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Gaikwad K, Ramakrishna G, Srivastava H, Saxena S, Kaila T, Tyagi A, Sharma P, Sharma S, Sharma R, Mahla HR, Kumar K, Sv AM, Solanke AU, Kalia P, Rao AR, Rai A, Sharma TR, Singh NK. The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes. Sci Rep 2023; 13:9941. [PMID: 37336893 DOI: 10.1038/s41598-023-33762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/18/2023] [Indexed: 06/21/2023] Open
Abstract
Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.
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Affiliation(s)
- Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.
| | | | | | - Swati Saxena
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - R Sharma
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - H R Mahla
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Amitha Mithra Sv
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pritam Kalia
- Division of Vegetable Sciences, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - A R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T R Sharma
- DDG (CS), Indian Council of Agricultural Research, New Delhi, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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Singh KP, Kumari P, Yadava DK. Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance. Front Genet 2022; 13:958217. [PMID: 36186472 PMCID: PMC9524822 DOI: 10.3389/fgene.2022.958217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba + B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n = 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used for de-novo assembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies.
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Affiliation(s)
| | - Preetesh Kumari
- Genetics Division, ICAR—Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Preetesh Kumari,
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3
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Chaudhary V, Jangra S, Yadav NR. In silico Identification of miRNAs and Their Targets in Cluster Bean for Their Role in Development and Physiological Responses. Front Genet 2022; 13:930113. [PMID: 35846150 PMCID: PMC9280363 DOI: 10.3389/fgene.2022.930113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Cluster bean popularly known as “guar” is a drought-tolerant, annual legume that has recently emerged as an economically important crop, owing to its high protein and gum content. The guar gum has wide range of applications in food, pharma, and mining industries. India is the leading exporter of various cluster bean-based products all across the globe. Non-coding RNAs (miRNAs) are involved in regulating the expression of the target genes leading to variations in the associated pathways or final protein concentrations. The understanding of miRNAs and their associated targets in cluster bean is yet to be used to its full potential. In the present study, cluster bean EST (Expressed Sequence Tags) database was exploited to identify the miRNA and their predicted targets associated with metabolic and biological processes especially response to diverse biotic and abiotic stimuli using in silico approach. Computational analysis based on cluster bean ESTs led to the identification of 57 miRNAs along with their targets. To the best of our knowledge, this is the first report on identification of miRNAs and their targets using ESTs in cluster bean. The miRNA related to gum metabolism was also identified. Most abundant miRNA families predicted in our study were miR156, miR172, and miR2606. The length of most of the mature miRNAs was found to be 21nt long and the range of minimal folding energy (MFE) was 5.8–177.3 (−kcal/mol) with an average value of 25.4 (−kcal/mol). The identification of cluster bean miRNAs and their targets is predicted to hasten the miRNA discovery, resulting in better knowledge of the role of miRNAs in cluster bean development, physiology, and stress responses.
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Reddy BM, Anthony Johnson AM, Jagadeesh Kumar N, Venkatesh B, Jayamma N, Pandurangaiah M, Sudhakar C. De novo Transcriptome Analysis of Drought-Adapted Cluster Bean (Cultivar RGC-1025) Reveals the Wax Regulatory Genes Involved in Drought Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:868142. [PMID: 35837463 PMCID: PMC9274130 DOI: 10.3389/fpls.2022.868142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Cluster bean (Cyamopsis tetragonoloba L.) is one of the multipurpose underexplored crops grown as green vegetable and for gum production in dryland areas. Cluster bean is known as relatively tolerant to drought and salinity stress. To elucidate the molecular mechanisms involved in the drought tolerance of cluster bean cultivar RGC-1025, RNA sequencing (RNA-seq) of the drought-stressed and control samples was performed. De novo assembly of the reads resulted in 66,838 transcripts involving 203 pathways. Among these transcripts, differentially expressed gene (DEG) analysis resulted in some of the drought-responsive genes expressing alpha dioxygenase 2, low temperature-induced 65 kDa protein (LDI65), putative vacuolar amino acid transporter, and late embryogenesis abundant protein (LEA 3). The analysis also reported drought-responsive transcription factors (TFs), such as NAC, WRKY, GRAS, and MYB families. The relative expression of genes by qRT-PCR revealed consistency with the DEG analysis. Key genes involved in the wax biosynthesis pathway were mapped using the DEG data analysis. These results were positively correlated with epicuticular wax content and the wax depositions on the leaf surfaces, as evidenced by scanning electron microscope (SEM) image analysis. Further, these findings support the fact that enhanced wax deposits on the leaf surface had played a crucial role in combating the drought stress in cluster beans under drought stress conditions. In addition, this study provided a set of unknown genes and TFs that could be a source of engineering tolerance against drought stress in cluster beans.
