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Grondin A, Natividad MA, Ogata T, Jan A, Gaudin ACM, Trijatmiko KR, Liwanag E, Maruyama K, Fujita Y, Yamaguchi-Shinozaki K, Nakashima K, Slamet-Loedin IH, Henry A. A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials. RICE (NEW YORK, N.Y.) 2024; 17:25. [PMID: 38592643 PMCID: PMC11003944 DOI: 10.1186/s12284-024-00705-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation. RESULTS Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of - 25 to - 75 kPa at a soil depth of 30 cm which reduced biomass by 30-55% and grain yield by 1-92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks. CONCLUSIONS Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.
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Affiliation(s)
- Alexandre Grondin
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
- Institut de Recherche Pour Le Développement, Université de Montpellier, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier, France
| | - Mignon A Natividad
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Takuya Ogata
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Asad Jan
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Biotechnology and Genetics Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Amélie C M Gaudin
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Kurniawan R Trijatmiko
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Evelyn Liwanag
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Kyonoshin Maruyama
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Yasunari Fujita
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Laboratory of Plant Molecular Physiology, The University of Tokyo, Tokyo, 113-8657, Japan
- Tokyo University of Agriculture, Research Institute for Agricultural and Life Sciences, Tokyo, Japan
| | - Kazuo Nakashima
- Food Program, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Inez H Slamet-Loedin
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Amelia Henry
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines.
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Dwivedi SK, Kumar S, Natividad MA, Quintana MR, Chinnusamy V, Henry A. Disentangling the Roles of Plant Water Status and Stem Carbohydrate Remobilization on Rice Harvest Index Under Drought. RICE (NEW YORK, N.Y.) 2023; 16:14. [PMID: 36930351 PMCID: PMC10023821 DOI: 10.1186/s12284-023-00631-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Harvest index is an important component of grain yield and is typically reduced by reproductive stage drought stress in rice. Multiple drought response mechanisms can affect harvest index including plant water status and the degree of stem carbohydrate mobilization during grain filling. In this study, we aimed to dissect the contributions of plant water status and stem carbohydrate mobilization to harvest index. Pairs of genotypes selected for contrasting harvest index but similar biomass and days to flowering were characterized at ICAR-RCER, Patna, India and at IRRI, Philippines. RESULTS Multiple traits were related with harvest index across experiments, including mobilization efficiency at both sites as indicated by groupings in principal component analysis, and plant water status as indicated by direct correlations. Biomass-related traits were positively correlated with harvest index at IRRI but biomass was negatively correlated with harvest index at ICER-RCER, Patna. We observed that some pairs of genotypes showed differences in harvest index across environments, whereas other showed differences in harvest index only under drought. Of all time points measured when all genotypes were considered together, the stem carbohydrate levels at maturity were most consistently (negatively) correlated with harvest index under drought, but not under well-watered conditions. However, in the pairs of genotypes grouped as those whose differences in harvest index were stable across environments, improved plant water status resulted in a greater ability to both accumulate and remobilize stored carbohydrate, i.e. starch. CONCLUSION By distinguishing between genotypes whose harvest index was improved across conditions as opposed to specifically under drought, we can attribute the mechanisms behind the stable high-harvest index genotypes to be more related to stem carbohydrate remobilization than to plant water status. The stable high-harvest index lines in this study (Aus 257 and Wanni Dahanala) may confer mechanisms to improve harvest index that are independent of drought response and therefore may be useful for breeding improved rice varieties.
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Affiliation(s)
- Sharad K Dwivedi
- ICAR - Research Complex for Eastern Region, Patna, Bihar, 800014, India
- ICAR - Central Institute for Subtropical Horticulture, Lucknow, 226101, India
| | - Santosh Kumar
- ICAR - Research Complex for Eastern Region, Patna, Bihar, 800014, India
| | - Mignon A Natividad
- International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | | | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna, 4031, Philippines.
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Fine Mapping and Cloning of a qRA2 Affect the Ratooning Ability in Rice ( Oryza sativa L.). Int J Mol Sci 2023; 24:ijms24020967. [PMID: 36674482 PMCID: PMC9863488 DOI: 10.3390/ijms24020967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Ratooning ability is a key factor that influences the ratoon rice yield in areas where light and temperature are not sufficient for second-season rice. Near-isogenic lines (NILs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, using 176 NILs, we identified a novel QTL for ratooning ability in NIL128. First, we mapped the QTL between the markers Indel12-29 and Indel12-31, which encompass a region of 233 kb. The rice genome annotation indicated the existence of three candidate genes in this region that may be related to ratooning ability. Through gene prediction and cDNA sequencing, we speculated that the target gene of ratooning ability is LOC_Os02g51930 which encodes cytokinin glucosyl transferases (CGTs), hereafter named qRA2. Further analysis showed that qra2 was a 1-bp substitution in the first exon in NIL128, which resulted in the premature termination of qRA2. The results of the knockdown experiment showed that the Jiafuzhan knockdown mutants exhibited the ratooning ability phenotype of NIL128. Interestingly, the qRA2 gene was found to improve ratooning ability without affecting major agronomic traits. These results will help us better understand the genetic basis of rice ratooning ability and provide a valuable gene resource for breeding strong ratoon rice varieties.
