1
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Thapa R, Tabien RE, Johnson CD, Septiningsih EM. Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress. BMC Genomics 2023; 24:185. [PMID: 37024819 PMCID: PMC10080786 DOI: 10.1186/s12864-023-09262-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take place independently or simultaneously and significantly affect rice plants during germination and seedling growth. Fortunately, a wide array of phenotypic responses conferring flooding stress and chilling stress tolerance exist within the rice germplasm, indicating the presence of different molecular mechanisms underlying tolerance to these stresses. Understanding these differences may assist in developing improved rice cultivars having higher tolerance to both stresses. In this study, we conducted a comparative global gene expression analysis of two rice genotypes with contrasting phenotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination. RESULTS The differential gene expression analysis revealed that 5571 differentially expressed genes (DEGs), 7206 DEGs, and 13279 DEGs were identified under anaerobic stress, cold stress, and combined stress, respectively. Genes involved in the carbohydrate metabolic process, glucosyltransferase activity, regulation of nitrogen compound metabolic process, protein metabolic process, lipid metabolic process, cellular nitrogen compound biosynthetic process, lipid biosynthetic process, and a microtubule-based process were enriched across all stresses. Notably, the common Gene Ontology (GO) analysis identified three hub genes, namely Os08g0176800 (similar to mRNA-associated protein mrnp 41), Os11g0454200 (dehydrin), and OS10g0505900 (expressed protein). CONCLUSION A large number of differentially expressed genes were identified under anaerobic, cold conditions during germination and the combination of the two stress conditions in rice. These results will assist in the identification of promising candidate genes for possible manipulation toward rice crops that are more tolerant under flooding and cold during germination, both independently and concurrently.
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Affiliation(s)
- Ranjita Thapa
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
- Present address: Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX, 77843, USA
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.
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2
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Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches. Mol Biol Rep 2023; 50:2795-2812. [PMID: 36592290 DOI: 10.1007/s11033-022-07853-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 01/03/2023]
Abstract
Natural and man-made ecosystems worldwide are subjected to flooding, which is a form of environmental stress. Genetic variability in the plant response to flooding involves variations in metabolism, architecture, and elongation development that are related with a low oxygen escape strategy and an opposing quiescence scheme that enables prolonged submergence endurance. Flooding is typically associated with a decrease in O2 in the cells, which is especially severe when photosynthesis is absent or limited, leading to significant annual yield losses globally. Over the past two decades, considerable advancements have been made in understanding of mechanisms of rice adaptation and tolerance to flooding/submergence. The mapping and identification of Sub1 QTL have led to the development of marker-assisted selection (MAS) breeding approach to improve flooding-tolerant rice varieties in submergence-prone ecosystems. The Sub1 incorporated in rice varieties showed tolerance during flash flood, but not during stagnant conditions. Hence, gene pyramiding techniques can be applied to combine/stack multiple resistant genes for developing flood-resilient rice varieties for different types of flooding stresses. This review contains an update on the latest advances in understanding the molecular mechanisms, metabolic adaptions, and genetic factors governing rice flooding tolerance. A better understanding of molecular genetics and adaptation mechanisms that enhance flood-tolerant varieties under different flooding regimes was also discussed.
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3
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Aswini K, Suman A, Sharma P, Singh PK, Gond S, Pathak D. Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity. FRONTIERS IN PLANT SCIENCE 2023; 14:1101818. [PMID: 37089648 PMCID: PMC10117849 DOI: 10.3389/fpls.2023.1101818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.
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Affiliation(s)
- Krishnan Aswini
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Archna Suman,
| | - Pushpendra Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shrikant Gond
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Devashish Pathak
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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4
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Thomson MJ, Biswas S, Tsakirpaloglou N, Septiningsih EM. Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement. Int J Mol Sci 2022; 23:ijms23126565. [PMID: 35743007 PMCID: PMC9223900 DOI: 10.3390/ijms23126565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
Advances in molecular technologies over the past few decades, such as high-throughput DNA marker genotyping, have provided more powerful plant breeding approaches, including marker-assisted selection and genomic selection. At the same time, massive investments in plant genetics and genomics, led by whole genome sequencing, have led to greater knowledge of genes and genetic pathways across plant genomes. However, there remains a gap between approaches focused on forward genetics, which start with a phenotype to map a mutant locus or QTL with the goal of cloning the causal gene, and approaches using reverse genetics, which start with large-scale sequence data and work back to the gene function. The recent establishment of efficient CRISPR-Cas-based gene editing promises to bridge this gap and provide a rapid method to functionally validate genes and alleles identified through studies of natural variation. CRISPR-Cas techniques can be used to knock out single or multiple genes, precisely modify genes through base and prime editing, and replace alleles. Moreover, technologies such as protoplast isolation, in planta transformation, and the use of developmental regulatory genes promise to enable high-throughput gene editing to accelerate crop improvement.