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Affiliation(s)
- B. Manohara Reddy
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur, India
| | | | - N. Jagadeesh Kumar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur, India
| | - Boya Venkatesh
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur, India
| | - N. Jayamma
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur, India
| | - Merum Pandurangaiah
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur, India
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Suranjika S, Pradhan S, Nayak SS, Parida A. De novo transcriptome assembly and analysis of gene expression in different tissues of moth bean (Vigna aconitifolia) (Jacq.) Marechal. BMC PLANT BIOLOGY 2022; 22:198. [PMID: 35428206 PMCID: PMC9013028 DOI: 10.1186/s12870-022-03583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The underutilized species Vigna aconitifolia (Moth Bean) is an important legume crop cultivated in semi-arid conditions and is valued for its seeds for their high protein content. It is also a popular green manure cover crop that offers many agronomic benefits including nitrogen fixation and soil nutrients. Despite its economic potential, genomic resources for this crop are scarce and there is limited knowledge on the developmental process of this plant at a molecular level. In the present communication, we have studied the molecular mechanisms that regulate plant development in V. aconitifolia, with a special focus on flower and seed development. We believe that this study will greatly enrich the genomic resources for this plant in form of differentially expressed genes, transcription factors, and genic molecular markers. RESULTS We have performed the de novo transcriptome assembly using six types of tissues from various developmental stages of Vigna aconitifolia (var. RMO-435), namely, leaves, roots, flowers, pods, and seed tissue in the early and late stages of development, using the Illumina NextSeq platform. We assembled the transcriptome to get 150938 unigenes with an average length of 937.78 bp. About 79.9% of these unigenes were annotated in public databases and 12839 of those unigenes showed a significant match in the KEGG database. Most of the unigenes displayed significant differential expression in the late stages of seed development as compared with leaves. We annotated 74082 unigenes as transcription factors and identified 12096 simple sequence repeats (SSRs) in the genic regions of V.aconitifolia. Digital expression analysis revealed specific gene activities in different tissues which were validated using Real-time PCR analysis. CONCLUSIONS The Vigna aconitifolia transcriptomic resources generated in this study provide foundational resources for gene discovery with respect to various developmental stages. This study provides the first comprehensive analysis revealing the genes involved in molecular as well as metabolic pathways that regulate seed development and may be responsible for the unique nutritive values of moth bean seeds. Hence, this study would serve as a foundation for characterization of candidate genes which would not only provide novel insights into understanding seed development but also provide resources for improved moth bean and related species genetic enhancement.
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Affiliation(s)
- Sandhya Suranjika
- Institute of Life Sciences (ILS), An autonomous Institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha India
- Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), KIIT Road, Patia, Bhubaneswar, Odisha India
| | - Seema Pradhan
- Institute of Life Sciences (ILS), An autonomous Institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha India
| | - Soumya Shree Nayak
- Institute of Life Sciences (ILS), An autonomous Institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha India
- Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), KIIT Road, Patia, Bhubaneswar, Odisha India
| | - Ajay Parida
- Institute of Life Sciences (ILS), An autonomous Institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha India
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Ansari MA, Bano N, Kumar A, Dubey AK, Asif MH, Sanyal I, Pande V, Pandey V. Comparative transcriptomic analysis and antioxidant defense mechanisms in clusterbean (Cyamopsis tetragonoloba (L.) Taub.) genotypes with contrasting drought tolerance. Funct Integr Genomics 2022; 22:625-642. [PMID: 35426545 DOI: 10.1007/s10142-022-00860-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 01/16/2023]
Abstract
To understand drought tolerance mechanism(s) in clusterbean (Cyamopsis tetragonoloba), we conducted physiological, biochemical, and de novo comparative transcriptome analysis of drought-tolerant (RGC-1002) and drought-sensitive (RGC-1066) genotypes subjected to 30 days of drought stress. Relative water content (RWC) was maintained in tolerant genotype but was reduced in sensitive genotype. Leaf pigment concentrations were higher in tolerant genotype. Net photosynthesis was significantly decreased in sensitive genotype but insignificant reduction was found in tolerant genotype. Enzymatic antioxidant (GR, APX, DHAR) activities were enhanced in tolerant genotype, while there were insignificant changes in these enzymes in sensitive genotype. The ratios of antioxidant molecules (ASC/DHA and GSH/GSSG) were higher in tolerant genotype as compared to sensitive genotype. In sensitive genotype, 6625 differentially expressed genes (DEGs) were upregulated and 5365 genes were downregulated. In tolerant genotype, 5206 genes were upregulated and 2793 genes were downregulated. In tolerant genotype, transketolase family protein, phosphoenolpyruvate carboxylase 3, temperature-induced lipocalin, and cytochrome oxidase were highly upregulated. Moreover, according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the drought tolerance may be attributed to upregulated starch and sucrose metabolism-related genes in tolerant genotype. Finally, quantitative real-time PCR confirmed the reproducibility of the RNA-seq data.
