1
|
Kumar M, Neeraj, Hada A, Somvanshi VS, Singh AK, Yadava YK, Jain PK, Gaikwad K, Sirohi A. A Draft Transcriptome Announcement of Anguina tritici. J Nematol 2024; 56:20240007. [PMID: 38510971 PMCID: PMC10954354 DOI: 10.2478/jofnem-2024-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Indexed: 03/22/2024] Open
Abstract
Anguina tritici, the wheat seed gall nematode, causes the 'ear-cockle' or seed gall disease of wheat (Triticum sp.), leading to an extensive decline of yield (30-70%) in underdeveloped wheat cultivating countries of the world. The nematode is known to survive in anhydrobiotic conditions for up to 32 years. Here, we present the first transcriptome assembly of A. tritici, which will be a valuable resource for understanding the genes responsible for nematode survival and above-ground plant parasitism. The final 133.2 Mb assembly consists of 105606 open reading frames (including isoforms) with the following BUSCO scores against Nematoda database: 80.3% complete (16.4% single copy and 63.9% duplicated), 2.1% fragmented, and 17.6% missing.
Collapse
Affiliation(s)
- Manish Kumar
- Division of Nematology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi-110012, India
| | - Neeraj
- Division of Nematology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi-110012, India
| | - Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi-110012, India
| | - Vishal Singh Somvanshi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi-110012, India
| | - Ashish Kumar Singh
- Division of Crop Protection, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand263601, India
| | - Yashwant Kumar Yadava
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kishore Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi-110012, India
| |
Collapse
|
2
|
Gupta NC, Yadav S, Arora S, Mishra DC, Budhlakoti N, Gaikwad K, Rao M, Prasad L, Rai PK, Sharma P. Draft genome sequencing and secretome profiling of Sclerotinia sclerotiorum revealed effector repertoire diversity and allied broad-host range necrotrophy. Sci Rep 2022; 12:21855. [PMID: 36528657 PMCID: PMC9759525 DOI: 10.1038/s41598-022-22028-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 10/07/2022] [Indexed: 12/23/2022] Open
Abstract
White mold commonly known as Sclerotinia sclerotiorum causes stem rot disease and has emerged as one of the major fungal pathogens of oilseed Brassica across the world. In the present study, consistently virulent S. sclerotiorum isolate "ESR-01" was sequenced and an assembly size of ~ 41 Mb with 328 scaffolds having N50 of 447,128 was obtained. Additionally, 27,450 single nucleotide polymorphisms (SNPs) were identified from 155 scaffolds against S. sclerotiorum 1980 isolate, with an average SNP density of ~ 1.5 per kb genome. 667 repetitive elements were identified and approximately comprised 7% of the total annotated genes. The DDE_1 with 454 in numbers was found to be the most abundant and accounts for 68% of the total predicted repetitive elements. In total, 3844 simple sequence repeats are identified in the 328 scaffolds. A total of 9469 protein-coding genes were predicted from the whole genome assembly with an average gene length of 1587 bp and their distribution as 230.95 genes per Mb in the genome. Out of 9469 predicted protein-coding genes, 529 genes were observed encoding the CAZymes (Carbohydrate-Active enzymes) capable of degradation of the complex polysaccharides. Glycosyltransferase (GT) families were most abundant (49.71%) among the predicted CAZymes and GT2 (23%), GT4 (20%), and glycoside hydrolase (GH) 23% with GH18 (11%) were the prominent cell wall degrading enzyme families in the ESR-01 secretome. Besides this, 156 genes essential for the pathogen-host interactions were also identified. The effector analysis in the whole genome proteomics dataset revealed a total of 57 effector candidates (ECs) and 27 of them were having their analogs whereas the remaining 30 were novel ones. Eleven selected ECs were validated experimentally by analyzing the expression profile of the ESR-01 isolate of S. sclerotiorum. Together, the present investigation offers a better understanding of the S. sclerotiorum genome, secretome, and its effector repertoire which will help in refining the present knowledge on S. sclerotiorum-Brassica interactions and necrotrophic lifestyle of the phytopathogen in general.
