1
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Rajkumar MS, Tembhare K, Garg R, Jain M. Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility and regulatory DNA elements under drought stress in rice cultivars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2063-2079. [PMID: 38859561 DOI: 10.1111/tpj.16864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/08/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Drought stress (DS) is one of the major constraints limiting yield in crop plants including rice. Gene regulation under DS is largely governed by accessibility of the transcription factors (TFs) to their cognate cis-regulatory elements (CREs). In this study, we used DNase I hypersensitive assays followed by sequencing to identify the accessible chromatin regions under DS in a drought-sensitive (IR64) and a drought-tolerant (N22) rice cultivar. Our results indicated that DNase I hypersensitive sites (DHSs) were highly enriched at transcription start sites (TSSs) and numerous DHSs were detected in the promoter regions. DHSs were concurrent with epigenetic marks and the genes harboring DHSs in their TSS and promoter regions were highly expressed. In addition, DS induced changes in DHSs (∆DHSs) in TSS and promoter regions were positively correlated with upregulation of several genes involved in drought/abiotic stress response, those encoding TFs and located within drought-associated quantitative trait loci, much preferentially in the drought-tolerant cultivar. The CREs representing the binding sites of TFs involved in DS response were detected within the ∆DHSs, suggesting differential accessibility of TFs to their cognate sites under DS in different rice cultivars, which may be further deployed for enhancing drought tolerance in rice.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Kunal Tembhare
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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2
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Chang Y, Fang Y, Liu J, Ye T, Li X, Tu H, Ye Y, Wang Y, Xiong L. Stress-induced nuclear translocation of ONAC023 improves drought and heat tolerance through multiple processes in rice. Nat Commun 2024; 15:5877. [PMID: 38997294 PMCID: PMC11245485 DOI: 10.1038/s41467-024-50229-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 07/04/2024] [Indexed: 07/14/2024] Open
Abstract
Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Despite hundreds of stress-related genes being identified, only a few have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, a hub stress regulator that integrates the regulations of both drought and heat tolerance in rice. ONAC023 positively regulates drought and heat tolerance at both seedling and reproductive stages. Notably, the functioning of ONAC023 is obliterated without stress treatment and can be triggered by drought and heat stresses at two layers. The expression of ONAC023 is induced in response to stress stimuli. We show that overexpressed ONAC23 is translocated to the nucleus under stress and evidence from protoplasts suggests that the dephosphorylation of the remorin protein OSREM1.5 can promote this translocation. Under drought or heat stress, the nuclear ONAC023 can target and promote the expression of diverse genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various processes including water transport, reactive oxygen species homeostasis, and alternative splicing. These results manifest that ONAC023 is fine-tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.
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Affiliation(s)
- Yu Chang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Jiahan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tiantian Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaokai Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ying Ye
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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3
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Zou C, Tan H, Huang K, Zhai R, Yang M, Huang A, Wei X, Mo R, Xiong F. Physiological Characteristic Changes and Transcriptome Analysis of Maize ( Zea mays L.) Roots under Drought Stress. Int J Genomics 2024; 2024:5681174. [PMID: 38269194 PMCID: PMC10807950 DOI: 10.1155/2024/5681174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/08/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
Water deficit is a key limiting factor for limiting yield in maize (Zea mays L.). It is crucial to elucidate the molecular regulatory networks of stress tolerance for genetic enhancement of drought tolerance. The mechanism of drought tolerance of maize was explored by comparing physiological and transcriptomic data under normal conditions and drought treatment at polyethylene glycol- (PEG-) induced drought stress (5%, 10%, 15%, and 20%) in the root during the seedling stage. The content of saccharide, SOD, CAT, and MDA showed an upward trend, proteins showed a downward trend, and the levels of POD first showed an upward trend and then decreased. Compared with the control group, a total of 597, 2748, 6588, and 5410 differentially expressed genes were found at 5%, 10%, 15%, and 20% PEG, respectively, and 354 common DEGs were identified in these comparisons. Some differentially expressed genes were remarkably enriched in the MAPK signaling pathway and plant hormone signal transduction. The 50 transcription factors (TFs) divided into 15 categories were screened from the 354 common DEGs during drought stress. Auxin response factor 10 (ARF10), auxin-responsive protein IAA9 (IAA9), auxin response factor 14 (ARF14), auxin-responsive protein IAA1 (IAA1), auxin-responsive protein IAA27 (IAA27), and 1 ethylene response sensor 2 (ERS2) were upregulated. The two TFs, including bHLH 35 and bHLH 96, involved in the MAPK signal pathway and plant hormones pathway, are significantly upregulated in 5%, 10%, 15%, and 20% PEG stress groups. The present study provides greater insight into the fundamental transcriptome reprogramming of grain crops under drought.
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Affiliation(s)
- Chenglin Zou
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Hua Tan
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Kaijian Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Ruining Zhai
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Meng Yang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Aihua Huang
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Xinxing Wei
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Runxiu Mo
- Maize Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
| | - Faqian Xiong
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China
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4
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Daryani P, Amirbakhtiar N, Soorni J, Loni F, Darzi Ramandi H, Shobbar ZS. Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach. RICE (NEW YORK, N.Y.) 2024; 17:7. [PMID: 38227151 DOI: 10.1186/s12284-024-00684-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.
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Affiliation(s)
- Parisa Daryani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nazanin Amirbakhtiar
- National Plant Gene Bank of Iran, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Jahad Soorni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Fatemeh Loni
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hadi Darzi Ramandi
- Department of Plant Production and Genetics, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
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5
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Singh P, Sundaram KT, Vinukonda VP, Venkateshwarlu C, Paul PJ, Pahi B, Gurjar A, Singh UM, Kalia S, Kumar A, Singh VK, Sinha P. Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties. Commun Biol 2024; 7:89. [PMID: 38216712 PMCID: PMC10786901 DOI: 10.1038/s42003-024-05769-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.
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Affiliation(s)
- Preeti Singh
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Krishna T Sundaram
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | | | | | - Pronob J Paul
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Bandana Pahi
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India
| | - Anoop Gurjar
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Uma Maheshwar Singh
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Sanjay Kalia
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, India
| | - Arvind Kumar
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India.
| | - Pallavi Sinha
- International Rice Research Institute (IRRI), South-Asia Hub, Hyderabad, India.