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Affiliation(s)
- Mohd Akram Ansari
- Plant Ecology and Climate Change Science Division, CSIR-NBRI, Lucknow, India. .,Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.
| | - Nasreen Bano
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Anil Kumar
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.,Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Arvind Kumar Dubey
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India.,Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Mehar Hasan Asif
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Indraneel Sanyal
- Plant Molecular Biology and Biotechnology Division, CSIR-NBRI, Lucknow, India
| | - Veena Pande
- Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, India
| | - Vivek Pandey
- Plant Ecology and Climate Change Science Division, CSIR-NBRI, Lucknow, India.
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Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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Acharya BR, Sandhu D, Dueñas C, Ferreira JFS, Grover KK. Deciphering Molecular Mechanisms Involved in Salinity Tolerance in Guar ( Cyamopsis tetragonoloba (L.) Taub.) Using Transcriptome Analyses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030291. [PMID: 35161272 PMCID: PMC8838131 DOI: 10.3390/plants11030291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/09/2023]
Abstract
Guar is a commercially important legume crop known for guar gum. Guar is tolerant to various abiotic stresses, but the mechanisms involved in its salinity tolerance are not well established. This study aimed to understand molecular mechanisms of salinity tolerance in guar. RNA sequencing (RNA-Seq) was employed to study the leaf and root transcriptomes of salt-tolerant (Matador) and salt-sensitive (PI 340261) guar genotypes under control and salinity. Our analyses identified a total of 296,114 unigenes assembled from 527 million clean reads. Transcriptome analysis revealed that the gene expression differences were more pronounced between salinity treatments than between genotypes. Differentially expressed genes associated with stress-signaling pathways, transporters, chromatin remodeling, microRNA biogenesis, and translational machinery play critical roles in guar salinity tolerance. Genes associated with several transporter families that were differentially expressed during salinity included ABC, MFS, GPH, and P-ATPase. Furthermore, genes encoding transcription factors/regulators belonging to several families, including SNF2, C2H2, bHLH, C3H, and MYB were differentially expressed in response to salinity. This study revealed the importance of various biological pathways during salinity stress and identified several candidate genes that may be used to develop salt-tolerant guar genotypes that might be suitable for cultivation in marginal soils with moderate to high salinity or using degraded water.
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Affiliation(s)
- Biswa R. Acharya
- U.S. Salinity Lab (USDA-ARS), 450 W Big Springs Road, Riverside, CA 92507, USA; (B.R.A.); (J.F.S.F.)
- College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA;
| | - Devinder Sandhu
- U.S. Salinity Lab (USDA-ARS), 450 W Big Springs Road, Riverside, CA 92507, USA; (B.R.A.); (J.F.S.F.)
- Correspondence: (D.S.); (K.K.G.)
| | - Christian Dueñas
- College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA;
| | - Jorge F. S. Ferreira
- U.S. Salinity Lab (USDA-ARS), 450 W Big Springs Road, Riverside, CA 92507, USA; (B.R.A.); (J.F.S.F.)
| | - Kulbhushan K. Grover
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
- Correspondence: (D.S.); (K.K.G.)
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Development of SNP Set for the Marker-Assisted Selection of Guar ( Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly. PLANTS 2021; 10:plants10102063. [PMID: 34685872 PMCID: PMC8539970 DOI: 10.3390/plants10102063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022]
Abstract
Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits.
