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Kumar N, Bharadwaj C, Sahu S, Shiv A, Shrivastava AK, Reddy SPP, Soren KR, Patil BS, Pal M, Soni A, Roorkiwal M, Varshney RK. Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea ( Cicer arietinum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2605-2619. [PMID: 34916736 PMCID: PMC8639897 DOI: 10.1007/s12298-021-01093-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 10/06/2021] [Accepted: 10/19/2021] [Indexed: 05/14/2023]
Abstract
LncRNAs (long noncoding RNAs) are 200 bp length crucial RNA molecules, lacking coding potential and having important roles in regulating gene expression, particularly in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in chickpea roots and predicted their intricate regulatory roles. A total of 3452 novel lncRNAs were identified to be distributed across all 08 chickpea chromosomes. On comparing salt-tolerant (ICCV 10, JG 11) and salt-sensitive cultivars (DCP 92-3, Pusa 256), 4446 differentially expressed lncRNAs were detected under various salt treatments. We predicted 3373 lncRNAs to be regulating their target genes in cis regulating manner and 80 unique lncRNAs were observed as interacting with 136 different miRNAs, as eTMs (endogenous target mimic) targets of miRNAs and implicated them in the regulatory network of salt stress response. Functional analysis of these lncRNA revealed their association in targeting salt stress response-related genes like potassium transporter, transporter family genes, serine/threonine-protein kinase, aquaporins like TIP1-2, PIP2-5 and transcription factors like, AP2, NAC, bZIP, ERF, MYB and WRKY. Furthermore, about 614 lncRNA-SSRs (simple sequence repeats) were identified as a new generation of molecular markers with higher efficiency and specificity in chickpea. Overall, these findings will pave the understanding of comprehensive functional role of potential lncRNAs, which can help in providing insight into the molecular mechanism of salt tolerance in chickpea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01093-0.
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Affiliation(s)
- Neeraj Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi 110012 India
| | - Aalok Shiv
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
- Present Address: ICAR-Indian Institute of Sugarcane Research, Lucknow, 226002 India
| | | | | | - Khela Ram Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 282 004 India
| | | | - Madan Pal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Anjali Soni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012 India
| | - Manish Roorkiwal
- Centre of Excellence in Genomics, ICRISAT, Hyderabad, 502324 India
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Ghangal R, Singh VK, Khemka NK, Rajkumar MS, Garg R, Jain M. Updates on Genomic Resources in Chickpea for Crop Improvement. Methods Mol Biol 2020; 2107:19-33. [PMID: 31893441 DOI: 10.1007/978-1-0716-0235-5_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In recent years, rapid advancement has been done in generation of genomic resources for the important legume crop chickpea. Here, we provide an update on important advancements made on availability of genomic resources for this crop. The availability of reference genome and transcriptome sequences, and resequencing of several accessions have enabled the discovery of gene space and molecular markers in chickpea. These resources have helped in elucidating evolutionary relationship and identification of quantitative trait loci for important agronomic traits. Gene expression in different tissues/organs during development and under abiotic/biotic stresses has been interrogated. In addition, single-base resolution DNA methylation patterns in different organs have been analyzed to understand gene regulation. Overall, we provide a consolidated overview of available genomic resources of chickpea that may help in fulfilling the promises for improvement of this important crop.
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Affiliation(s)
- Rajesh Ghangal
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vikash K Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Niraj K Khemka
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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Jha UC. Current advances in chickpea genomics: applications and future perspectives. PLANT CELL REPORTS 2018; 37:947-965. [PMID: 29860584 DOI: 10.1007/s00299-018-2305-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 05/27/2023]
Abstract
Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. BMC Genomics 2017; 18:878. [PMID: 29141604 PMCID: PMC5688659 DOI: 10.1186/s12864-017-4232-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/23/2017] [Indexed: 01/24/2023] Open
Abstract
Background Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level. Cajanus cajan, a leguminosae pulse crop grown in tropical and subtropical areas of the world, is a source of high value protein to vegetarians or very poor populations globally. Hence, genome-wide identification of miRNAs and lncRNAs in C. cajan is extremely important to understand their role in PTGR with a possible implication to generate improve variety of crops. Results We have identified 616 mature miRNAs in C. cajan belonging to 118 families, of which 578 are novel and not reported in MirBase21. A total of 1373 target sequences were identified for 180 miRNAs. Of these, 298 targets were characterized at the protein level. Besides, we have also predicted 3919 lncRNAs. Additionally, we have identified 87 of the predicted lncRNAs to be targeted by 66 miRNAs. Conclusions miRNA and lncRNAs in plants are known to control a variety of traits including yield, quality and stress tolerance. Owing to its agricultural importance and medicinal value, the identified miRNA, lncRNA and their targets in C. cajan may be useful for genome editing to improve better quality crop. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of C. cajan agricultural traits. Electronic supplementary material The online version of this article (10.1186/s12864-017-4232-2) contains supplementary material, which is available to authorized users.