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6
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Sankarapillai LV, Vijayaraghavareddy P, Nanaiah K, Arpitha GD, Chaitanya PM, Sathishraj R, Shindhe D, Vemanna RS, Yin X, Struik PC, Sreeman S. Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice. PHYSIOLOGIA PLANTARUM 2023; 175:e13992. [PMID: 37882292 DOI: 10.1111/ppl.13992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/29/2023] [Accepted: 08/03/2023] [Indexed: 10/27/2023]
Abstract
Water-saving attempts for rice cultivation often reduce yields. Maintaining productivity under drought is possible when rice genotypes are bred with improved metabolism and spikelet fertility. Although attempts have been made to introgress water mining and water use efficiency traits, combining acquired tolerance traits (ATTs), that is, specific traits induced or upregulated to better tolerate severe stress, appears equally important. In our study, we screened 90 rice germplasm accessions that represented the molecular and phenotypic variations of 851 lines of the 3 K rice panel. Utilising phenomics, we identified markers linked to ATTs through association analysis of over 0.2 million SNPs derived from whole-genome sequences. Propensity to respond to 'induction' stress varied significantly among genotypes, reflecting differences in cellular protection against oxidative stress. Among the ATTs, the hydroxyl radical and proline contents exhibited the highest variability. Furthermore, these significant variations in ATTs were strongly correlated with spikelet fertility. The 43 significant markers associated with ATTs were further validated using a different subset of contrasting genotypes. Gene expression studies and metabolomic profiling of two well-known contrasting genotypes, APO (tolerant) and IR64 (sensitive), identified two ATT genes: AdoMetDC and Di19. Our study highlights the relevance of polyamine biosynthesis in modulating ATTs in rice. Genotypes with superior ATTs and the associated markers can be effectively employed in breeding rice varieties with sustained spikelet fertility and grain yield under drought.
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Affiliation(s)
| | - Preethi Vijayaraghavareddy
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Karthik Nanaiah
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
| | | | | | - Rajendran Sathishraj
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Dhananjay Shindhe
- Department of Pathology and Microbiology, University of Nebraska Medical Centre, Omaha, Nebraska, USA
| | - Ramu S Vemanna
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University & Research, Wageningen, the Netherlands
| | - Sheshshayee Sreeman
- Department of Crop Physiology, University of Agricultural Sciences, Bengaluru, India
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7
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Krishna TPA, Veeramuthu D, Maharajan T, Soosaimanickam M. The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement. Curr Genomics 2023; 24:24-35. [PMID: 37920729 PMCID: PMC10334699 DOI: 10.2174/1389202924666230517115912] [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: 01/02/2023] [Revised: 03/31/2023] [Accepted: 04/14/2023] [Indexed: 11/04/2023] Open
Abstract
Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.
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Affiliation(s)
| | - Duraipandiyan Veeramuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
| | - Theivanayagam Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
| | - Mariapackiam Soosaimanickam
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India
- Department of Advanced Zoology & Biotechnology, Loyola College, Nungambakkam, Chennai, 600034, India
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8
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Shankar R, Dwivedi AK, Singh V, Jain M. Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance. PHYSIOLOGIA PLANTARUM 2023; 175:e13879. [PMID: 36805564 DOI: 10.1111/ppl.13879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.
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Affiliation(s)
- Rama Shankar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anuj Kumar Dwivedi
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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9
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Mahmood U, Li X, Fan Y, Chang W, Niu Y, Li J, Qu C, Lu K. Multi-omics revolution to promote plant breeding efficiency. FRONTIERS IN PLANT SCIENCE 2022; 13:1062952. [PMID: 36570904 PMCID: PMC9773847 DOI: 10.3389/fpls.2022.1062952] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.
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Affiliation(s)
- Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiaodong Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Chang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yue Niu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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10
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Improved drought tolerance of EMS mutagenized Alfalfa (Medicago sativa L.) mutants by in vitro screening at germination stage. Sci Rep 2022; 12:12693. [PMID: 35882960 PMCID: PMC9325702 DOI: 10.1038/s41598-022-16294-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
The objectives of this study were to determine drought tolerant novel mutant of alfalfa (Medicago sativa L.) genotypes by screening EMS mutagenized 340675 M3 seeds at germination stages in the presence of osmotic stress of 35% PEG6000. Root growth assay provided several drought tolerant candidate mutants. Of those, 4 mutants were further evaluated at water deficit conditions applied for 24 days after the first cutting at flowering bud stage. The results revealed that mutants determined as drought tolerant at germination stage were also tolerant to water deficit conditions. Protein content and superoxide dismutase values were found to be higher in all mutants than controls. Ascorbate peroxides, glutton reductase and lipid peroxidase values varied based on the mutant genotype and duration of drought stress. Drought stress significantly changed transcriptional levels of MtP5CS, MtDehyd, MseIF-2, MtRD2 and MsNAC genes. These results indicated that in vitro screening of alfalfa mutant seeds for osmatic tolerance at germination and early seedling growth stages was successfully able to determine the drought tolerant alfalfa mutants which were also tolerant to water deficit conditions after the first cutting at flowering bud stage.
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11
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Yilmaz EG, Tiryaki I, Sari U. Genetic variation among einkorn genotypes based on gene targeted functional markers and its possible relationship with drought tolerance at seed germination stage. Mol Biol Rep 2022; 49:7389-7398. [PMID: 35716281 DOI: 10.1007/s11033-022-07532-9] [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: 02/26/2022] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Einkorn wheat is one of the first primary genetic resources for discovery of new alleles related to biotic and abiotic stress tolerances for further genetic improvements while it became more popular especially for its native grain status as healthy food resources. Therefore, this study aims to determine germination parameters of 32 local einkorn (Triticum monococcum) genotypes collected from Kastamonu and its vicinity, Turkey under drought stress conditions, and to reveal the genetic relationship of those genotypes based on drought related gene targeted functional markers (GTFMs). METHODS AND RESULTS Germination test was conducted at 20 ± 0.5 °C in darkness with randomized complete block design with 4 replications. Seeds placed on double filter papers in a covered glass petri dishes (80 × 15 mm) were treated with polyethylene glycol (PEG6000) with a -0.23 MPa. The final germination percentages (FGPs), speed and span of germination parameters were determined. Drought stress severely worsened all germination parameters measured. The genotypes SG24 and SG12 were the most drought tolerant and sensitive genotypes based on 21.1% and 64.8% of reduction rates in FGPs, respectively. Twelve GTFMs produced a total of 32 bands and 26 of them were polymorphic. The mean polymorphism ratio of the markers and average band per marker were determined as 86.31% and 2.66, respectively. The highest polymorphism information content (PIC) was obtained from AIB1 gene marker (0.875). CONCLUSIONS This study revealed that there was a significant genetic variation for drought tolerance levels of local einkorn wheat genotypes at germination stage and drought related GTFMs can be used not only to reveal genetic variation but also to distinguish the drought tolerant genotypes.