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5
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Higgins S, Biswas S, Goff NK, Septiningsih EM, Kurouski D. Raman Spectroscopy Enables Non-invasive and Confirmatory Diagnostics of Aluminum and Iron Toxicities in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:754735. [PMID: 35651767 PMCID: PMC9149412 DOI: 10.3389/fpls.2022.754735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/28/2022] [Indexed: 05/26/2023]
Abstract
Metal toxicities can be detrimental to a plant health, as well as to the health of animals and humans that consume such plants. Metal content of plants can be analyzed using colorimetric, atomic absorption- or mass spectroscopy-based methods. However, these techniques are destructive, costly and laborious. In the current study, we investigate the potential of Raman spectroscopy (RS), a modern spectroscopic technique, for detection and identification of metal toxicities in rice. We modeled medium and high levels of iron and aluminum toxicities in hydroponically grown plants. Spectroscopic analyses of their leaves showed that both iron and aluminum toxicities can be detected and identified with ∼100% accuracy as early as day 2 after the stress initiation. We also showed that diagnostics accuracy was very high not only on early, but also on middle (day 4-day 8) and late (day 10-day 14) stages of the stress development. Importantly this approach only requires an acquisition time of 1 s; it is non-invasive and non-destructive to plants. Our findings suggest that if implemented in farming, RS can enable pre-symptomatic detection and identification of metallic toxins that would lead to faster recovery of crops and prevent further damage.
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Affiliation(s)
- Samantha Higgins
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Nicolas K. Goff
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, TX, United States
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Mittal L, Tayyeba S, Sinha AK. Finding a breather for Oryza sativa: Understanding hormone signalling pathways involved in rice plants to submergence stress. PLANT, CELL & ENVIRONMENT 2022; 45:279-295. [PMID: 34971465 DOI: 10.1111/pce.14250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/23/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
During the course of evolution, different ecotypes of rice (Oryza sativa L.) have evolved distinct strategies to cope with submergence stress. Such contrasting responses are mediated by plant hormones that are principle regulators of growth, development and responses to various biotic and abiotic stresses. These hormones act cooperatively and show extensive crosstalk which is mediated by key regulatory genes that serve as nodes of molecular communication. The presence or absence of such genes leads to significant changes in hormone signalling pathways and hence, governs the type of response that the plant will exhibit. As flooding is one of the leading causes of crop loss across all the major rice-producing countries, it is crucial to deeply understand the molecular nexus governing the response to submergence to produce flood resilient varieties. This review focuses on the hormonal signalling pathways that mediate two contrasting responses of the rice plant to submergence stress namely, rapid internode elongation to escape flood waters and quiescence response that enables the plant to survive under complete submergence. The significance of several key genes such as Sub1A-1, SLR1, SD1 and SK1/SK2, in defining the ultimate response to submergence has also been discussed.
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Affiliation(s)
- Lavanya Mittal
- National Institute of Plant Genome Research, New Delhi, India
| | - Sumaira Tayyeba
- National Institute of Plant Genome Research, New Delhi, India
| | - Alok K Sinha
- National Institute of Plant Genome Research, New Delhi, India
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7
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Toulotte JM, Pantazopoulou CK, Sanclemente MA, Voesenek LACJ, Sasidharan R. Water stress resilient cereal crops: Lessons from wild relatives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:412-430. [PMID: 35029029 PMCID: PMC9255596 DOI: 10.1111/jipb.13222] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Cereal crops are significant contributors to global diets. As climate change disrupts weather patterns and wreaks havoc on crops, the need for generating stress-resilient, high-yielding varieties is more urgent than ever. One extremely promising avenue in this regard is to exploit the tremendous genetic diversity expressed by the wild ancestors of current day crop species. These crop wild relatives thrive in a range of environments and accordingly often harbor an array of traits that allow them to do so. The identification and introgression of these traits into our staple cereal crops can lessen yield losses in stressful environments. In the last decades, a surge in extreme drought and flooding events have severely impacted cereal crop production. Climate models predict a persistence of this trend, thus reinforcing the need for research on water stress resilience. Here we review: (i) how water stress (drought and flooding) impacts crop performance; and (ii) how identification of tolerance traits and mechanisms from wild relatives of the main cereal crops, that is, rice, maize, wheat, and barley, can lead to improved survival and sustained yields in these crops under water stress conditions.
