approaches that specific geranylgeranylated ROPs modulate C. roseus MIA biosynthesis. Among the six C. roseus ROP GTPases (CrROPs), only CrROP3 and CrROP5, having a C-terminal CSIL motif, were specifically prenylated by PGGT-I. Additionally, their transcripts showed higher expression in most parts than other CrROPs. Protein-protein interaction studies revealed that CrROP3 and CrROP5, but not ΔCrROP3, ΔCrROP5, and CrROP2 lacking the CSIL motif, interacted with CrPGGT-I. Further, CrROP3 and CrROP5 exhibited nuclear localization, whereas CrROP2 was localized to the plasma membrane. In planta functional studies revealed that silencing of CrROP3 and CrROP5 negatively affected MIA biosynthesis, while their overexpression upregulated MIA formation. In contrast, silencing and overexpression of CrROP2 had no effect on MIA biosynthesis. Moreover, overexpression of ΔCrROP3 and ΔCrROP5 mutants devoid of sequence coding for the CSIL motif failed to enhance MIA biosynthesis. These results implicate that CrROP3 and CrROP5 have a positive regulatory role on MIA biosynthesis and thus shed light on how geranylgeranylated ROP GTPases mediate the modulation of specialized metabolism in C. roseus.
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Affiliation(s)
- Dikki Pedenla Bomzan
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anuj Sharma
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pamela Lemos Cruz
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Ines Carqueijeiro
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Léo Bellenger
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Avanish Rai
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
| | - Akshay Kumar Thippesh
- Department of Biotechnology and Crop Improvement, College of Horticulture, UHS Bagalkot, Mysuru 571130, India
| | - Venkatesha S Chinnegowda
- Department of Biotechnology and Crop Improvement, College of Horticulture, UHS Bagalkot, Mysuru 571130, India
| | - Durgesh Parihar
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Eric Ducos
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, BBV, EA2106, Universitéde de Tours, 37200 Tours, France
| | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Majeed Y, Zhu X, Zhang N, ul-Ain N, Raza A, Haider FU, Si H. Harnessing the role of mitogen-activated protein kinases against abiotic stresses in plants. FRONTIERS IN PLANT SCIENCE 2023; 14:932923. [PMID: 36909407 PMCID: PMC10000299 DOI: 10.3389/fpls.2023.932923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Crop plants are vulnerable to various biotic and abiotic stresses, whereas plants tend to retain their physiological mechanisms by evolving cellular regulation. To mitigate the adverse effects of abiotic stresses, many defense mechanisms are induced in plants. One of these mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signaling pathway used in the transduction of extracellular stimuli into intercellular responses. This stress signaling pathway is activated by a series of responses involving MAPKKKs→MAPKKs→MAPKs, consisting of interacting proteins, and their functions depend on the collaboration and activation of one another by phosphorylation. These proteins are key regulators of MAPK in various crop plants under abiotic stress conditions and also related to hormonal responses. It is revealed that in response to stress signaling, MAPKs are characterized as multigenic families and elaborate the specific stimuli transformation as well as the antioxidant regulation system. This pathway is directed by the framework of proteins and stopping domains confer the related associates with unique structure and functions. Early studies of plant MAPKs focused on their functions in model plants. Based on the results of whole-genome sequencing, many MAPKs have been identified in plants, such as Arbodiposis, tomato, potato, alfalfa, poplar, rice, wheat, maize, and apple. In this review, we summarized the recent work on MAPK response to abiotic stress and the classification of MAPK cascade in crop plants. Moreover, we highlighted the modern research methodologies such as transcriptomics, proteomics, CRISPR/Cas technology, and epigenetic studies, which proposed, identified, and characterized the novel genes associated with MAPKs and their role in plants under abiotic stress conditions. In-silico-based identification of novel MAPK genes also facilitates future research on MAPK cascade identification and function in crop plants under various stress conditions.
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Affiliation(s)
- Yasir Majeed
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Xi Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Noor ul-Ain
- Fujian Agricultural and Forestry University (FAFU) and University of Illinois Urbana-Champaign-School of Integrative Biology (UIUC-SIB) Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ali Raza
- College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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Morey KJ, Peebles CAM. Hairy roots: An untapped potential for production of plant products. FRONTIERS IN PLANT SCIENCE 2022; 13:937095. [PMID: 35991443 PMCID: PMC9389236 DOI: 10.3389/fpls.2022.937095] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in Catharanthus roseus hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.