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Affiliation(s)
- Enes Gokhan Yilmaz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Canakkale Onsekiz Mart University, Terzioglu Campus, 17020, Canakkale, Turkey
| | - Iskender Tiryaki
- Department of Agricultural Biotechnology, Faculty of Agriculture, Canakkale Onsekiz Mart University, Terzioglu Campus, 17020, Canakkale, Turkey.
| | - Ugur Sari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Canakkale Onsekiz Mart University, Terzioglu Campus, 17020, Canakkale, Turkey
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12
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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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13
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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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14
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Zargar SM, Mir RA, Ebinezer LB, Masi A, Hami A, Manzoor M, Salgotra RK, Sofi NR, Mushtaq R, Rohila JS, Rakwal R. Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:803603. [PMID: 35154193 PMCID: PMC8829427 DOI: 10.3389/fpls.2021.803603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.
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Affiliation(s)
- Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Ammarah Hami
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Najeebul Rehman Sofi
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Roohi Mushtaq
- Department of Biotechnology and Bioinformatics, SP College, Cluster University Srinagar, Srinagar, India
| | - Jai Singh Rohila
- Dale Bumpers National Rice Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Stuttgart, AR, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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15
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Radha B, Sunitha NC, Sah RP, T P MA, Krishna GK, Umesh DK, Thomas S, Anilkumar C, Upadhyay S, Kumar A, Ch L N M, S B, Marndi BC, Siddique KHM. Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:996514. [PMID: 36714754 PMCID: PMC9874338 DOI: 10.3389/fpls.2022.996514] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/05/2022] [Indexed: 05/12/2023]
Abstract
Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.
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Affiliation(s)
- Beena Radha
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Vellayani, Thiruvananthapuram, Kerala, India
| | | | - Rameswar P Sah
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Md Azharudheen T P
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - G K Krishna
- Department of Plant Physiology, Kerala Agricultural University-College of Agriculture, Thrissur, Kerala, India
| | - Deepika Kumar Umesh
- Mulberry Breeding & Genetics Section, Central Sericultural Research and Training Institute-Berhampore, Central Silk Board, Murshidabad, West Bengal, India
| | - Sini Thomas
- Department of Plant Physiology, Kerala Agricultural University-Regional Agricultural Research Station, Kumarakom, Kerala, India
| | - Chandrappa Anilkumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Sameer Upadhyay
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Awadhesh Kumar
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Manikanta Ch L N
- Department of Plant Physiology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Behera S
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Bishnu Charan Marndi
- Division of Crop Production, Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India
| | - Kadambot H M Siddique
- The University of Western Australia Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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16
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Billah M, Aktar S, Brestic M, Zivcak M, Khaldun ABM, Uddin MS, Bagum SA, Yang X, Skalicky M, Mehari TG, Maitra S, Hossain A. Progressive Genomic Approaches to Explore Drought- and Salt-Induced Oxidative Stress Responses in Plants under Changing Climate. PLANTS (BASEL, SWITZERLAND) 2021; 10:1910. [PMID: 34579441 PMCID: PMC8471759 DOI: 10.3390/plants10091910] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/17/2022]
Abstract
Drought and salinity are the major environmental abiotic stresses that negatively impact crop development and yield. To improve yields under abiotic stress conditions, drought- and salinity-tolerant crops are key to support world crop production and mitigate the demand of the growing world population. Nevertheless, plant responses to abiotic stresses are highly complex and controlled by networks of genetic and ecological factors that are the main targets of crop breeding programs. Several genomics strategies are employed to improve crop productivity under abiotic stress conditions, but traditional techniques are not sufficient to prevent stress-related losses in productivity. Within the last decade, modern genomics studies have advanced our capabilities of improving crop genetics, especially those traits relevant to abiotic stress management. This review provided updated and comprehensive knowledge concerning all possible combinations of advanced genomics tools and the gene regulatory network of reactive oxygen species homeostasis for the appropriate planning of future breeding programs, which will assist sustainable crop production under salinity and drought conditions.
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Affiliation(s)
- Masum Billah
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.B.); (T.G.M.)
| | - Shirin Aktar
- Institute of Tea Research, Chinese Academy of Agricultural Sciences, South Meiling Road, Hangzhou 310008, China;
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Marek Zivcak
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia;
| | | | - Md. Shalim Uddin
- Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh; (A.B.M.K.); (M.S.U.); (S.A.B.)
| | - Shamim Ara Bagum
- Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh; (A.B.M.K.); (M.S.U.); (S.A.B.)
| | - Xinghong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 61 Daizong St., Tai’an 271000, China;
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic;
| | - Teame Gereziher Mehari
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; (M.B.); (T.G.M.)
| | - Sagar Maitra
- Department of Agronomy, Centurion University of Technology and Management, Village Alluri Nagar, R.Sitapur 761211, Odisha, India;
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur 5200, Bangladesh
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17
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Janaki Ramayya P, Vinukonda VP, Singh UM, Alam S, Venkateshwarlu C, Vipparla AK, Dixit S, Yadav S, Abbai R, Badri J, T. R, Phani Padmakumari A, Singh VK, Kumar A. Marker-assisted forward and backcross breeding for improvement of elite Indian rice variety Naveen for multiple biotic and abiotic stress tolerance. PLoS One 2021; 16:e0256721. [PMID: 34473798 PMCID: PMC8412243 DOI: 10.1371/journal.pone.0256721] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/13/2021] [Indexed: 11/18/2022] Open
Abstract
The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY1.1, qDTY2.2 and qDTY4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.
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Affiliation(s)
| | | | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
| | - Shamshad Alam
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Challa Venkateshwarlu
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | | | - Shilpi Dixit
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Shailesh Yadav
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Jyothi Badri
- ICAR-Indian Institute of Rice Research (IIRR), Rajendra Nagar, Hyderabad, India
| | - Ram T.