Collapse
Affiliation(s)
- Navin C. Gupta
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sunita Yadav
- grid.463150.50000 0001 2218 1322Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shaweta Arora
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Dwijesh C. Mishra
- grid.463150.50000 0001 2218 1322Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Neeraj Budhlakoti
- grid.463150.50000 0001 2218 1322Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kishore Gaikwad
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Mahesh Rao
- grid.418105.90000 0001 0643 7375ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Lakshman Prasad
- grid.418196.30000 0001 2172 0814ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Pramod K. Rai
- grid.505951.d0000 0004 1768 6555ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan India
| | - Pankaj Sharma
- grid.505951.d0000 0004 1768 6555ICAR-Directorate of Rapeseed-Mustard Research, Bharatpur, Rajasthan India
| |
Collapse
|
3
|
Tyagi A, Sharma S, Ali S, Gaikwad K. Crosstalk between H 2 S and NO: an emerging signalling pathway during waterlogging stress in legume crops. Plant Biol (Stuttg) 2022; 24:576-586. [PMID: 34693601 DOI: 10.1111/plb.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
In legumes, waterlogging is a major detrimental factor leading to huge yield losses. Generally, legumes lack tolerance to submergence, and conventional breeding to develop tolerant varieties are limited due to the lack of tolerant germplasm and potential target genes. Moreover, our understanding of the various signalling cascades, their interactions and key pathways induced during waterlogging is limited. Here, we focus on the role of two important plant signalling molecules, viz. hydrogen sulphide (H2 S) and nitric oxide (NO), during waterlogging stress in legumes. Plants and soil microbes produce these signalling molecules both endogenously and exogenously under various stresses, including waterlogging. NO and H2 S are known to regulate key physiological pathways, such as stomatal closure, leaf senescence and regulation of numerous stress signalling pathways, while NO plays a pivotal role in adventitious root formation during waterlogging. The crosstalk between H2 S and NO is synergistic because of the resemblance of their physiological effects and proteomic functions, which mainly operate through cysteine-dependent post-translational modifications via S-nitrosation and persulfidation. Such knowledge has provided novel platforms for researchers to unravel the complexity associated with H2 S-NO signalling and interactions with plant stress hormones. This review provides an overall summary on H2 S and NO, including biosynthesis, biological importance, crosstalk, transporter regulation as well as understanding their role during waterlogging using 'multi-omics' approach. Understanding H2 S and NO signalling will help in deciphering the metabolic interactions and identifying key regulatory genes that could be used for developing waterlogging tolerance in legumes.
Collapse
Affiliation(s)
- A Tyagi
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - S Sharma
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - S Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan Gyeongbuk, Republic of Korea
| | - K Gaikwad
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| |
Collapse
|
4
|
Lal MK, Singh B, Tiwari RK, Kumar S, S G, Gaikwad K, Kumar A, Paul V, Singh MP. Interactive Effect of Retrogradation and Addition of Pulses, Cooking Oil on Predicted Glycemic Index and Resistant Starch of Potato. STARCH-STARKE 2022. [DOI: 10.1002/star.202100221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Milan Kumar Lal
- Division of Plant Physiology ICAR‐Indian Agricultural Research Insitute (ICAR‐IARI) New Delhi 110012 India
- Division of Crop Physiology Biochemistry and Post‐Harvest Technology ICAR‐Central Potato Research Institute (ICAR‐CPRI) Shimla Himachal Pradesh 171001 India
| | - Brajesh Singh
- Division of Crop Physiology Biochemistry and Post‐Harvest Technology ICAR‐Central Potato Research Institute (ICAR‐CPRI) Shimla Himachal Pradesh 171001 India
| | - Rahul Kumar Tiwari
- Division of Plant Physiology ICAR‐Indian Agricultural Research Insitute (ICAR‐IARI) New Delhi 110012 India
- Division of Crop Physiology Biochemistry and Post‐Harvest Technology ICAR‐Central Potato Research Institute (ICAR‐CPRI) Shimla Himachal Pradesh 171001 India
| | - Sudhir Kumar
- Division of Plant Physiology ICAR‐Indian Agricultural Research Insitute (ICAR‐IARI) New Delhi 110012 India
| | - Gopalakrishnan S
- Division of Genetics ICAR‐Indian Agricultural Research Institute (ICAR‐IARI) New Delhi 110012 India
| | - Kishore Gaikwad
- ICAR‐National Institute for Plant Biotechnology (ICAR‐NIPB) New Delhi 110012 India
| | - Awadhesh Kumar
- Division of Crop Physiology and Biochemistry ICAR‐National Rice Research Institute, (ICAR‐NRRI) Cuttack 753006 India
| | - Vijay Paul