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Affiliation(s)
- Justine M. Toulotte
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Chrysoula K. Pantazopoulou
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Maria Angelica Sanclemente
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Laurentius A. C. J. Voesenek
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Rashmi Sasidharan
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
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8
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Liang Y, Wang S, Harper CL, Subramanian NK, Tabien RE, Johnson CD, Bailey-Serres J, Septiningsih EM. Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1. PLANTS 2021; 10:plants10122740. [PMID: 34961210 PMCID: PMC8703405 DOI: 10.3390/plants10122740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
Abstract
Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).
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Affiliation(s)
- Yuya Liang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX 77843, USA; (S.W.); (C.D.J.)
| | - Chersty L. Harper
- Texas A&M AgriLife Research Center, Beaumont, TX 77713, USA; (C.L.H.); (R.E.T.)
| | - Nithya K. Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
| | - Rodante E. Tabien
- Texas A&M AgriLife Research Center, Beaumont, TX 77713, USA; (C.L.H.); (R.E.T.)
| | - Charles D. Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX 77843, USA; (S.W.); (C.D.J.)
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
- Correspondence:
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9
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Chattopadhyay K, Chakraborty K, Samal P, Sarkar RK. Identification of QTLs for stagnant flooding tolerance in rice employing genotyping by sequencing of a RIL population derived from Swarna × Rashpanjor. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2893-2909. [PMID: 35035143 PMCID: PMC8720131 DOI: 10.1007/s12298-021-01107-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/15/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
UNLABELLED In lowland rice ecosystems stagnant flooding or partial submergence has a significant negative impact on important yield attributing traits resulting in substantial grain yield reduction. Genetics of this stress is not yet studied intensively. Rashpanjor (IC 575321), a landrace from India, was identified and used as the tolerant donor for stagnant flooding and was crossed with high yielding variety Swarna to develop the RIL population for the present investigation. Yield and yield attributing traits of 180 F2:8 lines in rainfed non-stressed and stressed (stagnant flooding with 45 ± 5 cm standing water) conditions were recorded in the wet season of 2018 and stress susceptibility and tolerance indices of yield component traits were deduced. Homo-polymorphic high-quality SNPs between two parents derived from genotyping by sequencing were employed and 17 putative QTLs for plant height, shoot elongation, panicle number, grain weight, panicle length in control and stagnant flooding conditions were identified. Tolerance and susceptibility indexes for these traits were detected in chromosomes 1, 3, 4, 5, 6, 10, 11, and 12 with PVE ranging from 6.53 to 57.89%. Two major QTLs clusters were found for stress susceptibility index of grain and panicle weight on chromosome 1 and plant height in non-stress condition and stress tolerance index of elongation ability on chromosome 3. Putative functional genes present either in associated non-synonymous SNPs or inside the QTL regions were also predicted. Some of them were directly associated with ethylene biosynthesis and encoding auxin responsive factors for better adaptation under stagnant flooding and also coded for different transcription factors viz. NAC domain-binding protein, WRKY gene family, and MYB class known for ROS scavenging and production of metabolites to enhance tolerance to stagnant flooding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01107-x.
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Affiliation(s)
| | - Koushik Chakraborty
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - Prabhudatta Samal
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Ramani Kumar Sarkar
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
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10
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Kulkarni SR, Balachandran SM, Ulaganathan K, Balakrishnan D, Prasad ASH, Rekha G, Kousik MBVN, Hajira SK, Kale RR, Aleena D, Anila M, Punniakoti E, Dilip T, Pranathi K, Das MA, Shaik M, Chaitra K, Sinha P, Sundaram RM. Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population. 3 Biotech 2021; 11:513. [PMID: 34926111 DOI: 10.1007/s13205-021-03045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022] Open
Abstract
A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03045-7.