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10
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Chen C, Chu Y, Huang Q, Zhang W, Ding C, Zhang J, Li B, Zhang T, Li Z, Su X. Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency. BMC Genomics 2021; 22:697. [PMID: 34579659 PMCID: PMC8474845 DOI: 10.1186/s12864-021-07991-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nitrogen (N) is one of the main factors limiting the wood yield in poplar cultivation. Understanding the molecular mechanism of N utilization could play a guiding role in improving the nitrogen use efficiency (NUE) of poplar. Results In this study, three N-efficient genotypes (A1-A3) and three N-inefficient genotypes (C1-C3) of Populus deltoides were cultured under low N stress (5 μM NH4NO3) and normal N supply (750 μM NH4NO3). The dry matter mass, leaf morphology, and chlorophyll content of both genotypes decreased under N starvation. The low nitrogen adaptation coefficients of the leaves and stems biomass of group A were significantly higher than those of group C (p < 0.05). Interestingly, N starvation induced fine root growth in group A, but not in group C. Next, a detailed time-course analysis of enzyme activities and gene expression in leaves identified 2062 specifically differentially expressed genes (DEGs) in group A and 1118 in group C. Moreover, the sensitivity to N starvation of group A was weak, and DEGs related to hormone signal transduction and stimulus response played an important role in the low N response this group. Weighted gene co-expression network analysis identified genes related to membranes, catalytic activity, enzymatic activity, and response to stresses that might be critical for poplar’s adaption to N starvation and these genes participated in the negative regulation of various biological processes. Finally, ten influential hub genes and twelve transcription factors were identified in the response to N starvation. Among them, four hub genes were related to programmed cell death and the defense response, and PodelWRKY18, with high connectivity, was involved in plant signal transduction. The expression of hub genes increased gradually with the extension of low N stress time, and the expression changes in group A were more obvious than those in group C. Conclusions Under N starvation, group A showed stronger adaptability and better NUE than group C in terms of morphology and physiology. The discovery of hub genes and transcription factors might provide new information for the analysis of the molecular mechanism of NUE and its improvement in poplar. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07991-7.
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Affiliation(s)
- Cun Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Yanguang Chu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Qinjun Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Jing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Bo Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Zhenghong Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China. .,Key Laboratory of Tree Breeding and Cultivation, State Forestry and Grassland Administration, Beijing, China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu Province, China.
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Baruah PM, Krishnatreya DB, Bordoloi KS, Gill SS, Agarwala N. Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:221-236. [PMID: 33706183 DOI: 10.1016/j.plaphy.2021.02.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 05/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.
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Affiliation(s)
- Pooja Moni Baruah
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India
| | | | | | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124 001, India
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India.
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Sharma S, Tyagi A, Srivastava H, Ramakrishna G, Sharma P, Sevanthi AM, Solanke AU, Sharma R, Singh NK, Sharma TR, Gaikwad K. Exploring the edible gum (galactomannan) biosynthesis and its regulation during pod developmental stages in clusterbean using comparative transcriptomic approach. Sci Rep 2021; 11:4000. [PMID: 33597579 PMCID: PMC7890066 DOI: 10.1038/s41598-021-83507-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/19/2021] [Indexed: 12/02/2022] Open
Abstract
Galactomannan is a polymer of high economic importance and is extracted from the seed endosperm of clusterbean (C. tetragonoloba). In the present study, we worked to reveal the stage-specific galactomannan biosynthesis and its regulation in clusterbean. Combined electron microscopy and biochemical analysis revealed high protein and gum content in RGC-936, while high oil bodies and low gum content in M-83. A comparative transcriptome study was performed between RGC-936 (high gum) and M-83 (low gum) varieties at three developmental stages viz. 25, 39, and 50 days after flowering (DAF). Total 209,525, 375,595 and 255,401 unigenes were found at 25, 39 and 50 DAF respectively. Differentially expressed genes (DEGs) analysis indicated a total of 5147 shared unigenes between the two genotypes. Overall expression levels of transcripts at 39DAF were higher than 50DAF and 25DAF. Besides, 691 (RGC-936) and 188 (M-83) candidate unigenes that encode for enzymes involved in the biosynthesis of galactomannan were identified and analyzed, and 15 key enzyme genes were experimentally validated by quantitative Real-Time PCR. Transcription factor (TF) WRKY was observed to be co-expressed with key genes of galactomannan biosynthesis at 39DAF. We conclude that WRKY might be a potential biotechnological target (subject to functional validation) for developing high gum content varieties.
