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Prathyusha VB, Swathi E, Divya D, Reddy BVB, Bentur JS, Chalam VC, Wankhede DP, Singh K, Anitha K. Field and agroinoculation screening of national collection of urd bean ( Vigna mungo) germplasm accessions for new sources of mung bean yellow mosaic virus (MYMV) resistance. 3 Biotech 2023; 13:194. [PMID: 37206359 PMCID: PMC10188856 DOI: 10.1007/s13205-023-03610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Yellow mosaic disease (YMD) is a major problem in Urd bean (Vigna mungo L.) in India, which causes huge yield losses. Breeding for wide spectrum and durable Mungbean yellow mosaic virus (MYMV) resistance and cultivating resistant cultivars is the most appropriate and effective approach. However, the task has become challenging with the report of at least two species of the virus, viz., Mungbean yellow mosaic virus (MYMV) and Mungbean yellow mosaic India virus (MYMIV) and their recombinants; the existence of various isolates of these species with varied virulence and rapid mutations noted in the virus as well as in the whitefly vector population. Thus the present study was carried out to identify and characterize novel and diverse sources of YMV resistance and develop linked molecular markers for breeding durable and broadspectrum resistant urdbean cultivars against YMV. Towards this goal, we have screened 998 accessions of urdbean national collection of germplasm against YMD Hyderabad isolate both in a field under the natural level of disease incidence and through agro inoculation in the laboratory using viruliferous clones of the same isolate. Ten highly resistant accessions identified through repeated testing have been characterized in terms of reported linked markers. We attempted to see diversity among the ten resistant accessions reported here using earlier reported resistance-linked SCAR marker YMV1 and SSR CEDG180 marker. SCAR marker YMV1 did not amplify with any of the 10 accessions. But with CEDG180, results suggested that 10 accessions shortlisted through field and laboratory tests do not carry PU31 allele and this shows that it may be likely to carry novel gene(s). Further studies are needed to genetically characterize these new sources.
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Affiliation(s)
| | - E. Swathi
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Hyderabad, TG 500 030 India
| | - D. Divya
- Agri Biotech Foundation, Rajendranagar, Hyderabad, TG 500 030 India
| | - B. V. Bhaskar Reddy
- Regional Agricultural Research Station, Acharya NG Ranga Agricultural University, Tirupati, AP 517 502 India
| | - J. S. Bentur
- Agri Biotech Foundation, Rajendranagar, Hyderabad, TG 500 030 India
| | - V. Celia Chalam
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110 012 India
| | - D. P. Wankhede
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110 012 India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, 110 012 India
- Present Address: Head, Gene Bank, ICRISAT, Patancheru, TG 502324 India
| | - K. Anitha
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Hyderabad, TG 500 030 India
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Singh R, Singh A, Mahato AK, Paliwal R, Tiwari G, Kumar A. De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata. Int J Mol Sci 2023; 24:ijms24119212. [PMID: 37298166 DOI: 10.3390/ijms24119212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant.
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Affiliation(s)
- Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Ajay Kumar Mahato
- The Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Ritu Paliwal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Gunjan Tiwari
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Pootakham W, Nawae W, Naktang C, Sonthirod C, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Somta P, Laosatit K, Tangphatsornruang S. A chromosome-scale assembly of the black gram (Vigna mungo) genome. Mol Ecol Resour 2020; 21:238-250. [PMID: 32794377 DOI: 10.1111/1755-0998.13243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked-read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques yielded the first high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome-wide duplication event observed in the tetraploid créole bean (Vigna reflexo-pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full-length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high-quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker-assisted breeding and for future comparative genomics and phylogenetic studies in legume species.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
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Mehra R, Jasrotia RS, Mahajan A, Sharma D, Iquebal MA, Kaul S, Dhar MK. Transcriptome analysis of Snow Mountain Garlic for unraveling the organosulfur metabolic pathway. Genomics 2020; 112:99-107. [DOI: 10.1016/j.ygeno.2019.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/05/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]
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Liu JP, Hu J, Liu YH, Yang CP, Zhuang YF, Guo XL, Li YJ, Zhang L. Transcriptome analysis of Hevea brasiliensis in response to exogenous methyl jasmonate provides novel insights into regulation of jasmonate-elicited rubber biosynthesis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:349-358. [PMID: 29692543 PMCID: PMC5911270 DOI: 10.1007/s12298-018-0529-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/07/2018] [Accepted: 03/27/2018] [Indexed: 05/14/2023]
Abstract
The phytohomorne methyl jasmonate (MeJA) is known to trigger extensive reprogramming of gene expression leading to transcriptional activation of many secondary metabolic pathways. However, natural rubber is a commercially important secondary metabolite and little is known about the genetic and genomic basis of jasmonate-elicited rubber biosynthesis in rubber tree (Hevea brasiliensis). RNA sequencing (RNA-seq) of H. brasiliensis bark treated with 1 g lanolin paste containing 0.02% w/w MeJA for 24 h (M2) and 0.04% w/w MeJA for 24 h (M4) was performed. A total of 2950 and 2850 differentially expressed genes in M2 and M4 compared with control (C) were respectively detected. Key genes involved in 2-C-methyl-D-erythritol 4-phosphate, rubber biosynthesis, glycolysis and carbon fixation (Calvin cycle) pathway were found to be up-regulated by MeJA treatment. Particularly, the expression of 3-hydroxy-3-metylglutaryl coenzyme A reductase in MVA pathway was down-regulated by MeJA treatment, but the expression of farnesyl diphosphate synthase (FPS) and cis-prenyltransferase (CPT, or rubber transferase) in rubber biosynthesis pathway were up-regulated by MeJA treatment. Up-regulation of critical genes in JA biosynthesis in response to MeJA treatment exhibited the self-activation of JA biosynthesis. In addition, up-regulated genes of great regulatory importance in cross-talk between JA and other hormone signaling, and of transcriptional regulation were identified. The increased expression levels of FPS and CPT in rubber biosynthesis pathway possibly resulted in an increased latex production in rubber tree treated with MeJA. The present results provide insights into the mechanism by which MeJA activates the rubber biosynthesis and the transcriptome data can also serve as the foundation for future research into the molecular basis for MeJA regulation of other cellular processes.
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Affiliation(s)
- Jin-Ping Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Jin Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Yan-Hui Liu
- Center for Genomics and Biotechnology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Cui-Ping Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Yu-Fen Zhuang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Xiu-Li Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry Institute, Hainan University, Haikou, 570228 Hainan Province China
| | - Yi-Jian Li
- Service Center of Science and Technology, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan Province China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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