- Division of Plant Physiology ICAR‐Indian Agricultural Research Insitute (ICAR‐IARI) New Delhi 110012 India
| | - Madan Pal Singh
- Division of Plant Physiology ICAR‐Indian Agricultural Research Insitute (ICAR‐IARI) New Delhi 110012 India
| |
Collapse
|
5
|
Madhusudhan P, Sinha P, Rajput LS, Bhattacharya M, Sharma T, Bhuvaneshwari V, Gaikwad K, Krishnan SG, Singh AK. Effect of temperature on Pi54-mediated leaf blast resistance in rice. World J Microbiol Biotechnol 2019; 35:148. [PMID: 31549233 DOI: 10.1007/s11274-019-2724-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/06/2019] [Indexed: 12/19/2022]
Abstract
Assessment of temperature effect on plant resistance against diseases has become essential under climate change scenario as temperature rise is anticipated to modify host resistance. To determine temperature influence on resistance gene, a pair of near-isogenic rice lines differing for the Pi54 resistance gene was assessed against leaf blast. Blast resistance was determined as the extent of infection efficiency (IE) and sporulation (SP) at suboptimal (22 °C and 32 °C) and optimal temperature (27 °C) of pathogen aggressiveness. Relative resistance for IE and SP was higher at suboptimal temperature as compared to that of optimal temperature. Maximum level of resistance was at 22 °C where higher levels of expression of Pi54 and defence-regulatory transcription factor WRKY45 were also noted. At 32 °C, although some level of resistance noted, but level of Pi54 and WRKY45 expression was too low, suggesting that resistance recorded at higher temperature was due to reduced pathogen aggressiveness. At the optimal temperature for pathogen aggressiveness, comparatively lower levels of Pi54 and WRKY45 expression suggest possible temperature-induced interruption of the defence processes. The variation in resistance patterns modulated by temperature is appeared to be due to pathogen's sensitivity to temperature that leads to varying levels of Pi54 gene activation. Quick and violent activity of the pathogen at optimal temperature came into sight for the interruption of defence process activated by Pi54 gene. Evaluation of blast resistance genes under variable temperature conditions together with weather data could be applied in screening rice genotypes for selection of resistance having resilience to temperature rise.
Collapse
Affiliation(s)
- P Madhusudhan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Agricultural Research Station, Acharya N G Ranga Agricultural University, Nellore, Andhra Pradesh, 524003, India
| | - P Sinha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - L S Rajput
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Division of Plant Protection, ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, 452001, India
| | - M Bhattacharya
- Department of Agronomy, IOWA State University, Ames, IA, 5001-1051, USA
| | - Taru Sharma
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - V Bhuvaneshwari
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University, Maruteru, Andhra Pradesh, 534122, India
| | - Kishore Gaikwad
- National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| |
Collapse
|
6
|
Decatris M, Hayes M, Reed N, Bhalla V, Thomas J, Gaikwad K, Birchall K, Phillips A, Ryan P, Du Rand I, Taniere P. Programmed death-ligand 1 (PD-L1) expression and testing experience in a cohort of advanced non-small cell lung cancer (NSCLC) patients. Lung Cancer 2018. [DOI: 10.1016/s0169-5002(18)30126-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
7
|
Arora S, Mahato AK, Singh S, Mandal P, Bhutani S, Dutta S, Kumawat G, Singh BP, Chaudhary AK, Yadav R, Gaikwad K, Sevanthi AM, Datta S, Raje RS, Sharma TR, Singh NK. A high-density intraspecific SNP linkage map of pigeonpea (Cajanas cajan L. Millsp.). PLoS One 2017; 12:e0179747. [PMID: 28654689 PMCID: PMC5487049 DOI: 10.1371/journal.pone.0179747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 06/02/2017] [Indexed: 01/09/2023] Open
Abstract
Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm. Here, we present a dense intraspecific linkage map of pigeonpea comprising 932 markers that span a total adjusted map length of 1,411.83 cM. The consensus map is based on three different linkage maps that incorporate a large number of single nucleotide polymorphism (SNP) markers derived from next generation sequencing data, using Illumina GoldenGate bead arrays, and genotyping with restriction site associated DNA (RAD) sequencing. The genotyping-by-sequencing enhanced the marker density but was met with limited success due to lack of common markers across the genotypes of mapping population. The integrated map has 547 bead-array SNP, 319 RAD-SNP, and 65 simple sequence repeat (SSR) marker loci. We also show here correspondence between our linkage map and published genome pseudomolecules of pigeonpea. The availability of a high-density linkage map will help improve the anchoring of the pigeonpea genome to its chromosomes and the mapping of genes and quantitative trait loci associated with useful agronomic traits.