- ICAR-Indian Institute of Rice Research (IIRR), Rajendra Nagar, Hyderabad, India
| | | | - Vikas Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Arvind Kumar
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, India
- * E-mail:
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18
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Zhang A, Ji Y, Sun M, Lin C, Zhou P, Ren J, Luo D, Wang X, Ma C, Zhang X, Feng G, Nie G, Huang L. Research on the drought tolerance mechanism of Pennisetum glaucum (L.) in the root during the seedling stage. BMC Genomics 2021; 22:568. [PMID: 34301177 PMCID: PMC8305952 DOI: 10.1186/s12864-021-07888-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought is one of the major environmental stresses resulting in a huge reduction in crop growth and biomass production. Pearl millet (Pennisetum glaucum L.) has excellent drought tolerance, and it could be used as a model plant to study drought resistance. The root is a very crucial part of plant that plays important roles in plant growth and development, which makes it a focus of research. RESULTS In this study, we explored the mechanism of drought tolerance of pearl millet by comparing physiological and transcriptomic data under normal condition and drought treatment at three time points (1 h, 3 h and 7 h) in the root during the seedling stage. The relative electrical conductivity went up from 1 h to 7 h in both control and drought treatment groups while the content of malondialdehyde decreased. A total of 2004, 1538 and 605 differentially expressed genes were found at 1 h, 3 h and 7 h respectively and 12 genes showed up-regulation at all time points. Some of these differentially expressed genes were significantly enriched into 'metabolic processes', 'MAPK signaling pathway' and 'plant hormone signal transduction' such as the ABA signal transduction pathway in GO and KEGG enrichment analysis. CONCLUSIONS Pearl millet was found to have a quick drought response, which may occur before 1 h that contributes to its tolerance against drought stress. These results can provide a theoretical basis to enhance the drought resistance in other plant species.
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Affiliation(s)
- Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chuang Lin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Puding Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Juncai Ren
- College of Animal Science and Technology, Southwest University, Rongchang Campus, Chongqing, 402460, China
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Congyu Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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19
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Roy S, Verma BC, Banerjee A, Kumar J, Ray US, Mandal NP. Genetic diversity for drought and low-phosphorus tolerance in rice (Oryza sativa L.) varieties and donors adapted to rainfed drought-prone ecologies. Sci Rep 2021; 11:13671. [PMID: 34211096 PMCID: PMC8249610 DOI: 10.1038/s41598-021-93325-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/11/2021] [Indexed: 11/15/2022] Open
Abstract
Drought and phosphate availability are two major abiotic factors limiting productivity of rice in rainfed upland areas. There has been a constant need for new improved donor with tolerance to multiple abiotic stress conditions for rainfed rice breeding. In the present study, a set of 32 popular rice varieties and landraces were evaluated for drought and low-phosphorus (P) tolerance, and also characterized using grain yield under reproductive drought QTLs (DTY QTLs) and Pup1 linked/specific molecular markers. Twenty-seven genotypes were identified as tolerant to moderately tolerant to drought. The SSR markers linked to ten DTY QTLs classified the genotypes into two groups corresponding to aus and indica. The tolerant genotypes were distributed under both groups. Based on the core markers of Pup1 locus, complete tolerant haplotype was recorded in nine genotypes other than the tolerant check Dular. Nine more genotypes showed the incomplete tolerant haplotypes. The rice genotypes showed significantly high genetic variability for low-P tolerance in hydroponic study. A few genotypes revealed non-Pup1 type tolerance which needs further confirmation.
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Affiliation(s)
- Somnath Roy
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India.
| | - B C Verma
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India
| | - Amrita Banerjee
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India
| | - J Kumar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India
| | - Uday Sankar Ray
- Zonal Drought Resistant Paddy Research Station, Hathwara, Purulia, 723147, West Bengal, India
| | - N P Mandal
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India.
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Melandri G, AbdElgawad H, Floková K, Jamar DC, Asard H, Beemster GTS, Ruyter-Spira C, Bouwmeester HJ. Drought tolerance in selected aerobic and upland rice varieties is driven by different metabolic and antioxidative responses. PLANTA 2021; 254:13. [PMID: 34173050 PMCID: PMC8233253 DOI: 10.1007/s00425-021-03659-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/08/2021] [Indexed: 05/14/2023]
Abstract
Sugar-mediated osmotic acclimation and a strong antioxidative response reduce drought-induced biomass loss at the vegetative stage in rice. A clear understanding of the physiological and biochemical adaptations to water limitation in upland and aerobic rice can help to identify the mechanisms underlying their tolerance to low water availability. In this study, three indica rice varieties-IR64 (lowland), Apo (aerobic), and UPL Ri-7 (upland)-, that are characterized by contrasting levels of drought tolerance, were exposed to drought at the vegetative stage. Drought-induced changes in biomass, leaf metabolites and oxidative stress markers/enzyme activities were analyzed in each variety at multiple time points. The two drought-tolerant varieties, Apo and UPL Ri-7 displayed a reduced water use in contrast to the susceptible variety IR64 that displayed high water consumption and consequent strong leaf dehydration upon drought treatment. A sugar-mediated osmotic acclimation in UPL Ri-7 and a strong antioxidative response in Apo were both effective in limiting the drought-induced biomass loss in these two varieties, while biomass loss was high in IR64, also after recovery. A qualitative comparison of these results with the ones of a similar experiment conducted in the field at the reproductive stage showed that only Apo, which also in this stage showed the highest antioxidant power, was able to maintain a stable grain yield under stress. Our results show that different metabolic and antioxidant adaptations confer drought tolerance to aerobic and upland rice varieties in the vegetative stage. The effectiveness of these adaptations differs between developmental stages. Unraveling the genetic control of these mechanisms might be exploited in breeding for new rice varieties adapted to water-limited environments.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Kristýna Floková
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany AS CR and Palacký University, Olomouc, Czech Republic
| | - Diaan C Jamar
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Han Asard
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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21
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Panda S, Majhi PK, Anandan A, Mahender A, Veludandi S, Bastia D, Guttala SB, Singh SK, Saha S, Ali J. Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture. Int J Mol Sci 2021; 22:6058. [PMID: 34199720 PMCID: PMC8199995 DOI: 10.3390/ijms22116058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.
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Affiliation(s)
- Siddharth Panda
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (S.P.); (S.V.)
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India;
| | - Prasanta Kumar Majhi
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University (B.H.U.), Varanasi 221005, Uttar Pradesh, India; (P.K.M.); (S.K.S.)
| | - Annamalai Anandan
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (S.P.); (S.V.)