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Affiliation(s)
- Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | | | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.,DBT-National Agri-Food Biotechnology Institute, Mohali, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.
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Dhaliwal SK, Talukdar A, Gautam A, Sharma P, Sharma V, Kaushik P. Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review. Int J Mol Sci 2020; 21:E9615. [PMID: 33348635 PMCID: PMC7766301 DOI: 10.3390/ijms21249615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes' performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.
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Affiliation(s)
- Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India; (S.K.D.); (P.S.)
| | - Akshay Talukdar
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Ashish Gautam
- Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145, India;
| | - Pankaj Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India; (S.K.D.); (P.S.)
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
- Nagano University, Ueda 386-0031, Japan
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14
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Anas M, Liao F, Verma KK, Sarwar MA, Mahmood A, Chen ZL, Li Q, Zeng XP, Liu Y, Li YR. Fate of nitrogen in agriculture and environment: agronomic, eco-physiological and molecular approaches to improve nitrogen use efficiency. Biol Res 2020; 53:47. [PMID: 33066819 PMCID: PMC7565752 DOI: 10.1186/s40659-020-00312-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/20/2020] [Indexed: 11/10/2022] Open
Abstract
Nitrogen is the main limiting nutrient after carbon, hydrogen and oxygen for photosynthetic process, phyto-hormonal, proteomic changes and growth-development of plants to complete its lifecycle. Excessive and inefficient use of N fertilizer results in enhanced crop production costs and atmospheric pollution. Atmospheric nitrogen (71%) in the molecular form is not available for the plants. For world's sustainable food production and atmospheric benefits, there is an urgent need to up-grade nitrogen use efficiency in agricultural farming system. The nitrogen use efficiency is the product of nitrogen uptake efficiency and nitrogen utilization efficiency, it varies from 30.2 to 53.2%. Nitrogen losses are too high, due to excess amount, low plant population, poor application methods etc., which can go up to 70% of total available nitrogen. These losses can be minimized up to 15-30% by adopting improved agronomic approaches such as optimal dosage of nitrogen, application of N by using canopy sensors, maintaining plant population, drip fertigation and legume based intercropping. A few transgenic studies have shown improvement in nitrogen uptake and even increase in biomass. Nitrate reductase, nitrite reductase, glutamine synthetase, glutamine oxoglutarate aminotransferase and asparagine synthetase enzyme have a great role in nitrogen metabolism. However, further studies on carbon-nitrogen metabolism and molecular changes at omic levels are required by using "whole genome sequencing technology" to improve nitrogen use efficiency. This review focus on nitrogen use efficiency that is the major concern of modern days to save economic resources without sacrificing farm yield as well as safety of global environment, i.e. greenhouse gas emissions, ammonium volatilization and nitrate leaching.
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Affiliation(s)
- Muhammad Anas
- College of Agriculture, Guangxi University, Nanning, 530005, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Krishan K Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | | | - Aamir Mahmood
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Zhong-Liang Chen
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China
| | - Qiang Li
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Xu-Peng Zeng
- College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yang Liu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, 530007, China.
| | - Yang-Rui Li
- College of Agriculture, Guangxi University, Nanning, 530005, China.
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, Guangxi, China.
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Grigoreva E, Ulianich P, Ben C, Gentzbittel L, Potokina E. First Insights into the Guar (Cyamopsis tetragonoloba (L.) Taub.) Genome of the ‘Vavilovskij 130’ Accession, Using Second and Third-Generation Sequencing Technologies. RUSS J GENET+ 2019. [DOI: 10.1134/s102279541911005x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar ( Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. Int J Genomics 2019; 2019:7295859. [PMID: 31687376 PMCID: PMC6800914 DOI: 10.1155/2019/7295859] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/23/2019] [Accepted: 09/05/2019] [Indexed: 11/17/2022] Open
Abstract
The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2 × 100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.