Collapse
Affiliation(s)
- Sheetal Arora
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Ajay Kumar Mahato
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Sangeeta Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Paritra Mandal
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Shefali Bhutani
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Sutapa Dutta
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Giriraj Kumawat
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Bikram Pratap Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | - Rekha Yadav
- Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - K. Gaikwad
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | | | - Ranjeet S. Raje
- Division of Genetics, Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Tilak R. Sharma
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- * E-mail:
| |
Collapse
|
8
|
Abstract
OBJECTIVE To measure physical activity in children with wasting and to look for association between poor physical activity and wasting. METHODS Physical activity was measured in 56 children with wasting, using Childrens Activity Rating Scale, and compared with age- and sex-matched controls. RESULTS A significant association was found between poor physical activity and malnutrition as determined by weight-for-height Z Score <-2 (P=0.001) and mid-upper-arm circumference (P=0.002). MAIN CONCLUSION Physical activity can be used as clinical parameter to assess malnutrition.
Collapse
Affiliation(s)
- M Girish
- Department of Pediatrics, NKP Salve Institute of Medical Sciences, and *Department of Preventive and Community Medicine, Government Medical College, Nagpur, Maharashtra, India. Correspondence to: Dr Meenakshi Girish, 101, Shubham Enclave, Darda Marg, Rahate Colony, Nagpur 440 022, Maharashtra, India.
| | | | | | | | | |
Collapse
|
9
|
Bakshi AV, Bharath R, Gupta S, Nair R, Shet T, Ghadyalpatil NS, Kaushal R, Gaikwad K, Kannan S, Parikh PM. Evaluation of efficacy and safety of neoadjuvant chemotherapy with weekly paclitaxel in patients with locally advanced and large operable breast cancer. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.11593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
10
|
Bharath R, Menon H, Ghadyalpatil NS, Prabhash K, Hingmire SS, Karanth N, Jain K, Gaikwad K, Agarwal JP, Parikh PM. Treatment outcomes in patients with extensive stage small cell lung cancer - Experience from a tertiary Indian cancer centre. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.19129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
11
|
Meur G, Gaikwad K, Bhat SR, Prakash S, Kirti PB. Homeotic-like modification of stamens to petals is associated with aberrant mitochondrial gene expression in cytoplasmic male sterile Ogura Brassica juncea. J Genet 2006; 85:133-9. [PMID: 17072082 DOI: 10.1007/bf02729019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We have previously reported correction of severe leaf chlorosis in the cytoplasmic male sterile Ogura (also called Ogu) Brassica juncea line carrying Ogura cytoplasm by plastid substitution via protoplast fusion. Two cybrids obtained from the fusion experiment, Og1 and Og2, were green and carried the plastid genome of B. juncea cv. RLM198. While Og1 displayed normal flower morphology comparable to that of its euplasmic B. juncea counterpart except for sterile anthers, Og2 retained homeotic-like floral modification of stamens to petal-like structures and several other floral deformities observed in the chlorotic (Ogu) B. juncea cv. RLM198 (or OgRLM). With respect to the mitochondrial genome, Og1 showed 81% genetic similarity to the fertile cultivar RLM while Og2 showed 93% similarity to OgRLM. In spite of recombination and rearrangements in the mitochondrial genomes in the cybrids, expression patterns of 10 out of 11 mitochondrial genes were similar in all the three CMS lines; the only exception was atp6, whose expression was altered. While Og1 showed normal atp6 transcript similar to that in RLM, in Og2 and OgRLM weak expression of a longer transcript was detected. These results suggest that the homeotic-like changes in floral patterning leading to petaloid stamens in Og2 and OgRLM may be associated with aberrant mitochondrial gene expression.