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Jiang M, Guo K, Wang J, Wu Y, Shen X, Huang L. Current status and prospects of rice canopy temperature research. Food Energy Secur 2022. [DOI: 10.1002/fes3.424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Min Jiang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University Yangzhou China
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Kefan Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University Yangzhou China
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Jiaqi Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University Yangzhou China
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Yunfei Wu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University Yangzhou China
| | - Xinping Shen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University Yangzhou China
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
| | - Lifen Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology Agricultural College of Yangzhou University Yangzhou China
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain Crops Yangzhou University Yangzhou China
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He N, Zhan G, Huang F, Abou-Elwafa SF, Yang D. Fine Mapping and Cloning of a Major QTL qph12, Which Simultaneously Affects the Plant Height, Panicle Length, Spikelet Number and Yield in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:878558. [PMID: 35693171 PMCID: PMC9187155 DOI: 10.3389/fpls.2022.878558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Plant height is one of the most important agronomical traits in rice (Oryza sativa L.). Introducing the semidwarf rice in the 1960s significantly enhanced the rice yield potential in Asia. Implementing near-isogenic lines (NILs) is the most powerful tool for the identification and fine mapping of quantitative trait loci (QTLs). In this study, 176 NILs were produced from the crossing and back-crossing of two rice cultivars. Specifically, the indica rice cultivar Jiafuzhan served as a recipient, and the restorer japonica cultivar Hui1586 served as a donor. Using the 176 NILs, we identified a novel major QTL for reduced plant height in the NIL36 line. The qph12 QTL was mapped to a 31 kb genomic region between the indel markers Indel12-29 and Indel12-31. The rice genome annotation indicated the presence of three candidate genes in this genomic region. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os12g40890 (qPH12) is the target gene in the NIL36 line. Further analysis showed that the qph12 QTL is caused by a 1 bp deletion in the first exon that resulted in premature termination of the qPH12. Knockout experiments showed that the qph12 QTL is responsible for the reduced plant height phenotype of the NIL36 line. Although the qph12 gene from the NIL36 line showed a shorter panicle length, fewer spikelets per panicle and a lower plant grain yield, the plant also exhibited a lower plant height. Taken together, our results revealed that the qph12 have good specific application prospects in future rice breeding.
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Affiliation(s)
- Niqing He
- Rice Research Institute, Fujian High Quality Rice Research and Development Center, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Guanping Zhan
- Rice Research Institute, Fujian High Quality Rice Research and Development Center, Fujian Academy of Agricultural Sciences, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fenghuang Huang
- Rice Research Institute, Fujian High Quality Rice Research and Development Center, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | | | - Dewei Yang
- Rice Research Institute, Fujian High Quality Rice Research and Development Center, Fujian Academy of Agricultural Sciences, Fuzhou, China
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Khanna A, Anumalla M, Catolos M, Bartholomé J, Fritsche-Neto R, Platten JD, Pisano DJ, Gulles A, Sta Cruz MT, Ramos J, Faustino G, Bhosale S, Hussain W. Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines. RICE (NEW YORK, N.Y.) 2022; 15:14. [PMID: 35247120 PMCID: PMC8898209 DOI: 10.1186/s12284-022-00559-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Estimating genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI's rice drought breeding program was used to estimate the genetic trends and assess the breeding program's success. We also identified top-performing lines based on grain yield breeding values as an elite panel for implementing future population improvement-based breeding schemes. A two-stage approach of pedigree-based mixed model analysis was used to analyze the data and extract the breeding values and estimate the genetic trends for grain yield under non-stress, drought, and in combined data of non-stress and drought. Lower grain yield values were observed in all the drought trials. Heritability for grain yield estimates ranged between 0.20 and 0.94 under the drought trials and 0.43-0.83 under non-stress trials. Under non-stress conditions, the genetic gain of 0.21% (10.22 kg/ha/year) for genotypes and 0.17% (7.90 kg/ha/year) for checks was observed. The genetic trend under drought conditions exhibited a positive trend with the genetic gain of 0.13% (2.29 kg/ha/year) for genotypes and 0.55% (9.52 kg/ha/year) for checks. For combined analysis showed a genetic gain of 0.27% (8.32 kg/ha/year) for genotypes and 0.60% (13.69 kg/ha/year) for checks was observed. For elite panel selection, 200 promising lines were selected based on higher breeding values for grain yield and prediction accuracy of > 0.40. The breeding values of the 200 genotypes formulating the core panel ranged between 2366.17 and 4622.59 (kg/ha). A positive genetic rate was observed under all the three conditions; however, the rate of increase was lower than the required rate of 1.5% genetic gain. We propose a recurrent selection breeding strategy within the elite population with the integration of modern tools and technologies to boost the genetic gains in IRRI's drought breeding program. The elite breeding panel identified in this study forms an easily available and highly enriched genetic resource for future recurrent selection programs to boost the genetic gains.
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Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Jérôme Bartholomé
- AGAP Institute, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Roberto Fritsche-Neto
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - John Damien Platten
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Daniel Joseph Pisano
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Alaine Gulles
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Joie Ramos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Gem Faustino
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
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7
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Sanchez J, Kaur PP, Pabuayon ICM, Karampudi NBR, Kitazumi A, Sandhu N, Catolos M, Kumar A, de Los Reyes BG. DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds. THE PLANT GENOME 2022; 15:e20168. [PMID: 34806842 DOI: 10.1002/tpg2.20168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.
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Affiliation(s)
- Jacobo Sanchez
- Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, USA
| | | | | | | | - Ai Kitazumi
- Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, USA
| | - Nitika Sandhu
- International Rice Research Institute, Los Banos, Philippines
- Current address: School of Agricultural Biotechnology, Punjab Agricultural Univ., Ludhiana, India
| | | | - Arvind Kumar
- International Rice Research Institute, Los Banos, Philippines
- Current address: International Crops Research Institute for the Semi-Arid Tropics, Petancheru, India
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Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
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Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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9
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Kumar S, Tripathi S, Singh SP, Prasad A, Akter F, Syed MA, Badri J, Das SP, Bhattarai R, Natividad MA, Quintana M, Venkateshwarlu C, Raman A, Yadav S, Singh SK, Swain P, Anandan A, Yadaw RB, Mandal NP, Verulkar SB, Kumar A, Henry A. Rice breeding for yield under drought has selected for longer flag leaves and lower stomatal density. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4981-4992. [PMID: 33852008 PMCID: PMC8219034 DOI: 10.1093/jxb/erab160] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/10/2021] [Indexed: 05/11/2023]
Abstract
Direct selection for yield under drought has resulted in the release of a number of drought-tolerant rice varieties across Asia. In this study, we characterized the physiological traits that have been affected by this strategy in breeding trials across sites in Bangladesh, India, and Nepal. Drought- breeding lines and drought-tolerant varieties showed consistently longer flag leaves and lower stomatal density than our drought-susceptible check variety, IR64. The influence of environmental parameters other than drought treatments on leaf traits was evidenced by close grouping of treatments within a site. Flag-leaf length and width appeared to be regulated by different environmental parameters. In separate trials in the Philippines, the same breeding lines studied in South Asia showed that canopy temperature under drought and harvest index across treatments were most correlated with grain yield. Both atmospheric and soil stress strengthened the relationships between leaf traits and yield. The stable expression of leaf traits among genotypes and the identification of the environmental conditions in which they contribute to yield, as well as the observation that some breeding lines showed longer time to flowering and higher canopy temperature than IR64, suggest that selection for additional physiological traits may result in further improvements of this breeding pool.