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Liu Z, Zhang Y, Ou L, Kang L, Liu Y, Lv J, Wei G, Yang B, Yang S, Chen W, Dai X, Li X, Zhou S, Zhang Z, Ma Y, Zou X. Identification and characterization of novel microRNAs for fruit development and quality in hot pepper (Capsicum annuum L.). Gene 2017; 608:66-72. [PMID: 28122266 DOI: 10.1016/j.gene.2017.01.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs which play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are involved in fruit development in model plants. However, the miRNAs related to fruit development and quality in hot pepper (Capsicum annuum L.) remains unknown. In this study, small RNA populations from different fruit ripening stages and different varieties were compared using next-generation sequencing technology. Totally, 59 known miRNAs and 310 novel miRNAs were identified from four libraries using miRDeep2 software. For these novel miRNAs, 656 targets were predicted and 402 of them were annotated. GO analysis and KEGG pathways suggested that some of the predicted miRNAs targeted genes involved in starch sucrose metabolism and amino sugar as well as nucleotide sugar metabolism. Quantitative RT-PCR validated the contrasting expression patterns between several miRNAs and their target genes. These results will provide an important foundation for future studies on the regulation of miRNAs involved in fruit development and quality.
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Affiliation(s)
- Zhoubin Liu
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Yuping Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Lijun Ou
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Linyu Kang
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Yuhua Liu
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Junheng Lv
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China
| | - Ge Wei
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Bozhi Yang
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Sha Yang
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Wenchao Chen
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Xiongze Dai
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Xuefeng Li
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Shudong Zhou
- Hunan Vegetable Research Institute, Changsha 410125, China
| | - Zhuqing Zhang
- Hunan Vegetable Research Institute, Changsha 410125, China.
| | - Yanqing Ma
- Hunan Vegetable Research Institute, Changsha 410125, China.
| | - Xuexiao Zou
- Longping Branch, Graduate School of Hunan university, Changsha 410125, China; Hunan Vegetable Research Institute, Changsha 410125, China.
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Srivastava S, Zheng Y, Kudapa H, Jagadeeswaran G, Hivrale V, Varshney RK, Sunkar R. High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:46-57. [PMID: 25900565 DOI: 10.1016/j.plantsci.2015.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 05/04/2023]
Abstract
Among legumes, chickpea (Cicer arietinum L.) is the second most important crop after soybean. MicroRNAs (miRNAs) play important roles by regulating target gene expression important for plant development and tolerance to stress conditions. Additionally, recently discovered phased siRNAs (phasiRNAs), a new class of small RNAs, are abundantly produced in legumes. Nevertheless, little is known about these regulatory molecules in chickpea. The small RNA population was sequenced from leaves and flowers of chickpea to identify conserved and novel miRNAs as well as phasiRNAs/phasiRNA loci. Bioinformatics analysis revealed 157 miRNA loci for the 96 highly conserved and known miRNA homologs belonging to 38 miRNA families in chickpea. Furthermore, 20 novel miRNAs belonging to 17 miRNA families were identified. Sequence analysis revealed approximately 60 phasiRNA loci. Potential target genes likely to be regulated by these miRNAs were predicted and some were confirmed by modified 5' RACE assay. Predicted targets are mostly transcription factors that might be important for developmental processes, and others include superoxide dismutases, plantacyanin, laccases and F-box proteins that could participate in stress responses and protein degradation. Overall, this study provides an inventory of miRNA-target gene interactions for chickpea, useful for the comparative analysis of small RNAs among legumes.
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Affiliation(s)
- Sangeeta Srivastava
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, Yunnan 650500, China
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India
| | - Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Vandana Hivrale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India; School of Plant Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA.