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Affiliation(s)
- Swapnil Ravindra Kulkarni
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - S M Balachandran
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Ulaganathan
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, 500007 India
| | - Divya Balakrishnan
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - A S Hari Prasad
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - G Rekha
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M B V N Kousik
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - S K Hajira
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Ravindra Ramarao Kale
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - D Aleena
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M Anila
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - E Punniakoti
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - T Dilip
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Pranathi
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - M Ayyappa Das
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Mastanbee Shaik
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - K Chaitra
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - Pragya Sinha
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
| | - R M Sundaram
- Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS) 500030 India
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11
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Liang Y, Biswas S, Kim B, Bailey-Serres J, Septiningsih EM. Improved Transformation and Regeneration of Indica Rice: Disruption of SUB1A as a Test Case via CRISPR-Cas9. Int J Mol Sci 2021; 22:ijms22136989. [PMID: 34209672 PMCID: PMC8269137 DOI: 10.3390/ijms22136989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 12/27/2022] Open
Abstract
Gene editing by use of clustered regularly interspaced short palindromic repeats (CRISPR) has become a powerful tool for crop improvement. However, a common bottleneck in the application of this approach to grain crops, including rice (Oryza sativa), is efficient vector delivery and calli regeneration, which can be hampered by genotype-dependent requirements for plant regeneration. Here, methods for Agrobacterium-mediated and biolistic transformation and regeneration of indica rice were optimized using CRISPR-Cas9 gene-editing of the submergence tolerance regulator SUBMERGENCE 1A-1 gene of the cultivar Ciherang-Sub1. Callus induction and plantlet regeneration methods were optimized for embryogenic calli derived from immature embryos and mature seed-derived calli. Optimized regeneration (95%) and maximal editing efficiency (100%) were obtained from the immature embryo-derived calli. Phenotyping of T1 seeds derived from the edited T0 plants under submergence stress demonstrated inferior phenotype compared to their controls, which phenotypically validates the disruption of SUB1A-1 function. The methods pave the way for rapid CRISPR-Cas9 gene editing of recalcitrant indica rice cultivars.
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Affiliation(s)
- Yuya Liang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (S.B.); (B.K.)
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (S.B.); (B.K.)
| | - Backki Kim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (S.B.); (B.K.)
- Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Botany and Plant Sciences, University of California, Riverside, CA 92521, USA;
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (S.B.); (B.K.)
- Correspondence:
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12
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Panda D, Barik J, Sarkar RK. Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice. Curr Genomics 2021; 22:41-58. [PMID: 34045923 PMCID: PMC8142345 DOI: 10.2174/1389202922666210114104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/16/2020] [Accepted: 12/26/2020] [Indexed: 12/16/2022] Open
Abstract
Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.
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Affiliation(s)
- Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput-764 020, Odisha, India
| | - Jijnasa Barik
- Department of Biodiversity and Conservation of Natural Resources, Central University of Odisha, Koraput-764 020, Odisha, India
| | - Ramani K Sarkar
- ICAR-National Rice Research Institute, Cuttack-753 006, Odisha, India
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13
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Kulkarni SR, Balachandran SM, Ulaganathan K, Balakrishnan D, Praveen M, Prasad ASH, Fiyaz RA, Senguttuvel P, Sinha P, Kale RR, Rekha G, Kousik MBVN, Harika G, Anila M, Punniakoti E, Dilip T, Hajira SK, Pranathi K, Das MA, Shaik M, Chaitra K, Rao PK, Gangurde SS, Pandey MK, Sundaram RM. Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping. Sci Rep 2020; 10:13695. [PMID: 32792551 PMCID: PMC7427098 DOI: 10.1038/s41598-020-70637-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/10/2020] [Indexed: 01/27/2023] Open
Abstract
The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.
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Affiliation(s)
- Swapnil Ravindra Kulkarni
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - S M Balachandran
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India.
| | - K Ulaganathan
- Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, India
| | - Divya Balakrishnan
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Praveen
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - A S Hari Prasad
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - R A Fiyaz
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - P Senguttuvel
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Pragya Sinha
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Ravindra R Kale
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - G Rekha
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M B V N Kousik
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - G Harika
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Anila
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - E Punniakoti
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - T Dilip
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - S K Hajira
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - K Pranathi
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - M Ayyappa Das
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Mastanbee Shaik
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - K Chaitra
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - P Koteswara Rao
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - R M Sundaram
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, 500030, India.