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Affiliation(s)
- Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - Santosh Tripathi
- Nepal Agricultural Research Council Regional Agriculture Research Station, Nepalgunj, Khajura, Banke, Nepal
- Regional Agricultural Research Station, Tarahara, Sunsari, Nepal
| | | | - Archana Prasad
- Indira Gandhi Agricultural University, Raipur, Chhattisgarh, India
| | - Fahamida Akter
- Bangladesh Rice Research Institute, Regional Station, Rajshahi, Bangladesh
| | - Md Abu Syed
- Bangladesh Rice Research Institute, Regional Station, Rajshahi, Bangladesh
| | - Jyothi Badri
- ICAR Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana, India
| | - Sankar Prasad Das
- ICAR Research Complex for North Eastern Hill Region, Lembucherra, Tripura, India
| | - Rudra Bhattarai
- Regional Agricultural Research Station, Tarahara, Sunsari, Nepal
| | | | - Marinell Quintana
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Challa Venkateshwarlu
- International Rice Research Institute South Asia Hub, ICRISAT, Patancheru, Telangana, India
| | - Anitha Raman
- International Rice Research Institute South Asia Hub, ICRISAT, Patancheru, Telangana, India
| | - Shailesh Yadav
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | - Padmini Swain
- ICAR National Rice Research Institute, Cuttack, Odisha, India
| | - A Anandan
- ICAR National Rice Research Institute, Cuttack, Odisha, India
| | - Ram Baran Yadaw
- National Rice Research Program, Hardinath, Baniniya, Janakpurdham, Nepal
| | - Nimai P Mandal
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand, India
| | - S B Verulkar
- Indira Gandhi Agricultural University, Raipur, Chhattisgarh, India
| | - Arvind Kumar
- International Rice Research Institute South Asia Hub, ICRISAT, Patancheru, Telangana, India
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Correspondence:
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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11
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Torres RO, Natividad MA, Quintana MR, Henry A. Ratooning as a management strategy for lodged or drought-damaged rice crops. CROP SCIENCE 2020; 60:367-380. [PMID: 32536700 PMCID: PMC7282670 DOI: 10.1002/csc2.20007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/09/2019] [Indexed: 06/11/2023]
Abstract
Rice (Oryza sativa L.) plants have the ability to develop ratoon tillers if the terminal growing point is lost, such as when the panicle has been aborted, matured, or harvested. We examined postharvest and midseason ratooning as management strategies for damaged rice crops, both in irrigated and rainfed conditions. Genotypic variation was observed in terms of postharvest ratoon tillering, midseason ratoon crop growth after lodging, and midseason ratoon crop growth after drought stress. The genotypic variation in postharvest ratoon tillering was related to stem carbohydrate levels at the time of main crop harvest and was affected by soil moisture levels at the time of main crop harvest. Drought-tolerant varieties did not consistently show improved ratoon crop growth. After lodging, cutting stems at a height of 30 cm produced the highest numbers of ratoon tillers, and the contribution of the ratoon crop to the total harvestable grain yield was highest when the ratoon crop was initiated at earlier growth stages. The highest ratoon grain yields recovered from lodged crops ranged up to 3.58 t ha-1. Total grain yield after drought was improved by trimming the leaves and panicles only in certain conditions and did not appear to be correlated with stem carbohydrate levels. These results suggest that management strategies may be recommended to farmers that exploit the ratooning ability of rice for improved recovery after midseason crop damage.
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Affiliation(s)
- Rolando O. Torres
- Systems Physiology Cluster, Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLaguna4031Philippines
| | - Mignon A. Natividad
- Systems Physiology Cluster, Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLaguna4031Philippines
| | - Marinell R. Quintana
- Systems Physiology Cluster, Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLaguna4031Philippines
| | - Amelia Henry
- Systems Physiology Cluster, Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLaguna4031Philippines
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12
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Mohd Ikmal A, Nurasyikin Z, Tuan Nur Aqlili Riana TA, Puteri Dinie Ellina Z, Wickneswari R, Noraziyah AAS. Drought Yield QTL ( qDTY) with Consistent Effects on Morphological and Agronomical Traits of Two Populations of New Rice ( Oryza sativa) Lines. PLANTS (BASEL, SWITZERLAND) 2019; 8:E186. [PMID: 31238548 PMCID: PMC6630983 DOI: 10.3390/plants8060186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/03/2022]
Abstract
Drought has been a major limiting factor for rice production. Drought yield QTLs (qDTYs; QTLs = quantitative trait loci) were pyramided into MRQ74 and MR219 to produce drought tolerant lines. In this study, new drought tolerant MRQ74 and MR219 pyramided lines (PLs) were evaluated under drought stress (RS) and non-stress (NS) conditions to evaluate the effects of different qDTYs combinations on morphological and agronomical traits. MRQ74 PLs having qDTY12.1 possessed the best root length (RL) under both RS and NS but the effect was only significant for MR219 PLs under RS. Some qDTYs combinations also found to have consistent effect on the same trait of both populations. PLs with only qDTY12.1 showed the highest grain yield (GY) under RS in both populations which means qDTY12.1 controlled RL and caused higher GY under drought condition. The interaction of major-effect qDTY12.1 with qDTY2.2 also shows significant effect on leaf rolling (LR) of both PL populations. These qDTYs proved to be beneficial in improving traits related to drought tolerance. Selected PLs with qDTY12.1 combinations also found to have better RL and root weight (RW) under RS. Improvement of morphological and agronomical traits led to higher GY of PLs. Therefore, qDTY12.1 either is present singly or in combination with other qDTYs was the best qDTY due to its consistent effect on morphological and agronomical traits and GY across populations under RS and NS.