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines;
| | - Sumanth Veludandi
- Crop Improvement Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India; (S.P.); (S.V.)
| | - Debendranath Bastia
- Department of Plant Breeding and Genetics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India;
| | - Suresh Babu Guttala
- Department of Genetics and Plant Breeding, Naini Agricultural Institute, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Prayagraj 211007, Uttar Pradesh, India;
| | - Shravan Kumar Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University (B.H.U.), Varanasi 221005, Uttar Pradesh, India; (P.K.M.); (S.K.S.)
| | - Sanjoy Saha
- Crop Production Division, Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack 753006, Odisha, India;
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines;
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22
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Rabara RC, Msanne J, Basu S, Ferrer MC, Roychoudhury A. Coping with inclement weather conditions due to high temperature and water deficit in rice: An insight from genetic and biochemical perspectives. PHYSIOLOGIA PLANTARUM 2021; 172:487-504. [PMID: 33179306 DOI: 10.1111/ppl.13272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Climatic fluctuations, temperature extremes, and water scarcity are becoming increasingly unpredictable with the passage of time. Such environmental atrocities have been the scourge of agriculture over the ages, bringing with them poor harvests and threat of famine. Rice production, owing to its high-water requirement for cultivation, is highly vulnerable to the threat of changing climate, particularly prolonged drought and high temperature, individually or in combination. Amidst all the abiotic stresses, heat and drought are considered as the most important concurrent stressors, largely affecting rice yield and productivity under the current scenario. Such threats heighten the need for new breeding and cultivation strategies in generating abiotic stress-resilient rice varieties with better yield potential. Responses of rice to these stresses can be categorized at the morphological, physiological and biochemical levels. This review examines the physiological and molecular mechanism, in the form of up regulation of several defense machineries of rice varieties to cope with drought stress (DS), high temperature stress (HTS), and their combination (DS-HTS). Genotypic differences among rice varieties in their tolerance ability have also been addressed. The review also appraises research studies conducted in rice regarding various phenotypic traits, genetic loci and response mechanisms to stress conditions to help craft new breeding strategies for improved tolerance to DS and HTS, singly or in combination. The review also encompasses the gene regulatory networks and transcription factors, and their cross-talks in mediating tolerance to such stresses. Understanding the epigenetic regulation, involving DNA methylation and histone modification during such hostile situations, will also play a crucial role in our comprehensive understanding of combinatorial stress responses. Taken together, this review consolidates current research and available information on promising rice cultivars with desirable traits as well as advocates synergistic and complementary approaches in molecular and systems biology to develop new rice breeds that favorably respond to DS-HTS-induced abiotic stress.
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Affiliation(s)
- Roel C Rabara
- Department of Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joseph Msanne
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Supratim Basu
- New Mexico Consortium, Los Alamos, NM, New Mexico, United States of America
| | - Marilyn C Ferrer
- Genetic Resources Division, Philippine Rice Research Institute, Science City of Muñoz, Nueva Ecija, Philippines
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, West Bengal, India
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23
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Ghazy MI, Salem KFM, Sallam A. Utilization of genetic diversity and marker-trait to improve drought tolerance in rice (Oryza sativa L.). Mol Biol Rep 2020; 48:157-170. [PMID: 33300089 DOI: 10.1007/s11033-020-06029-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/20/2020] [Indexed: 01/31/2023]
Abstract
Drought stress is one of the main problems for the rice crop, as it reduces the production and productivity of the grain yield significantly. In Egypt, many restrictions were made on the cultivation of rice due to its high-water demand. Producing promising drought-tolerant rice cultivars combined with high yielding is one of the main targets for rice breeders. A set of 22 highly diverse rice genotypes were evaluated under normal and drought conditions. Morphological, physiological, and yield traits were recorded on each genotype. Drought susceptibility index (DSI) was estimated for six yield traits to identify the most drought-tolerant rice genotypes. A high genetic variation was found among genotypes tested in the experiment. Under normal conditions, the highest phenotypic correlation was found between grain yield (GY) and sterility percentage (SP) (- 0.73**), while it was among GY and chlorophyll content (CC) (0.82**) under drought conditions. To identify quantitative trait loci (QTL) controlling yielding traits under drought and normal, a single marker analysis was performed between all yield traits under both conditions and a set of 106 simple sequence repeat (SSR) marker alleles. The genetic association analysis revealed 14 and 17 QTL under drought and normal conditions, respectively. The most drought-tolerant genotypes were selected based on phenotypic traits, the number of QTL in each selected genotype, and the level of genetic diversity existed among the genotypes. As a result, five genotypes (Giza 178, IET1444, GZ1368-S-5-4, Nahda, Giza 14) were identified as the most promising drought-tolerant rice genotypes. Eight QTL controlling drought tolerance were identified in Giza 178, Nahda, and GZ1368-S-5-4, while four QTL were found in IET1444. The number of different QTLs were estimated among the five selected genotypes. Giza 178 and GZ1368-S-5-4 shared the same QTLs. Seven different QTLs were found among Nahda, IET1444, GZ1368-S-5-4, and Giza 14. Combining information from phenotypic traits, genetic diversity analysis, and QTL analysis was very useful in identifying the true drought-tolerant rice genotypes that can be used for crossing in the future breeding program.
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Affiliation(s)
- Mohamed I Ghazy
- Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Sakha, Kafr Elsheikh, 33717, Egypt
| | - Khaled F M Salem
- Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City, Egypt
- Department of Biology, College of Science and Humanitarian Studies, Shaqra University, Qwaieah, Saudi Arabia
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt.