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Elucidation of Galactomannan Biosynthesis Pathway Genes through Transcriptome Sequencing of Seeds Collected at Different Developmental Stages of Commercially Important Indian Varieties of Cluster Bean (Cyamopsis tetragonoloba L.). Sci Rep 2019; 9:11539. [PMID: 31395961 PMCID: PMC6687724 DOI: 10.1038/s41598-019-48072-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
Cyamopsis tetragonoloba (L) endosperm predominantly contains guar gum a polysaccharide, which has tremendous industrial applications in food, textile, paper, oil drilling and water treatment. In order to understand the genes controlling galactomannan biosynthesis, mRNA was isolated from seeds collected at different developmental stages; young pods, mature pods and young leaf from two guar varieties, HG365 and HG870 and subjected to Illumina sequencing. De novo assembly of fourteen individual read files from two varieties of guar representing seven developmental stages gave a total of 1,13,607 contigs with an N50 of 1,244 bases. Annotation of assemblies with GO mapping revealed three levels of distribution, namely, Biological Processes, Molecular Functions and Cellular Components. GO studies identified major genes involved in galactomannan biosynthesis: Cellulose synthase D1 (CS D1) and GAUT-like gene families. Among the polysaccharide biosynthetic process (GO:0000271) genes the transcript abundance for CS was found to be predominantly more in leaf samples, whereas, the transcript abundance for GAUT-like steadily increased from 65% to 90% and above from stage1 to stage5 indicating accumulation of galactomannan in developing seeds; and validated by qRT-PCR analysis. Galactomannan quantification by HPLC showed HG365 (12.98–20.66%) and HG870 (7.035–41.2%) gradually increasing from stage1 to stage 5 (10–50 DAA) and highest accumulation occurred in mature and dry seeds with 3.8 to 7.1 fold increase, respectively. This is the first report of transcriptome sequencing and complete profiling of guar seeds at different developmental stages, young pods, mature pods and young leaf material from two commercially important Indian varieties and elucidation of galactomannan biosynthesis pathway. It is envisaged that the data presented herein will be very useful for improvement of guar through biotechnological interventions in future.
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Tyagi A, Sandhya, Sharma P, Saxena S, Sharma R, Amitha Mithra SV, Solanke AU, Singh NK, Sharma TR, Gaikwad K. The genome size of clusterbean (Cyamopsis tetragonoloba) is significantly smaller compared to its wild relatives as estimated by flow cytometry. Gene 2019; 707:205-211. [PMID: 30898697 DOI: 10.1016/j.gene.2019.02.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/04/2019] [Accepted: 02/28/2019] [Indexed: 02/06/2023]
Abstract
Clusterbean (C. tetragonoloba) is an important, leguminous vegetable and industrial crop with vast genetic diversity but meager genetic, cytological and genomic information. In the present study, an optimized procedure of flow cytometry was used to estimate the genome size of three clusterbean species, represented by C. tetragonoloba (cv. RGC-936) and two wild relatives (C. serreta and C. senegalensis). For accurate estimation of genomic content, singlet G0/G1 populations of multiple tissues such as leaves, hypocotyl, and matured seeds were determined and used along with three different plant species viz. Pisum sativum (as primary), Oryza sativa, and Glycine max (secondary), as external and internal reference standards. Seed tissue of the test sample and G. max provided the best estimate of nuclear DNA content in comparison to other sample tissues and reference standards. The genome size of C. tetragonoloba was detemined at 580.9±0.02Mbp (1C), while that of C. serreta and C. senegalensis was estimated at 979.6±0.02Mbp (1C) and 943.4±0.03Mbp (1C), respectively. Thus, the wild relatives harbor, nearly double the genome content of the cultivated cluster bean. Findings of this study will enrich genomic database of the legume family and can serve as the starting point for clusterbean evolutionary and genomics studies.