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Affiliation(s)
- Asmuni Mohd Ikmal
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
| | - Zainuddin Nurasyikin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
| | | | | | - Ratnam Wickneswari
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
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13
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Henry A, Stuart-Williams H, Dixit S, Kumar A, Farquhar G. Stomatal conductance responses to evaporative demand conferred by rice drought-yield quantitative trait locus qDTY 12.1. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:660-669. [PMID: 32172773 PMCID: PMC7734198 DOI: 10.1071/fp18126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 03/02/2019] [Indexed: 05/24/2023]
Abstract
Rice quantitative trait locus (QTL) qDTY12.1 is a major-effect drought yield QTL that was identified from a cross of Vandana (recipient parent) and Way Rarem (donor parent) through breeding efforts to improve rice yield under upland drought stress conditions. The two main physiological effects previously observed to be related to the presence of qDTY12.1 were (i) increased lateral root growth, and (ii) increased transpiration efficiency. Since relatively more progress has thus far been made on characterising the lateral root growth response related to qDTY12.1, the present study focussed on characterising how qDTY12.1 confers higher transpiration efficiency under upland drought stress in the Vandana background. In a series of field experiments in which stomatal conductance was measured across different times of day in four qDTY12.1 near isogenic lines (NILs), the NILs and Way Rarem showed consistently higher stomatal conductance than Vandana under conditions of low vapour pressure deficit (VPD) and low photosynthetically active radiation (PAR), and consistently lower stomatal conductance than Vandana under high VPD and high PAR. Leaf δ18O was higher in the qDTY12.1 NIL than in Vandana, and although this trend was previously observed for leaf δ13C it appeared to be more consistent across measurement dates and treatments for leaf δ18O. The qDTY12.1 NILs and Way Rarem tended to show greater large vein to small vein interveinal distance and mesophyll area than Vandana, also consistent across treatments. In terms of aquaporin-related plant hydraulics, variation among NILs in terms of aquaporin inhibition of root hydraulic conductivity (Lpr) was observed, with the highest-yielding NIL showing a lack of Lpr inhibition similar to Way Rarem. The results reported here suggest that the effects of qDTY12.1 are in response not only to soil moisture, but also to atmospheric conditions. An interaction among multiple mechanisms including leaf anatomy and aquaporin function appear to confer the transpiration efficiency effect of qDTY12.1.
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Affiliation(s)
- Amelia Henry
- International Rice Research Institute, DAPO Box 7777 Metro Manila, Philippines; and Corresponding author.
| | - Hilary Stuart-Williams
- Research School of Biology, Robertson Building (46), Sullivan's Creek Road, Australian National University, Canberra, ACT 2601, Australia
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777 Metro Manila, Philippines
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777 Metro Manila, Philippines
| | - Graham Farquhar
- Research School of Biology, Robertson Building (46), Sullivan's Creek Road, Australian National University, Canberra, ACT 2601, Australia
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14
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Sabar M, Shabir G, Shah SM, Aslam K, Naveed SA, Arif M. Identification and mapping of QTLs associated with drought tolerance traits in rice by a cross between Super Basmati and IR55419-04. BREEDING SCIENCE 2019; 69:169-178. [PMID: 31086495 PMCID: PMC6507710 DOI: 10.1270/jsbbs.18068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Water stress, in a climate change scenario is one of the major threats for sustainable rice productivity. Combining drought resistance with yield and desirable economic traits is the most promising solution for the researchers. Although several studies resulted in the identification of QTLs for drought resistance in rice, but none of them serve as a milestone. Therefore, there is always a quest to find the new QTLs. The present investigation was carried out to map QTLs involved in drought resistance and yield related parameter in a cross of IR55419-04 and Super Basmati. An F2 population of 418 individuals was used as the mapping population. The raised nursery was transplanted in lyzimeters. Two extreme sets of tolerant (23 Nos.) and sensitive (23 Nos.) individuals were selected based on total water uptake under water stress conditions. Two hundred thirty microsatellite markers staggered on the whole genome were used for identifying polymorphic markers between the two parents. The selected 73 polymorphic microsatellites were used to genotype individuals and were scattered on a distance of 1735 cM on all 12 linkage groups. QTL analysis was performed by using the WinQTL Cartographer 2.5 V. A total of 21 QTLs were detected using composite interval mapping. The QTLs relating to drought tolerance at the vegetative stage were found on chromosome 1. Novel genomic regions were detected in the marker interval RM520-RM143 and RM168-RM520. The region has a significant QTL qTWU3.1 for total water uptake. Root morphological trait QTLs were found on chromosome 3. QTLs responsible for additive effects were due to the alleles of the IR55419-04. These novel QTLs can be used for marker assisted breeding to develop new drought-tolerant rice varieties and fine mapping can be used to explore the functional relationship between the QTLs and phenotypic traits.