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24
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Vishnukiran T, Neeraja CN, Jaldhani V, Vijayalakshmi P, Raghuveer Rao P, Subrahmanyam D, Voleti SR. A major pleiotropic QTL identified for yield components and nitrogen content in rice (Oryza sativa L.) under differential nitrogen field conditions. PLoS One 2020; 15:e0240854. [PMID: 33079957 PMCID: PMC7575116 DOI: 10.1371/journal.pone.0240854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 10/04/2020] [Indexed: 11/22/2022] Open
Abstract
To identify the genomic regions for yield and NUE of rice genotypes and lines with promising yield under low N, a recombinant inbred population (RIL) developed between BPT5204 (a mega variety known for its quality) and PTB1 (variety with high NUE) was evaluated for consecutive wet and dry seasons under low nitrogen (LN) and recommended nitrogen (RN) field conditions. A set of 291 RILs were characterized for 24 traits related to leaf, agro-morphological, yield, N content and nitrogen use efficiency indices. More than 50 RILs were found promising with grain yield >10 g under LN. Parental polymorphism survey with 297 SSRs and selective genotyping revealed five genomic regions associated with yield under LN, which were further saturated with polymorphic SSRs. Thirteen promising SSRs were identified out of 144 marker trait associations under LN using single marker analysis. Composite interval mapping showed 37 QTL under LN with five pleiotropic QTL. A major stable pleiotropic (RM13201—RM13209) from PTB1 spanning 825.4 kb region associated with straw N % (SNP) in both treatments across seasons and yield and yield related traits in WS appears to be promising for the MAS. Another major QTL (RM13181-RM13201) was found to be associated with only relative trait parameters of biomass, grain and grain nitrogen. These two major pleiotropic QTL (RM13201-RM13209 and RM13181-RM13201) on chromosome 2 were characterized for their positive allele effect and could be deployed for the development of rice varieties with NUE.
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Affiliation(s)
- T. Vishnukiran
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - C. N. Neeraja
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
- * E-mail:
| | - V. Jaldhani
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Vijayalakshmi
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Raghuveer Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D. Subrahmanyam
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S. R. Voleti
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
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25
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Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
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Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
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26
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Kumar A, Sandhu N, Venkateshwarlu C, Priyadarshi R, Yadav S, Majumder RR, Singh VK. Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag. Sci Rep 2020; 10:13073. [PMID: 32753648 PMCID: PMC7403580 DOI: 10.1038/s41598-020-70132-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.
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Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, Metro Manila, Philippines. .,IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, India.
| | - Nitika Sandhu
- International Rice Research Institute, Metro Manila, Philippines.,Punjab Agricultural University, Ludhiana, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Rahul Priyadarshi
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India.,International Rice Research Institute, Guwahati, Assam, India
| | - Shailesh Yadav
- International Rice Research Institute, Metro Manila, Philippines
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
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27
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Melandri G, Prashar A, McCouch SR, van der Linden G, Jones HG, Kadam N, Jagadish K, Bouwmeester H, Ruyter-Spira C. Association mapping and genetic dissection of drought-induced canopy temperature differences in rice. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1614-1627. [PMID: 31846000 PMCID: PMC7031080 DOI: 10.1093/jxb/erz527] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/16/2019] [Indexed: 05/07/2023]
Abstract
Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= -0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Ankush Prashar
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Susan R McCouch
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Gerard van der Linden
- Wageningen UR Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Hamlyn G Jones
- Plant Science Division, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, UK
- School of Plant Biology, University of Western Australia, Perth, Australia
| | - Niteen Kadam
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
- International Rice Research Institute, Los Baños, Philippines
- Department of Plant Biology and Institute of Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Krishna Jagadish
- International Rice Research Institute, Los Baños, Philippines
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
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28
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Melandri G, AbdElgawad H, Riewe D, Hageman JA, Asard H, Beemster GTS, Kadam N, Jagadish K, Altmann T, Ruyter-Spira C, Bouwmeester H. Biomarkers for grain yield stability in rice under drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:669-683. [PMID: 31087074 PMCID: PMC6946010 DOI: 10.1093/jxb/erz221] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/10/2019] [Indexed: 05/23/2023]
Abstract
Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in the field and were, at the reproductive stage, exposed to either well-watered or drought conditions to identify the metabolic processes associated with drought-induced grain yield loss. Photorespiration, protein degradation, and nitrogen recycling were the main processes involved in the drought-induced leaf metabolic reprogramming. Molecular markers of drought tolerance and sensitivity in terms of grain yield were identified using a multivariate model based on the values of the metabolites and enzyme activities across the population. The model highlights the central role of the ascorbate-glutathione cycle, particularly dehydroascorbate reductase, in minimizing drought-induced grain yield loss. In contrast, malondialdehyde was an accurate biomarker for grain yield loss, suggesting that drought-induced lipid peroxidation is the major constraint under these conditions. These findings highlight new breeding targets for improved rice grain yield stability under drought.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | - Jos A Hageman
- Wageningen University and Research, Biometris, Wageningen, The Netherlands
| | - Han Asard
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
| | - Gerrit T S Beemster
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
| | - Niteen Kadam
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
- International Rice Research Institute, Los Baños, Philippines
| | - Krishna Jagadish
- International Rice Research Institute, Los Baños, Philippines
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
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Genetic Mapping Identifies Consistent Quantitative Trait Loci for Yield Traits of Rice under Greenhouse Drought Conditions. Genes (Basel) 2020; 11:genes11010062. [PMID: 31948113 PMCID: PMC7017276 DOI: 10.3390/genes11010062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 12/31/2019] [Accepted: 01/03/2020] [Indexed: 11/17/2022] Open
Abstract
Improving drought resistance in crops is imperative under the prevailing erratic rainfall patterns. Drought affects the growth and yield of most modern rice varieties. Recent breeding efforts aim to incorporate drought resistance traits in rice varieties that can be suitable under alternative irrigation schemes, such as in a (semi)aerobic system, as row (furrow-irrigated) rice. The identification of quantitative trait loci (QTLs) controlling grain yield, the most important trait with high selection efficiency, can lead to the identification of markers to facilitate marker-assisted breeding of drought-resistant rice. Here, we report grain yield QTLs under greenhouse drought using an F2:3 population derived from Cocodrie (drought sensitive) × Nagina 22 (N22) (drought tolerant). Eight QTLs were identified for yield traits under drought. Grain yield QTL under drought on chromosome 1 (phenotypic variance explained (PVE) = 11.15%) co-localized with the only QTL for panicle number (PVE = 37.7%). The drought-tolerant parent N22 contributed the favorable alleles for all QTLs except qGN3.2 and qGN5.1 for grain number per panicle. Stress-responsive transcription factors, such as ethylene response factor, WD40 domain protein, zinc finger protein, and genes involved in lipid/sugar metabolism were linked to the QTLs, suggesting their possible role in drought tolerance mechanism of N22 in the background of Cocodrie, contributing to higher yield under drought.