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Singh A, Singh Y, Mahato AK, Jayaswal PK, Singh S, Singh R, Yadav N, Singh AK, Singh PK, Singh R, Kumar R, Septiningsih EM, Balyan HS, Singh NK, Rai V. Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance. Sci Rep 2020; 10:8621. [PMID: 32451398 PMCID: PMC7248102 DOI: 10.1038/s41598-020-65588-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/28/2020] [Indexed: 11/24/2022] Open
Abstract
Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars.
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Affiliation(s)
- Anuradha Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Yashi Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Ajay K Mahato
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Pawan K Jayaswal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Sangeeta Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Renu Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Neera Yadav
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - A K Singh
- Department of Crop Physiology, Narendra Deo University of Agriculture & Technology, Ayodhya, UP, India
| | - P K Singh
- Department of Genetics and Plant Breeding, Banaras Hindu University, Varanasi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Rajesh Kumar
- Department of Genetics and Plant Breeding, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Endang M Septiningsih
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Department of Soil and Crop Sciences, Texas A & M University, TX, 77843, USA
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.
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15
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Kato Y, Collard BCY, Septiningsih EM, Ismail AM. Increasing flooding tolerance in rice: combining tolerance of submergence and of stagnant flooding. ANNALS OF BOTANY 2020; 124:1199-1210. [PMID: 31306479 PMCID: PMC6944782 DOI: 10.1093/aob/mcz118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Rice ecosystems in the tropical coastal areas are subject to two types of flooding stress: transient complete submergence and long-term water stagnation (stagnant flooding). Here, we aimed to dissect the mechanisms for stagnant flooding tolerance of rice genotypes carrying SUB1, a quantitative trait locus for submergence tolerance. METHODS We screened 80 elite genotypes under stagnant flooding stress in the lowland rice fields in the wet and dry seasons, and examined the tolerance mechanisms of promising genotypes for the two following seasons. KEY RESULTS Yield reduction under stagnant flooding averaged 48 % in the dry season and 89 % in the wet season. Elite genotypes carrying SUB1 showed 49 % lower yield than those without SUB1 under stagnant flooding, with no differences under shallow water conditions. However, we identified a few high-yielding Sub1 genotypes that were as tolerant of stagnant flooding as a reference genotype that lacked SUB1. These genotypes had intermediate stature with more shoot elongation in response to rising water than a moderately tolerant Sub1 reference variety, resulting in greater canopy expansion and higher yield. It was important to increase lodging resistance, since plant height >140 cm increased lodging under stagnant flooding. The culm diameter was closely associated with culm strength; reduced aerenchyma formation and increased lignin accumulation in the culm should increase lodging resistance. CONCLUSIONS The study demonstrated a successful combination of submergence and stagnant flooding tolerance in a rice breeding programme, and identified elite Sub1 genotypes that also tolerate stagnant flooding. Our results will support genetic improvement of Sub1 varieties for stagnant flooding tolerance.
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Affiliation(s)
- Yoichiro Kato
- International Rice Research Institute, Metro Manila, Philippines
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Bertrand C Y Collard
- International Rice Research Institute, Metro Manila, Philippines
- Yanco Agricultural Institute, Department of Primary Industries, New South Wales, Australia
| | - Endang M Septiningsih
- International Rice Research Institute, Metro Manila, Philippines
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
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Barik J, Panda D, Mohanty SK, Lenka SK. Leaf photosynthesis and antioxidant response in selected traditional rice landraces of Jeypore tract of Odisha, India to submergence. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:847-863. [PMID: 31404200 PMCID: PMC6656848 DOI: 10.1007/s12298-019-00671-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/26/2019] [Accepted: 04/26/2019] [Indexed: 05/11/2023]
Abstract
Submergence tolerance in rice is important for improving yield under rain-fed lowland rice ecosystem. In this study, five traditional rice landraces having submergence tolerance phenotype were selected. These five rice landraces were chosen based on the submergence-tolerance screening of 88 rice landraces from various lowland areas of Jeypore tract of Odisha in our previous study. These five rice landraces were further used for detailed physiological assessment under control, submergence and subsequent re-aeration to judge their performance under different duration of submergence. Seedling survival was significantly decreased with the increase of plant height and significant varietal difference was observed after 14 days of complete submergence. Results showed that submergence progressively declined the leaf photosynthetic rate, stomatal conductance, instantaneous water use efficiency, carboxylation efficiency, photosystem II (PSII) activity and chlorophyll, with greater effect observed in susceptible check variety (IR 42). Notably, higher activities of antioxidative enzymes and ascorbate level were observed in traditional rice landraces and were found comparable with the tolerant check variety (FR 13A). Taken together, three landraces such as Samudrabali, Basnamundi and Gadaba showed better photosynthetic activity than that of tolerant check variety (FR 13A) and showed superior antioxidant response to submergence and subsequent re-aeration. These landraces can be considered as potential donors for the future submergence tolerance breeding program.
