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Beena R, Kirubakaran S, Nithya N, Manickavelu A, Sah RP, Abida PS, Sreekumar J, Jaslam PM, Rejeth R, Jayalekshmy VG, Roy S, Manju RV, Viji MM, Siddique KHM. Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces. BMC Plant Biol 2021; 21:484. [PMID: 34686134 PMCID: PMC8539776 DOI: 10.1186/s12870-021-03272-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/29/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. RESULTS Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. CONCLUSION The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.
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Affiliation(s)
- Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | | | - Narayanan Nithya
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Alagu Manickavelu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala India
| | - Rameshwar Prasad Sah
- Indian Council of Agricultural Research (ICAR)-Central Rice Research Institute, currently named National Rice Research Institute (NRRI), Cuttack, Odisha India
| | - Puthenpeedikal Salim Abida
- Regional Agricultural Research Station, Pattambi, Kerala Agricultural University, Palakkad, Kerala India
| | - Janardanan Sreekumar
- Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram, Kerala India
| | | | - Rajendrakumar Rejeth
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Vijayalayam Gengamma Jayalekshmy
- Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Stephen Roy
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Ramakrishnan Vimala Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Mariasoosai Mary Viji
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
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Rejeth R, Manikanta CLN, Beena R, Stephen R, Manju RV, Viji MM. Water stress mediated root trait dynamics and identification of microsatellite markers associated with root traits in rice ( Oryza sativa L.). Physiol Mol Biol Plants 2020; 26:1225-1236. [PMID: 32549685 PMCID: PMC7266872 DOI: 10.1007/s12298-020-00809-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
To identify microsatellite markers associated with root traits for drought tolerance in rice (Oryza sativa L.) a study was conducted at Department of Plant Physiology, College of Agriculture, Trivandrum, Kerala Agricultural University. A set of thirty-five rice genotypes were exposed to water stress and evaluated for physio-morphological components as indices of water stress tolerance. Observations were made on leaf rolling score and root traits, especially the root length, root dry weight, root volume and root shoot ratio at booting stage. As of the data obtained, ten tolerant and ten susceptible varieties were selected for bulk line analysis to identify the DNA markers linked with target gene conferring drought tolerance. Out of 150 SSR primers screened, RM474 showed polymorphism between the tolerant and susceptible bulks. Individual genotypes of the bulks also showed the same product size of the respective tolerant and susceptible bulks.
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Affiliation(s)
- R. Rejeth
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Ch. L. N. Manikanta
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R. Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Roy Stephen
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R. V. Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - M. M. Viji
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
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Rejeth R, Manikanta CLN, Beena R, Stephen R, Manju RV, Viji MM. Water stress mediated root trait dynamics and identification of microsatellite markers associated with root traits in rice ( Oryza sativa L.). Physiol Mol Biol Plants 2020; 26:1225-1236. [PMID: 32549685 DOI: 10.1007/s12298-020-00809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 03/30/2020] [Indexed: 05/26/2023]
Abstract
To identify microsatellite markers associated with root traits for drought tolerance in rice (Oryza sativa L.) a study was conducted at Department of Plant Physiology, College of Agriculture, Trivandrum, Kerala Agricultural University. A set of thirty-five rice genotypes were exposed to water stress and evaluated for physio-morphological components as indices of water stress tolerance. Observations were made on leaf rolling score and root traits, especially the root length, root dry weight, root volume and root shoot ratio at booting stage. As of the data obtained, ten tolerant and ten susceptible varieties were selected for bulk line analysis to identify the DNA markers linked with target gene conferring drought tolerance. Out of 150 SSR primers screened, RM474 showed polymorphism between the tolerant and susceptible bulks. Individual genotypes of the bulks also showed the same product size of the respective tolerant and susceptible bulks.
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Affiliation(s)
- R Rejeth
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Ch L N Manikanta
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - Roy Stephen
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - R V Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
| | - M M Viji
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala 695522 India
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