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QTLian breeding for climate resilience in cereals: progress and prospects. Funct Integr Genomics 2019; 19:685-701. [PMID: 31093800 DOI: 10.1007/s10142-019-00684-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 04/05/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
Abstract
The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consumed globally. Drought, waterlogging, heat, salinity, and mineral toxicity are the key abiotic stresses drastically affecting crop yield. Conventional plant breeding approaches towards abiotic stress tolerance have gained success to limited extent, due to the complex (multigenic) nature of these stresses. Progress in breeding climate-resilient crop plants has gained momentum in the last decade, due to improved understanding of the physiochemical and molecular basis of various stresses. A good number of genes have been characterized for adaptation to various stresses. In the era of novel molecular markers, mapping of QTLs has emerged as viable solution for breeding crops tolerant to abiotic stresses. Therefore, molecular breeding-based development and deployment of high-yielding climate-resilient crop cultivars together with climate-smart agricultural practices can pave the path to enhanced crop yields for smallholder farmers in areas vulnerable to the climate change. Advances in fine mapping and expression studies integrated with cheaper prices offer new avenues for the plant breeders engaged in climate-resilient plant breeding, and thereby, hope persists to ensure food security in the era of climate change.
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Meena RK, Bhusal N, Kumar K, Jain R, Jain S. Intervention of molecular breeding in water saving rice production system: aerobic rice. 3 Biotech 2019; 9:133. [PMID: 30863712 PMCID: PMC6405779 DOI: 10.1007/s13205-019-1657-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/27/2019] [Indexed: 01/01/2023] Open
Abstract
The aerobic rice system/methods developed to tackle shortage of water, is a sustainable method to enhance rice productivity. Approximately 50% of irrigation water could be saved using this system in contrast to lowland rice cultivation. The crop can be directly seeded or transplanted in dry soil in this system rather than irrigated system of rice production. Here in this review we had tried to present all the important development made in regards to aerobic rice. Many QTLs responsible for aerobic traits in rice that have been mapped already are enlisted here. Brief comparisons of aerobic rice and conventional rice, further improvements made in aerobic rice have also been discussed.
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Affiliation(s)
- Rahul Kumar Meena
- Department of Molecular Biology and Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Nabin Bhusal
- Department of Genetics and Plant Breeding, Agriculture and Forestry University Rampur, Chitwan, 13712, Nepal
| | - Kuldeep Kumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Rajinder Jain
- Department of Molecular Biology and Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Sunita Jain
- Department of Molecular Biology and Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
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Phule AS, Barbadikar KM, Maganti SM, Seguttuvel P, Subrahmanyam D, Babu MBBP, Kumar PA. RNA-seq reveals the involvement of key genes for aerobic adaptation in rice. Sci Rep 2019; 9:5235. [PMID: 30918284 PMCID: PMC6437204 DOI: 10.1038/s41598-019-41703-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 03/01/2019] [Indexed: 12/24/2022] Open
Abstract
Adaptation of rice to the aerobic condition is needed to cope with the water scarcity as well as to ensure sustainable yield in future. To understand the molecular mechanisms responsible for aerobic adaptation in rice, we performed RNA-seq analysis of root and shoot i.e. developing panicle tissues at panicle initiation stage in two cultivars adapted to aerobic (CR Dhan 202) and traditional transplanted anaerobic (BPT 5204) conditions. The RNA-seq data emanated from 1.65 billion clean reads with approximately 37 million reads per sample. The number of differentially expressed transcripts was higher in the root than that in the shoot under both aerobic and anaerobic conditions. The transcription factors viz. MADS4, MADS5, MADS6, MADS7, MADS15 and transporters involved in sugar (SWEET3A) and nutrient uptake (PHT1;6, MDR-like ABC and vacuolar iron transporter homolog 2) were highly and uniquely expressed in the aerobic adapted cultivar (AAC) CR Dhan 202 under aerobic condition indicating their role in adaptation. The hormones such as ethylene and abscisic acid might be significantly involved in imparting aerobic adaptation. The higher expression of root related genes in the AAC under aerobic conditions suggests the involvement and sensitivity of roots to the water limiting condition. The metabolic activities are also more pronounced in the roots which impart rigorous plant establishment under the aerobic condition. The presence of alternative splice variants in the transcripts viz. Tetratrico peptide repeat (TPR) domain containing protein and GOLDEN2-LIKE1 (GLK1) additionally confirms that post transcriptional regulation is also crucial for aerobic adaptation. The QTLs related to root traits and stress tolerance harboring the uniquely expressed genes, which were identified in the present study can be deployed in molecular breeding programs to develop elite, high yielding aerobic rice cultivars.
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Affiliation(s)
- Amol S Phule
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Hyderabad, 30, India
| | - Kalyani M Barbadikar
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - Sheshu Madhav Maganti
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - P Seguttuvel
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - D Subrahmanyam
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - M B B Prasad Babu
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India
| | - Polumetla A Kumar
- Biotechnology Division, ICAR-Indian Institute of Rice Research, Hyderabad, 30, India.
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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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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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Mishra SS, Behera PK, Kumar V, Lenka SK, Panda D. Physiological characterization and allelic diversity of selected drought tolerant traditional rice ( Oryza sativa L.) landraces of Koraput, India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1035-1046. [PMID: 30425421 PMCID: PMC6214433 DOI: 10.1007/s12298-018-0606-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 05/25/2023]
Abstract
Water-deficit stress tolerance in rice is important for maintaining stable yield, especially under rain-fed ecosystem. After a thorough drought-tolerance screening of more than 130 rice genotypes from various regions of Koraput in our previous study, six rice landraces were selected for drought tolerance capacity. These six rice landraces were further used for detailed physiological and molecular assessment under control and simulated drought stress conditions. After imposing various levels of drought stress, leaf photosynthetic rate (PN), photochemical efficiency of photosystem II (Fv/Fm), SPAD chlorophyll index, membrane stability index and relative water content were found comparable with the drought-tolerant check variety (N22). Compared to the drought-susceptible variety IR64, significant positive attributes and varietal differences were observed for all the above physiological parameters in drought-tolerant landraces. Genetic diversity among the studied rice landraces was assessed using 19 previously reported drought tolerance trait linked SSR markers. A total of 50 alleles with an average of 2.6 per locus were detected at the loci of the 19 markers across studied rice genotypes. The Nei's genetic diversity (He) and the polymorphism information content (PIC) ranged from 0.0 to 0.767 and 0.0 to 0.718, respectively. Seven SSR loci, such as RM324, RM19367, RM72, RM246, RM3549, RM566 and RM515, showed the highest PIC values and are thus, useful in assessing the genetic diversity of studied rice lines for drought tolerance. Based on the result, two rice landraces (Pandkagura and Mugudi) showed the highest similarity index with tolerant check variety. However, three rice landraces (Kalajeera, Machhakanta and Haldichudi) are more diverse and showed highest genetic distance with N22. These landraces can be considered as the potential genetic resources for drought breeding program.