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Affiliation(s)
- Muhammad Sabar
- Rice Research Institute, Kala Shah Kaku,
Lahore,
Pakistan
| | - Ghulam Shabir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University,
Multan,
Pakistan
| | - Shahid Masood Shah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus,
Abbottabad, 22010,
Pakistan
- Corresponding author (e-mail: )
| | - Kashif Aslam
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University,
Multan,
Pakistan
| | - Shahzad Amir Naveed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences,
Beijing,
China
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering (NIBGE),
Faisalabad, 38000,
Pakistan
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15
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Sandhu N, Dixit S, Swamy BPM, Raman A, Kumar S, Singh SP, Yadaw RB, Singh ON, Reddy JN, Anandan A, Yadav S, Venkataeshwarllu C, Henry A, Verulkar S, Mandal NP, Ram T, Badri J, Vikram P, Kumar A. Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas. RICE (NEW YORK, N.Y.) 2019; 12:8. [PMID: 30778782 PMCID: PMC6379507 DOI: 10.1186/s12284-019-0269-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/11/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY1.1, qDTY2.1, qDTY3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal. RESULTS Grain yield advantage of the NILs with qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 and qDTY2.1 + qDTY3.1 + Sub1 ranged from 76 to 2479 kg ha- 1 and 396 to 2376 kg ha- 1 under non-stress (NS) respectively and 292 to 1118 kg ha- 1 and 284 to 2086 kg ha- 1 under reproductive drought stress (RS), respectively. The NIL, IR96322-34-223-B-1-1-1-1 having qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321-1447-651-B-1-1-2 having qDTY1.1 + qDTY3.1 + Sub 1 and IR 94391-131-358-19-B-1-1-1 having qDTY3.1 + Sub1 have been released as varieties Bahuguni dhan-1' and 'Bahuguni dhan-2' respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322-34-223-B-1-1-1-1, IR 96321-1447-651-B-1-1-2 and IR 94391-131-358-19-B-1-1-1 respectively on 6 K SNP Infinium chip. CONCLUSION The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha- 1 under reproductive stage drought stress and 0.1 to 1.0 t ha- 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.
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Affiliation(s)
- Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, India
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Anitha Raman
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar India
| | - S. P. Singh
- Bihar Agricultural University, Sabour, Bihar India
| | - R. B. Yadaw
- National Rice Research Program Hardinath, Dhanusha, Nepal
| | - O. N. Singh
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - J. N. Reddy
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - A. Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Challa Venkataeshwarllu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Amelia Henry
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Satish Verulkar
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh India
| | - N. P. Mandal
- Central Rainfed Upland Rice Research station, National Rice Research Institute, Hazaribagh, Jharkhand India
| | - T. Ram
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jyothi Badri
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Prashant Vikram
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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16
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Vemanna RS, Bakade R, Bharti P, Kumar MKP, Sreeman SM, Senthil-Kumar M, Makarla U. Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:193. [PMID: 30894866 PMCID: PMC6415615 DOI: 10.3389/fpls.2019.00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Due to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.
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Affiliation(s)
- Ramu S. Vemanna
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
- Regional Center for Biotechnology, Faridabad, India
- *Correspondence: Ramu S. Vemanna, ;
| | - Rahul Bakade
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | - Pooja Bharti
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agriculture Sciences, Bengaluru, India
| | | | | | - Udayakumar Makarla
- Department of Crop Physiology, University of Agriculture Sciences, Bengaluru, India
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17
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Grondin A, Dixit S, Torres R, Venkateshwarlu C, Rogers E, Mitchell-Olds T, Benfey PN, Kumar A, Henry A. Physiological mechanisms contributing to the QTL qDTY 3.2 effects on improved performance of rice Moroberekan x Swarna BC 2F 3:4 lines under drought. RICE (NEW YORK, N.Y.) 2018; 11:43. [PMID: 30066052 PMCID: PMC6068063 DOI: 10.1186/s12284-018-0234-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/09/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Traditional rice (Oryza sativa) varieties are valuable resources for the improvement of drought resistance. qDTY3.2 is a drought-yield quantitative trait locus that was identified in a population derived from the traditional variety Moroberekan and the drought-susceptible variety Swarna. In this study, our aim was to characterize the physiological mechanisms associated with qDTY3.2. Our approach was to phenotype fifteen BC2F3:4 lines for shoot and root drought resistance-related traits as compared to Swarna in the field under well-watered and drought stress conditions. Four BC2F3:4 lines contrasting for yield under drought were selected for detailed characterization of shoot morphology, water use related traits, flowering time and root system architecture in the field as well as in controlled environments (lysimeters in a greenhouse, and gel imaging platform in a growth chamber). RESULTS Across five field experiments, grain yield correlated significantly with root growth along the soil profile, flowering time, and canopy temperature under drought conditions. The four selected BC2F3:4 lines showed earlier flowering time, reduced distribution of root growth to shallow soil layers which resulted in lower water uptake (between 0 and 30 cm) and drought-induced increased distribution of root growth to deep soil layers (between 30 and 60 cm) as compared to Swarna in the field. Root system architecture phenotypes were confirmed in whole root systems in lysimeters, and corresponded to higher numbers of root tips in a gel imaging platform, highlighting the potential stability of some root traits across different growth stages and systems. CONCLUSIONS We conclude that earlier flowering time, reduced shallow root growth, and drought-induced increased deep root growth are associated with the presence of qDTY3.2 since these phenotypes were consistently observed in the selected QTL lines with full introgression of qDTY3.2. We hypothesize that the qDTY3.2 associated RSA phenotypes led to better use of water and metabolic resources which, combined with earlier flowering time, improved yield under drought.