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Affiliation(s)
- Jijnasa Barik
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764021 India
| | - Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764021 India
| | | | - Sangram K. Lenka
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana 122 001 India
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17
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Analysis of the distribution of assimilation products and the characteristics of transcriptomes in rice by submergence during the ripening stage. BMC Genomics 2019; 20:18. [PMID: 30621581 PMCID: PMC6323827 DOI: 10.1186/s12864-018-5320-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 11/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Research on the submergence stress of rice has concentrated on the quiescence strategy to survive in long-term flooding conditions based on Submergence-1A (SUB1A). In the case of the ripening period, it is important that submergence stress can affect the quality as well as the survival of rice. Therefore, it is essential to understand the changes in the distribution of assimilation products in grain and ripening characteristics in submergence stress conditions. However, such studies have been insufficient at the physiological and molecular biological levels. Results We confirmed that the distribution rate of assimilation products in grain was decreased by submergence treatment. These results were caused by an increase in the distribution rate of assimilation products to the stem according to escape strategy. To understand this phenomenon at the molecular level, we analyzed the relative expression levels of genes related to sucrose metabolism, and found that the sucrose phosphate synthase gene (OsSPS), which induces the accumulation of sucrose in tissues, was decreased in the seeds and leaves, but not in the stems. Furthermore, the sucrose transporter gene (OsSUT) related to sucrose transport decreased in the seeds and leaves, but increased in stems. We also analyzed the biological metabolic processes related to starch and sucrose synthesis, carbon fixation, and glycolysis using the KEGG mapper with selected differentially expressed genes (DEGs) in seeds, stems, and leaves caused by submergence treatment. We found that the expression of genes for each step related to starch and D-glucose synthesis was down-regulated in the seeds and leaves but up-regulated in the stem. Conclusion The results of this study provide basic data for the development of varieties and corresponding technologies adapted to submergence conditions, through understanding the action network of the elements that change in the submergence condition, as well as information regarding useful DEGs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5320-7) contains supplementary material, which is available to authorized users.
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18
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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19
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Thomson MJ, Singh N, Dwiyanti MS, Wang DR, Wright MH, Perez FA, DeClerck G, Chin JH, Malitic-Layaoen GA, Juanillas VM, Dilla-Ermita CJ, Mauleon R, Kretzschmar T, McCouch SR. Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. RICE (NEW YORK, N.Y.) 2017; 10:40. [PMID: 28856618 PMCID: PMC5577349 DOI: 10.1186/s12284-017-0181-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/25/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit "sweet spot" for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice. RESULTS Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina's production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material. CONCLUSIONS The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.
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Affiliation(s)
- Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Houston, TX, 77843, USA.
| | - Namrata Singh
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
| | - Maria S Dwiyanti
- International Rice Research Institute, Los Baños, Philippines
- Present address: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Diane R Wang
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
| | - Mark H Wright
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
- Department of Genetics, Stanford School of Medicine, Stanford, California, 94305, USA
| | - Francisco Agosto Perez
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
| | - Genevieve DeClerck
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
- Present address: DeClerck Design, LLC, Freeville, NY, USA
| | - Joong Hyoun Chin
- International Rice Research Institute, Los Baños, Philippines
- Present address: Graduate School of Integrated Bioindustry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, South Korea
| | | | | | - Christine J Dilla-Ermita
- International Rice Research Institute, Los Baños, Philippines
- Present address: Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA
| | - Ramil Mauleon
- International Rice Research Institute, Los Baños, Philippines
| | | | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA.
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