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Affiliation(s)
- Anshika Tyagi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Sandhya
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Swati Saxena
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ramavtar Sharma
- ICAR-Central Arid Zone Research Institute (CAZRI), Jodhpur, India
| | - S V Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
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Thakur O, Randhawa GS. Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots. BMC Genomics 2018; 19:951. [PMID: 30572838 PMCID: PMC6302463 DOI: 10.1186/s12864-018-5205-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/28/2018] [Indexed: 12/11/2022] Open
Abstract
Background Guar [Cyamopsis tetragonoloba, L. Taub.] is an important industrial crop because of the commercial applications of the galactomannan gum contained in its seeds. Plant breeding programmes based on marker-assisted selection require a rich resource of molecular markers. As limited numbers of such markers are available for guar, molecular breeding programmes have not been undertaken for the genetic improvement of this important crop. Hence, the present work was done to enrich the molecular markers resource of guar by identifying high quality SSR, SNP and InDel markers from the RNA-Seq data of the roots of two guar varieties. Results We carried out RNA-Seq analysis of the roots of two guar varieties, namely, RGC-1066 and M-83. A total of 102,479 unigenes with an average length of 1016 bp were assembled from about 30 million high quality pair-end reads generated by an Illumina HiSeq 2500 platform. The assembled unigenes had 86.55% complete and 97.71% partially conserved eukaryotic genes (CEGs). The functional annotation of assembled unigenes using BLASTX against six databases showed that the guar unigenes were most similar to Glycine max. We could assign GO terms to 45,200 unigenes using the UniProt database. The screening of 102,479 unigenes with MISA and SAMtools version 1.4 softwares resulted in the identification of 25,040 high-confidence molecular markers which consisted of 18,792 SSRs, 5999 SNPs and 249 InDels. These markers tagged most of the genes involved in root development, stress tolerance and other general metabolic activities. Each of the 25,040 molecular markers was characterized, particularly with respect to its position in the unigene. For 71% of the molecular markers, we could determine the names, products and functions of the unigenes. About 80% of the markers, from a random sample of molecular markers, showed PCR amplification. Conclusions We have identified and characterized 25,040 high confidence SSR, SNP and InDel molecular markers in guar. It is expected that these markers will be useful in molecular breeding programmes and will also be helpful in studying molecular mechanisms of root development, stress tolerance and gum synthesis in guar. Electronic supplementary material The online version of this article (10.1186/s12864-018-5205-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Omika Thakur
- Department of Biotechnology, Indian Institute of Technology Roorkee, -247667, Roorkee, Uttarakhand, India
| | - Gursharn Singh Randhawa
- Department of Biotechnology, Indian Institute of Technology Roorkee, -247667, Roorkee, Uttarakhand, India. .,Present address: Department of Biochemistry & Biotechnology, Sardar Bhagwan Singh University, Balawala, Dehradun, Uttarakhand, 248161, India.
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20
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Tyagi A, Nigam D, S. V. AM, Solanke AU, Singh NK, Sharma TR, Gaikwad K. Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1241-1257. [PMID: 29193664 PMCID: PMC5978871 DOI: 10.1111/pbi.12866] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 05/13/2023]
Abstract
Owing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC-936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP- D-glucose 4-epimerase) and validated as targets for three novel miRNAs, that is Ct-miR3130, Ct-miR3135 and Ct-miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan-producing species.
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Affiliation(s)
- Anshika Tyagi
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | - Deepti Nigam
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | | | | | | | - Tilak R. Sharma
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
- Present address:
National Agri‐Food Biotechnology InstituteMohaliIndia
| | - Kishor Gaikwad
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
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Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism-Related Genes. Genes (Basel) 2018; 9:genes9040206. [PMID: 29641510 PMCID: PMC5924548 DOI: 10.3390/genes9040206] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 11/26/2022] Open
Abstract
The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and Nagina 22 (N22) under optimal (N+) and chronic starvation (N−) of nitrogen (N) from 15-day-old root and shoot tissues. The two genotypes were found to be contrasting in their response to N−; IR64 root architecture and root dry weight remained almost equivalent to that under N+ conditions, while N22 showed high foraging ability but a substantial reduction in biomass under N−. Similarly, the photosynthetic pigments showed a drastic reduction in N22 under low N, while IR64 was more resilient. Nitrate reductase showed significantly low specific activity under N− in both genotypes. Glutamate synthase (GOGAT) and citrate synthase CS activity were highly reduced in N22 but not in IR64. Transcriptome analysis of these genotypes revealed nearly double the number of genes to be differentially expressed (DEGs) in roots (1016) compared to shoots (571). The response of the two genotypes to N starvation was distinctly different reflecting their morphological/biochemical response with just two and eight common DEGs in the root and shoot tissues. There were a total of 385 nitrogen-responsive DEGs (106 in shoots and 279 in roots) between the two genotypes. Fifty-two of the 89 DEGs identified as specific to N22 root tissues were also found to be differentially expressed between the two genotypes under N−. Most of these DEGs belonged to starch and chloroplast metabolism, followed by membrane and signaling proteins. Physical mapping of DEGs revealed 95 DEGs in roots and 76 in shoots to be present in quantitative trait loci (QTL) known for NUE.
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