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Affiliation(s)
- Alexandre Grondin
- International Rice Research Institute, Los Baños, Laguna Philippines
- Present address: UMR DIADE, Institut de Recherche pour le Développement/Université de Montpellier, Montpellier, France
| | - Shalabh Dixit
- International Rice Research Institute, Los Baños, Laguna Philippines
| | - Rolando Torres
- International Rice Research Institute, Los Baños, Laguna Philippines
| | - Challa Venkateshwarlu
- International Rice Research Institute South Asia Hub, ICRISAT, Patancheru, Telangana India
| | - Eric Rogers
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC USA
| | - Thomas Mitchell-Olds
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC USA
| | - Philip N. Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC USA
| | - Arvind Kumar
- International Rice Research Institute, Los Baños, Laguna Philippines
- International Rice Research Institute South Asia Hub, ICRISAT, Patancheru, Telangana India
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna Philippines
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18
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Mohd Ikmal A, Nurasyikin Z, Kumar A, Noraziyah AAS. Evaluation of morpho-physiological traits of MRQ74 pyramided lines with drought yield QTLs. EUPHYTICA 2018; 214:98. [DOI: 10.1007/s10681-018-2178-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/13/2018] [Indexed: 09/02/2023]
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19
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Torres RO, Henry A. Yield stability of selected rice breeding lines and donors across conditions of mild to moderately severe drought stress. FIELD CROPS RESEARCH 2018; 220:37-45. [PMID: 29725159 PMCID: PMC5891920 DOI: 10.1016/j.fcr.2016.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although mild to moderately severe drought stress may have less of an effect on rice grain yield than severe drought stress during reproductive stage, its prevalence across rice farmers' fields at the global level may be more economically significant. In this study, field experiments were conducted on selected genotypes with known tolerance to severe reproductive-stage drought in order to identify those that would produce high and stable grain yield across seasons and soil moisture conditions varying from well-watered to mild and moderately severe drought stress. Mild stress generally occurred during wet seasons and moderate stress happened during dry seasons. The drought stress was mild enough such that the time to flowering was similar under drought stress and well-watered conditions in either season. However, significant grain yield reductions were incurred even at mild drought levels. Using an AMMI1 biplot analysis, IR83142-B-7-B-B, Binuhangin, IR77298-14-1-2-13, IR70215-70-CPA-3-4-1-3 and IR77298-14-1-2 were identified as the genotypes with the highest and most stable grain yields in both well-watered and mild to moderately severe drought stress environments. In a characterization of traits conferring drought tolerance among the highest yielding genotypes under mild to moderate drought stress, genotypes Binuhangin and IR70215-70-CPA-3-4-1-3 stood out for multiple physiological traits under drought. However, no direct correlations among genotypes between stomatal conductance, normalized difference vegetation index (NDVI) or root dry weight with grain or total dry matter yield were observed under any soil moisture level. These results reflect the complex interaction of drought response traits contributing to grain yield. The genotypic variation and physiological responses observed in this study point to the potential of developing varieties targeted to mild and moderate drought stress using yield as the selection criterion.
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20
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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21
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Dhakarey R, Raorane ML, Treumann A, Peethambaran PK, Schendel RR, Sahi VP, Hause B, Bunzel M, Henry A, Kohli A, Riemann M. Physiological and Proteomic Analysis of the Rice Mutant cpm2 Suggests a Negative Regulatory Role of Jasmonic Acid in Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2017; 8:1903. [PMID: 29250082 PMCID: PMC5715382 DOI: 10.3389/fpls.2017.01903] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/20/2017] [Indexed: 05/18/2023]
Abstract
It is widely known that numerous adaptive responses of drought-stressed plants are stimulated by chemical messengers known as phytohormones. Jasmonic acid (JA) is one such phytohormone. But there are very few reports revealing its direct implication in drought related responses or its cross-talk with other phytohormones. In this study, we compared the morpho-physiological traits and the root proteome of a wild type (WT) rice plant with its JA biosynthesis mutant coleoptile photomorphogenesis 2 (cpm2), disrupted in the allene oxide cyclase (AOC) gene, for insights into the role of JA under drought. The mutant had higher stomatal conductance, higher water use efficiency and higher shoot ABA levels under severe drought as compared to the WT. Notably, roots of cpm2 were better developed compared to the WT under both, control and drought stress conditions. Root proteome was analyzed using the Tandem Mass Tag strategy to better understand this difference at the molecular level. Expectedly, AOC was unique but notably highly abundant under drought in the WT. Identification of other differentially abundant proteins (DAPs) suggested increased energy metabolism (i.e., increased mobilization of resources) and reactive oxygen species scavenging in cpm2 under drought. Additionally, various proteins involved in secondary metabolism, cell growth and cell wall synthesis were also more abundant in cpm2 roots. Proteome-guided transcript, metabolite, and histological analyses provided further insights into the favorable adaptations and responses, most likely orchestrated by the lack of JA, in the cpm2 roots. Our results in cpm2 are discussed in the light of JA crosstalk to other phytohormones. These results together pave the path for understanding the precise role of JA during drought stress in rice.
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Affiliation(s)
- Rohit Dhakarey
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
- International Rice Research Institute, Los Baños, Philippines
| | - Manish L. Raorane
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
- International Rice Research Institute, Los Baños, Philippines
| | - Achim Treumann
- Newcastle University Protein and Proteome Analysis, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | | | - Rachel R. Schendel
- Department of Food Chemistry and Phytochemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Vaidurya P. Sahi
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Bettina Hause
- Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Mirko Bunzel
- Department of Food Chemistry and Phytochemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Philippines
| | - Ajay Kohli
- International Rice Research Institute, Los Baños, Philippines
| | - Michael Riemann
- Molecular Cell Biology, Institute of Botany, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions. PLoS One 2017; 12:e0186382. [PMID: 29045473 PMCID: PMC5647096 DOI: 10.1371/journal.pone.0186382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/30/2017] [Indexed: 12/13/2022] Open
Abstract
A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line. In this study, more drought-responsive microRNAs were identified in the inflorescence tissues of IR64, IR77298-14-1-2-10 and IR87705-7-15-B via next-generation sequencing. Among the 32 families of inflorescence-specific non-conserved microRNAs that were identified, 22 families were up-regulated in IR87705-7-15-B. Overall 9 conserved and 34 non-conserved microRNA families were found as drought-responsive in rice inflorescence with 5 conserved and 30 non-conserved families induced in the IR87705-7-15-B. The observation of more drought-responsive non-conserved microRNAs may imply their prominence over conserved microRNAs in drought response mechanisms of rice inflorescence. Gene Ontology annotation analysis on the target genes of drought-responsive microRNAs identified in IR87705-7-15-B revealed over-representation of biological processes including development, signalling and response to stimulus. Particularly, four inflorescence-specific microRNAs viz. osa-miR5485, osa-miR5487, osa-miR5492 and osa-miR5517, and two non-inflorescence specific microRNAs viz. osa-miR169d and osa-miR169f.2 target genes that are involved in flower or embryonic development. Among them, osa-miR169d, osa-miR5492 and osa-miR5517 are related to flowering time control. It is also worth mentioning that osa-miR2118 and osa-miR2275, which are implicated in the biosynthesis of rice inflorescence-specific small interfering RNAs, were induced in IR87705-7-15-B but repressed in IR77298-14-1-2-10. Further, gene search within qDTY4.1 QTL region had identified multiple copies of NBS-LRR resistance genes (potential target of osa-miR2118), subtilisins and genes implicated in stomatal movement, ABA metabolism and cuticular wax biosynthesis.