Collapse
Affiliation(s)
- Gargi Meur
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500 046, India
| | | | | | | | | |
Collapse
|
12
|
Sharma TR, Madhav MS, Singh BK, Shanker P, Jana TK, Dalal V, Pandit A, Singh A, Gaikwad K, Upreti HC, Singh NK. High-resolution mapping, cloning and molecular characterization of the Pi-k ( h ) gene of rice, which confers resistance to Magnaporthe grisea. Mol Genet Genomics 2005; 274:569-78. [PMID: 16228246 DOI: 10.1007/s00438-005-0035-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Accepted: 06/03/2005] [Indexed: 10/25/2022]
Abstract
In order to understand the molecular mechanisms involved in the gene-for-gene type of pathogen resistance, high-resolution genetic and physical mapping of resistance loci is required to facilitate map-based cloning of resistance genes. Here, we report the molecular mapping and cloning of a dominant gene (Pi-k ( h )) present in the rice line Tetep, which is associated with resistance to rice blast disease caused by Magnaporthe grisea. This gene is effective against M. grisea populations prevalent in the Northwestern Himalayan region of India. Using 178 sequence tagged microsatellite, sequence-tagged site, expressed sequence tag and simple sequence repeat (SSR) markers to genotype a population of 208 F(2) individuals, we mapped the Pi-k ( h ) gene between two SSR markers (TRS26 and TRS33) which are 0.7 and 0.5 cM away, respectively, and can be used in marker-assisted-selection for blast-resistant rice cultivars. We used the markers to identify the homologous region in the genomic sequence of Oryza sativa cv. Nipponbare, and a physical map consisting of two overlapping bacterial artificial chromosome and P1 artificial chromosome clones was assembled, spanning a region of 143,537 bp on the long arm of chromosome 11. Using bioinformatic analyses, we then identified a candidate blast-resistance gene in the region, and cloned the homologous sequence from Tetep. The putative Pi-k ( h ) gene cloned from Tetep is 1.5 kbp long with a single ORF, and belongs to the nucleotide binding site-leucine rich repeat class of disease resistance genes. Structural and expression analysis of the Pi-k ( h ) gene revealed that its expression is pathogen inducible.
Collapse
Affiliation(s)
- T R Sharma
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Baldev A, Gaikwad K, Kirti PB, Mohapatra T, Prakash S, Chopra VL. Recombination between chloroplast genomes of Trachystoma ballii and Brassica juncea following protoplast fusion. Mol Gen Genet 1998; 260:357-61. [PMID: 9870700 DOI: 10.1007/s004380050904] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We document here the presence of a recombinant plastome in a cytoplasmic male sterile (CMS) line of Brassica juncea developed from the somatic hybrid Trachystoma ballii + B. juncea. Restriction endonuclease digestion of the chloroplast (cp) DNA has revealed that the recombinant plastome gives rise to novel fragments in addition to the parent-specific fragments. Analysis of the 16S rRNA region by Southern hybridization shows no variation between B. juncea, T. ballii and the CMS line. The rbcL gene region of the recombinant plastome is identical to that in T. ballii. Analysis with probes for psbA and psbD using single and double DNA digests indicates that the hybridization patterns of the recombinant plastome are identical to those of the parents in digests obtained with some restriction enzymes, while novel bands hybridize to probes in other digests. In the psbA region, a B. juncea-specific PstI site and a T. ballii-specific EcoRI site are found in the recombinant plastome. The pshD region of the recombinant plastome contains a B. juncea-specific HindIII site and T. ballii-specific BamHI and HpaII sites. These results indicate the occurrence of intergenomic recombination between the chloroplasts of T. ballii and B. juncea in the somatic hybrid from which the CMS line was developed. The recombined plastome appears to be a mosaic of fragments specific to both parents and the recombination event has occurred in the single-copy regions. These recombinational events have not caused any imbalance in the recombinant plastome in terms of chloroplast-related functions, which have remained stable over generations.
Collapse
Affiliation(s)
- A Baldev
- National Research Centre for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi
| | | | | | | | | | | |
Collapse
|