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Liu Y, Patra B, Singh SK, Paul P, Zhou Y, Li Y, Wang Y, Pattanaik S, Yuan L. Terpenoid indole alkaloid biosynthesis in Catharanthus roseus: effects and prospects of environmental factors in metabolic engineering. Biotechnol Lett 2021; 43:2085-2103. [PMID: 34564757 PMCID: PMC8510960 DOI: 10.1007/s10529-021-03179-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/28/2021] [Indexed: 11/10/2022]
Abstract
Plants synthesize a vast array of specialized metabolites that primarily contribute to their defense and survival under adverse conditions. Many of the specialized metabolites have therapeutic values as drugs. Biosynthesis of specialized metabolites is affected by environmental factors including light, temperature, drought, salinity, and nutrients, as well as pathogens and insects. These environmental factors trigger a myriad of changes in gene expression at the transcriptional and posttranscriptional levels. The dynamic changes in gene expression are mediated by several regulatory proteins that perceive and transduce the signals, leading to up- or down-regulation of the metabolic pathways. Exploring the environmental effects and related signal cascades is a strategy in metabolic engineering to produce valuable specialized metabolites. However, mechanistic studies on environmental factors affecting specialized metabolism are limited. The medicinal plant Catharanthus roseus (Madagascar periwinkle) is an important source of bioactive terpenoid indole alkaloids (TIAs), including the anticancer therapeutics vinblastine and vincristine. The emerging picture shows that various environmental factors significantly alter TIA accumulation by affecting the expression of regulatory and enzyme-encoding genes in the pathway. Compared to our understanding of the TIA pathway in response to the phytohormone jasmonate, the impacts of environmental factors on TIA biosynthesis are insufficiently studied and discussed. This review thus focuses on these aspects and discusses possible strategies for metabolic engineering of TIA biosynthesis. PURPOSE OF WORK: Catharanthus roseus is a rich source of bioactive terpenoid indole alkaloids (TIAs). The objective of this work is to present a comprehensive account of the influence of various biotic and abiotic factors on TIA biosynthesis and to discuss possible strategies to enhance TIA production through metabolic engineering.
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Affiliation(s)
- Yongliang Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Sanjay Kumar Singh
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Priyanka Paul
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Yan Zhou
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Yongqing Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Ling Yuan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, Kentucky 40546 USA
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Salama IM, Eliwa NE, Mohamed MH. Effect of UV-A on vincristine biosynthesis and related peroxidase isozyme changes in Catharanthus roseus. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2020. [DOI: 10.1080/16878507.2020.1777658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- I. M. Salama
- Natural Products Research Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - N. E. Eliwa
- Natural Products Research Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
| | - M. H. Mohamed
- Natural Products Research Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority, Cairo, Egypt
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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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Mohanta TK, Arora PK, Mohanta N, Parida P, Bae H. Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants. BMC Genomics 2015; 16:58. [PMID: 25888265 PMCID: PMC4363184 DOI: 10.1186/s12864-015-1244-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes. Results A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with Arabidopsis or Oryza MAPKs. Conclusion We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tapan Kumar Mohanta
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Pankaj Kumar Arora
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
| | - Nibedita Mohanta
- Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa, 757003, India.
| | - Pratap Parida
- Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam, 786004, India.
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook, 712749, Republic of Korea.
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Liao X, Peng F, Forni S, McLaren D, Plastow G, Stothard P. Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome 2013; 56:592-8. [DOI: 10.1139/gen-2013-0082] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Genetic variation in Gir cattle (Bos indicus) has so far not been well characterized. In this study, we used whole genome sequencing of three Gir bulls and a pooled sample from another 11 bulls to identify polymorphisms and loci under selection. A total of 9 990 733 single nucleotide polymorphisms (SNPs) and 604 308 insertion/deletions (indels) were discovered in Gir samples, of which 62.34% and 83.62%, respectively, are previously unknown. Moreover, we detected 79 putative selective sweeps using the sequence data of the pooled sample. One of the most striking sweeps harbours several genes belonging to the cathelicidin gene family, such as CAMP, CATHL1, CATHL2, and CATHL3, which are related to pathogen- and parasite-resistance. Another interesting region harbours genes encoding mitogen-activated protein kinases, which are involved in directing cellular responses to a variety of stimuli, such as osmotic stress and heat shock. These findings are particularly interesting because Gir is resistant to hot temperatures and tropical diseases. This initial selective sweep analysis of Gir cattle has revealed a number of loci that could be important for their adaptation to tropical climates.
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Affiliation(s)
- Xiaoping Liao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Fred Peng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Selma Forni
- Genus plc, 100 Bluegrass Commons Boulevard, Suite 2200, Hendersonville, TN 37075, USA
| | | | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
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