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Li S, Zuo Q, Wang X, Ma W, Jin X, Shi J, Ben-Gal A. Characterizing roots and water uptake in a ground cover rice production system. PLoS One 2017; 12:e0180713. [PMID: 28686687 PMCID: PMC5501594 DOI: 10.1371/journal.pone.0180713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 06/20/2017] [Indexed: 11/18/2022] Open
Abstract
Background and aims Water-saving ground cover rice production systems (GCRPS) are gaining popularity in many parts of the world. We aimed to describe the characteristics of root growth, morphology, distribution, and water uptake for a GCRPS. Methods A traditional paddy rice production system (TPRPS) was compared with GCRPS in greenhouse and field experiments. In the greenhouse, GCRPS where root zone average soil water content was kept near saturation (GCRPSsat), field capacity (GCRPSfwc) and 80% field capacity (GCRPS80%), were evaluated. In a two-year field experiment, GCRPSsat and GCRPS80% were applied. Results Similar results were found in greenhouse and field experiments. Before mid-tillering the upper soil temperature was higher for GCRPS, leading to enhanced root dry weight, length, surface area, specific root length, and smaller diameter of roots but lower water uptake rate per root length compared to TPRPS. In subsequent growth stages, the reduced soil water content under GCRPS caused that the preponderance of root growth under GCRPSsat disappeared in comparison to TPRPS. Under other GCRPS treatments (GCRPSfwc and GCRPS80%), significant limitation on root growth, bigger root diameter and higher water uptake rate per root length were found. Conclusions Discrepancies in soil water and temperature between TPRPS and GCRPS caused adjustments to root growth, morphology, distribution and function. Even though drought stress was inevitable after mid-tillering under GCRPS, especially GCRPS80%, similar or even enhanced root water uptake capacity in comparison to TPRPS might promote allocation of photosynthetic products to shoots and increase water productivity.
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Affiliation(s)
- Sen Li
- Department of Soil and Water Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
- Key Laboratory of Arable Land Conservation (North China), Ministry of Agriculture, Beijing, China
| | - Qiang Zuo
- Department of Soil and Water Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
- Key Laboratory of Arable Land Conservation (North China), Ministry of Agriculture, Beijing, China
| | - Xiaoyu Wang
- Department of Soil and Water Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
- Key Laboratory of Arable Land Conservation (North China), Ministry of Agriculture, Beijing, China
| | - Wenwen Ma
- Department of Soil and Water Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
- Key Laboratory of Arable Land Conservation (North China), Ministry of Agriculture, Beijing, China
| | - Xinxin Jin
- Department of Soil and Water Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
- Key Laboratory of Arable Land Conservation (North China), Ministry of Agriculture, Beijing, China
| | - Jianchu Shi
- Department of Soil and Water Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
- Key Laboratory of Arable Land Conservation (North China), Ministry of Agriculture, Beijing, China
- * E-mail:
| | - Alon Ben-Gal
- Soil, Water and Environmental Sciences, Agricultural Research Organization, Gilat Research Center, Negev, Israel
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Kim TH, Hur YJ, Han SI, Cho JH, Kim KM, Lee JH, Song YC, Kwon YU, Shin D. Drought-tolerant QTL qVDT11 leads to stable tiller formation under drought stress conditions in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:131-138. [PMID: 28167026 DOI: 10.1016/j.plantsci.2016.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/23/2016] [Accepted: 11/21/2016] [Indexed: 05/27/2023]
Abstract
Drought is an important limiting factor for rice production, but the genetic mechanisms of drought tolerance is poorly understood. Here, we screened 218 rice varieties to identify 32 drought-tolerant varieties. The variety Samgang exhibited strong drought tolerance and stable yield in rain-fed conditions and was selected for further study. To identify QTLs for drought tolerance, we examined visual drought tolerance (VDT) and relative water content (RWC) phenotypes in a doubled haploid (DH) population of 101 individuals derived from a cross between Samgang and Nagdong (a drought-sensitive variety). Three QTLs from Samgang were identified for VDT and explained 41.8% of the phenotypic variance. In particular, qVDT11 contributed 20.3% of the phenotypic variance for RWC. To determine QTL effects on drought tolerance in rain-fed paddy conditions, seven DH lines were selected according to the number of QTLs they contained. Of the drought-tolerance-associated QTLs, qVDT2 and qVDT6 did not affect tiller formation, but qVDT11 increased tiller number. Tiller formation was most stable when qVDT2 and qVDT11 were combined. DH lines with both of these drought-tolerance-associated QTLs exhibited the most stable tiller formation. Together, these results suggest that qVDT11 is important for drought tolerance and stable tiller formation in rain-fed paddy fields.
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Affiliation(s)
- Tae-Heon Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Yeon-Jae Hur
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Sang-Ik Han
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Jun-Hyun Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Kyung-Min Kim
- College of Agriculture and Life Science, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Jong-Hee Lee
- Research Policy Bureau, Rural Development Administration, Jeonju 54875, Republic of Korea.
| | - You-Chun Song
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Yeong-Up Kwon
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
| | - Dongjin Shin
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea.
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Khan A, Sovero V, Gemenet D. Genome-assisted Breeding For Drought Resistance. Curr Genomics 2016; 17:330-42. [PMID: 27499682 PMCID: PMC4955035 DOI: 10.2174/1389202917999160211101417] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 11/30/2022] Open
Abstract
Drought stress caused by unpredictable precipitation poses a major threat to food production worldwide, and its impact is only expected to increase with the further onset of climate change. Understanding the effect of drought stress on crops and plants' response is critical for developing improved varieties with stable high yield to fill a growing food gap from an increasing population depending on decreasing land and water resources. When a plant encounters drought stress, it may use multiple response types, depending on environmental conditions, drought stress intensity and duration, and the physiological stage of the plant. Drought stress responses can be divided into four broad types: drought escape, drought avoidance, drought tolerance, and drought recovery, each characterized by interacting mechanisms, which may together be referred to as drought resistance mechanisms. The complex nature of drought resistance requires a multi-pronged approach to breed new varieties with stable and enhanced yield under drought stress conditions. High throughput genomics and phenomics allow marker-assisted selection (MAS) and genomic selection (GS), which offer rapid and targeted improvement of populations and identification of parents for rapid genetic gains and improved drought-resistant varieties. Using these approaches together with appropriate genetic diversity, databases, analytical tools, and well-characterized drought stress scenarios, weather and soil data, new varieties with improved drought resistance corresponding to grower preferences can be introduced into target regions rapidly.