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Kohli D, Joshi G, Deokar AA, Bhardwaj AR, Agarwal M, Katiyar-Agarwal S, Srinivasan R, Jain PK. Identification and characterization of Wilt and salt stress-responsive microRNAs in chickpea through high-throughput sequencing. PLoS One 2014; 9:e108851. [PMID: 25295754 PMCID: PMC4190074 DOI: 10.1371/journal.pone.0108851] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/25/2014] [Indexed: 11/19/2022] Open
Abstract
Chickpea (Cicer arietinum) is the second most widely grown legume worldwide and is the most important pulse crop in the Indian subcontinent. Chickpea productivity is adversely affected by a large number of biotic and abiotic stresses. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several biotic and abiotic stresses. This study is the first attempt to identify chickpea miRNAs that are associated with biotic and abiotic stresses. The wilt infection that is caused by the fungus Fusarium oxysporum f.sp. ciceris is one of the major diseases severely affecting chickpea yields. Of late, increasing soil salinization has become a major problem in realizing these potential yields. Three chickpea libraries using fungal-infected, salt-treated and untreated seedlings were constructed and sequenced using next-generation sequencing technology. A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume-specific miRNAs, including miR5213, miR5232, miR2111 and miR2118, were found in all of the libraries. Poly(A)-based qRT-PCR (Quantitative real-time PCR) was used to validate eleven conserved and five novel miRNAs. miR530 was highly up regulated in response to fungal infection, which targets genes encoding zinc knuckle- and microtubule-associated proteins. Many miRNAs responded in a similar fashion under both biotic and abiotic stresses, indicating the existence of cross talk between the pathways that are involved in regulating these stresses. The potential target genes for the conserved and novel miRNAs were predicted based on sequence homologies. miR166 targets a HD-ZIPIII transcription factor and was validated by 5′ RLM-RACE. This study has identified several conserved and novel miRNAs in the chickpea that are associated with gene regulation following exposure to wilt and salt stress.
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Affiliation(s)
- Deshika Kohli
- NRC on Plant Biotechnology, IARI Campus (PUSA), New Delhi, India
| | - Gopal Joshi
- Department of Botany, North campus, University of Delhi, Delhi, India
| | | | - Ankur R. Bhardwaj
- Department of Botany, North campus, University of Delhi, Delhi, India
| | - Manu Agarwal
- Department of Botany, North campus, University of Delhi, Delhi, India
| | | | | | - Pradeep Kumar Jain
- NRC on Plant Biotechnology, IARI Campus (PUSA), New Delhi, India
- * E-mail:
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Liew LC, Singh MB, Bhalla PL. Unique and conserved features of floral evocation in legumes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:714-728. [PMID: 24930396 DOI: 10.1111/jipb.12187] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
Legumes, with their unique ability to fix atmospheric nitrogen, play a vital role in ensuring future food security and mitigating the effects of climate change because they use less fossil energy and produce less greenhouse gases compared with N-fertilized systems. Grain legumes are second only to cereal crops as a source of human and animal food, and they contribute approximately one third of the protein consumed by the human population. The productivity of seed crops, such as grain legumes, is dependent on flowering. Despite the genetic variation and importance of flowering in legume production, studies of the molecular pathways that control flowering in legumes are limited. Recent advances in genomics have revealed that legume flowering pathways are divergent from those of such model species as Arabidopsis thaliana. Here, we discuss the current understanding of flowering time regulation in legumes and highlight the unique and conserved features of floral evocation in legumes.
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Affiliation(s)
- Lim Chee Liew
- Plant Molecular Biology and Biotechnology Laboratory, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria, 3010, Australia
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Characterization of conserved microRNAs from five different cucurbit species using computational and experimental analysis. Biochimie 2014; 102:137-44. [PMID: 24657600 DOI: 10.1016/j.biochi.2014.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
MicroRNAs (miRNAs) are ∼21 nt non-coding small RNAs which regulate gene expression at the post-transcriptional level in plants and animals. Until recently, only limited numbers of miRNAs were identified in Cucurbitaceae, a large flowering plant family. In this study, 220 potential miRNA candidates were identified from five species of Cucurbitaceae family using a comparative genome-based computational analysis. A comprehensive bioinformatic analysis of EST (expressed sequence tag) and GSS (genomic survey sequence) data of five cucurbit species showed that at least 41, 108, 21, 17 and 33 miRNAs existed in Cucumis sativus, Cucumis melo, Citrullus lanatus, Siraitia grosvenorii and Cucurbita pepo, respectively. Quantitative real-time PCR (qRT-PCR) analysis revealed the differentially expression levels of miRNAs in the four tissues of cucumber and melon. These identified miRNAs in the five species potentially targeted 578 protein-coding genes and one target of the C. melo miRNA cme-miR160a-5p was verified by 5' RLM-RACE. GO and KEGG analysis suggested that many melon miRNAs might involve in nucleotide metabolism, oxidative phosphorylation, cell redox homeostasis and signal transduction.
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Abstract
Conserved microRNAs and their targets in chickpea Programmed ribosomal frameshifting controls telomere length in yeast Enoxacin inhibits growth of prostate cancer cells and restores microRNA processing Transcriptional regulatory network shapes genome structure of S. cerevisiae
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