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Affiliation(s)
- Awais Khan
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
| | - Valpuri Sovero
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
| | - Dorcus Gemenet
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
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26
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Ma Y, Kan G, Zhang X, Wang Y, Zhang W, Du H, Yu D. Quantitative Trait Loci (QTL) Mapping for Glycinin and β-Conglycinin Contents in Soybean (Glycine max L. Merr.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3473-83. [PMID: 27070305 DOI: 10.1021/acs.jafc.6b00167] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Compared to β-conglycinin, glycinin contains 3-4 times the methionine and cysteine (sulfur-containing amino acids), accounting for approximately 40 and 30%, respectively, of the total storage protein in soybean. Increasing the soybean storage protein content while improving the ratio of glycinin to β-conglycinin is of great significance for soybean breeding and soy food products. The objective of this study is to analyze the genetic mechanism regulating the glycinin and β-conglycinin contents of soybean by using a recombinant inbred line (RIL) population derived from a cross between Kefeng No. 1 and Nannong 1138-2. Two hundred and twenty-one markers were used to map quantitative trait loci (QTLs) for glycinin (11S) and β-conglycinin (7S) contents, the ratio of glycinin to β-conglycinin (RGC), and the sum of glycinin and β-conglycinin (SGC). A total of 35 QTLs, 3 pairs of epistatic QTLs, and 5 major regions encompassing multiple QTLs were detected. Genes encoding the subunits of β-conglycinin were localized to marker intervals sat_418-satt650 and sat_196-sat_303, which are linked to RGC and SGC; marker sat_318, associated with 11S, 7S, and SGC, was located near Glyma10g04280 (Gy4), which encodes a subunit of glycinin. These results, which take epistatic interactions into account, will improve our understanding of the genetic basis of 11S and 7S contents and will lay a foundation for marker-assisted selection (MAS) breeding of soybean and improving the quality of soybean products.
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Affiliation(s)
- Yujie Ma
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Xinnan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Yongli Wang
- Biofuels Institute, School of the Environment, Jiangsu University , Zhenjiang 212013, China
| | - Wei Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Hongyang Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 210095, China
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Yang D, Ye X, Zheng X, Cheng C, Ye N, Huang F. Development and Evaluation of Chromosome Segment Substitution Lines Carrying Overlapping Chromosome Segments of the Whole Wild Rice Genome. FRONTIERS IN PLANT SCIENCE 2016; 7:1737. [PMID: 27933072 PMCID: PMC5121215 DOI: 10.3389/fpls.2016.01737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/04/2016] [Indexed: 05/04/2023]
Abstract
Common wild rice (Oryza rufipogon Griff.) represents an important resource for rice improvement. Genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) are most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, 146 CSSLs were produced; they were derived from the crossing and back-crossing of two rice cultivars: Dongnanihui 810 (Oryza sativa L.), an indica rice cultivar as the recipient, and ZhangPu wild rice, a wild rice cultivar as the donor. First, a physical map of the 146 CSSLs was constructed using 149 molecular markers. Based on this map, the total size of the 147 substituted segments in the population was 1145.65 Mb, or 3.04 times that of the rice genome. To further facilitate gene mapping, heterozygous chromosome segment substitution lines (HCSSLs) were also produced, which were heterozygous in the target regions. Second, a physical map of the 244 HCSSLs was produced using 149 molecular markers. Based on this map, the total length of substituted segments in the HCSSLs was 1683.75 Mb, or 4.47 times the total length of the rice genome. Third, using the 146 CSSLs, two QTLs for plant height, and one major QTL for apiculus coloration were identified. Using the two populations of HCSSLs, the qPa-6-2 gene was precisely mapped to an 88 kb region. These CSSLs and HCSSLs may, therefore, provide powerful tools for future whole genome large-scale gene discovery in wild rice, providing a foundation enabling the development of new rice varieties. This research will also facilitate fine mapping and cloning of quantitative trait genes, providing for the development of superior rice varieties.
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28
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Moumeni A, Satoh K, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S. Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit. BMC Genomics 2015; 16:1110. [PMID: 26715311 PMCID: PMC4696290 DOI: 10.1186/s12864-015-2335-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 12/19/2015] [Indexed: 02/05/2023] Open
Abstract
Background Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. This work will help differentiate mechanisms of tolerance in contrasting NILs and accelerate molecular breeding programs to improve drought tolerance in this crop. Results The two pairs of rice NILs, developed at the International Rice Research Institute, along with the drought-susceptible parent, IR64, showed distinct gene-expression profiles in leaves under different water-deficit (WD) treatments. Drought tolerance in the highly drought-tolerant NIL (DTN), IR77298-14-1-2-B-10, could be attributed to the up-regulation of genes with calcium ion binding, transferase, hydrolase and transcription factor activities, whereas in the moderate DTN, IR77298-5-6-B-18, genes with transporter, catalytic and structural molecule activities were up-regulated under WD. In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively. In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD. Conclusions We report here that the two pairs of NILs with different levels of drought tolerance may elucidate potential mechanisms and pathways through transcriptome data from leaf tissue. The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2335-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Moumeni
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), PO Box 145, Postal Code 46191-91951, Km8 Babol Rd., Amol, Mazandaran, Iran.
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Ramiah Venuprasad
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines. .,Africa Rice Centre (AfricaRice), Ibadan station, c/o IITA, PMB 5320 Oyo road, Ibadan, Nigeria.
| | - Rachid Serraj
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines. .,Agricultural Research (CGIAR ISPC), FAO, Rome, Italy.
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines.
| | - Hei Leung
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines.
| | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
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