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Affiliation(s)
- Swati S. Mishra
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764 021 India
| | - Prafulla K. Behera
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764 021 India
| | - Vajinder Kumar
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, 110012 India
| | - Sangram K. Lenka
- TERI, Deakin NanoBiotechnology Centre, The Energy and Resources Institute, Gurugram, Haryana 122 001 India
| | - Debabrata Panda
- Department of Biodiversity and Conservation of Natural Resources, Central University of Orissa, Koraput, Odisha 764 021 India
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Kumar A, Sandhu N, Dixit S, Yadav S, Swamy BPM, Shamsudin NAA. Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought. RICE (NEW YORK, N.Y.) 2018; 11:35. [PMID: 29845495 PMCID: PMC5975061 DOI: 10.1186/s12284-018-0227-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/21/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies. RESULTS Based on class analysis of the QTL combinations, the identified superior QTL classes in F3/BC1F3/BC2F3 generations with positive QTL x QTL and QTL x background interactions that were captured through phenotyping maintained its superiority in yield under non-stress (NS) and reproductive-stage drought stress (RS) across advanced generations in all five studies. The marker-assisted selection breeding strategy combining both genotyping and phenotyping in early generation significantly reduced the number of genotypes to be carried forward. The strategy presented in this study providing genotyping and phenotyping cost savings of 25-68% compared with the traditional marker-assisted selection approach. The QTL classes, Sub1 + qDTY 1.1 + qDTY 2.1 + qDTY 3.1 and Sub1 + qDTY 2.1 + qDTY 3.1 in Swarna-Sub1, Sub1 + qDTY 1.1 + qDTY 1.2 , Sub1 + qDTY 1.1 + qDTY 2.2 and Sub1 + qDTY 2.2 + qDTY 12.1 in IR64-Sub1, qDTY 2.2 + qDTY 4.1 in Samba Mahsuri, Sub1 + qDTY 3.1 + qDTY 6.1 + qDTY 6.2 and Sub1 + qDTY 6.1 + qDTY 6.2 in TDK1-Sub1 and qDTY 12.1 + qDTY 3.1 and qDTY 2.2 + qDTY 3.1 in MR219 had shown better and consistent performance under NS and RS across generations over other QTL classes. CONCLUSION "Deployment of this procedure will save time and resources and will allow breeders to focus and advance only germplasm with high probability of improved performance. The identification of superior QTL classes and capture of positive QTL x QTL and QTL x background interactions in early generation and their consistent performance in subsequent generations across five backgrounds supports the efficacy of a combined MAS breeding strategy".
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Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Current address: Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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Tabkhkar N, Rabiei B, Samizadeh Lahiji H, Hosseini Chaleshtori M. Genetic Variation and Association Analysis of the SSR Markers Linked to the Major Drought-Yield QTLs of Rice. Biochem Genet 2018; 56:356-374. [PMID: 29478138 DOI: 10.1007/s10528-018-9849-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/20/2018] [Indexed: 01/18/2023]
Abstract
Drought is one of the major abiotic stresses, which hampers the production of rice worldwide. Informative molecular markers are valuable tools for improving the drought tolerance in various varieties of rice. The present study was conducted to evaluate the informative simple sequence repeat (SSR) markers in a diverse set of rice genotypes. The genetic diversity analyses of the 83 studied rice genotypes were performed using 34 SSR markers closely linked to the major quantitative trait loci (QTLs) of grain yield under drought stress (qDTYs). In general, our results indicated high levels of polymorphism. In addition, we screened these rice genotypes at the reproductive stage under both drought stress and nonstressful conditions. The results of the regression analysis demonstrated a significant relationship between 11 SSR marker alleles and the plant paddy weight under stressful conditions. Under the nonstressful conditions, 16 SSR marker alleles showed a significant correlation with the plant paddy weight. Finally, four markers (RM279, RM231, RM166, and RM231) demonstrated a significant association with the plant paddy weight under both stressful and nonstressful conditions. These informative-associated alleles may be useful for improving the crop yield under both drought stress and nonstressful conditions in breeding programs.
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Affiliation(s)
- Narjes Tabkhkar
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Babak Rabiei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
| | - Habibollah Samizadeh Lahiji
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Maryam Hosseini Chaleshtori
- Rice Research Institute of Iran (RRII), Agriculture Research Education and Extension Organization (AREEO), Rasht, Iran
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Positive interactions of major-effect QTLs with genetic background that enhances rice yield under drought. Sci Rep 2018; 8:1626. [PMID: 29374240 PMCID: PMC5786057 DOI: 10.1038/s41598-018-20116-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/08/2018] [Indexed: 12/19/2022] Open
Abstract
To improve the grain yield of the lowland-adapted popular rice variety Samba Mahsuri under reproductive-stage drought (RS) and to understand the interactions between drought QTLs, two mapping populations were developed using marker-assisted selection (MAS) and marker-assisted recurrent selection (MARS). The mean grain yield of pyramided lines (PLs) with qDTY 2.2 + qDTY 4.1 in MAS is significantly higher under RS and irrigated control than lines with single QTLs. Among MARS PLs, lines with four qDTYs (qDTY 1.1 + qDTY 2.1 + qDTY 3.1 + qDTY 11.1 ) and two QTLs (qDTY 1.1 + qDTY 11.1 ) yielded higher than PLs with other qDTY combinations. The selected PLs showed a yield advantage of 0.3-2.0 t ha-1 under RS. An allelic profile of MAS PLs having same qDTY combination but with different yields under drought was studied. Hierarchical clustering grouped together the selected lines with high yield under drought. Epistasis test showed the interaction of qDTY 4.1 and qDTY 9.1 loci with qDTY 7.1 significantly increased yield under drought and all the lines with higher yield under drought possessed the conserved region of qDTY 7.1 on chromosome 7. The positive interactions among QTLs, effectiveness of QTLs in different backgrounds, introgression of DTY QTLs together with resistance to biotic stresses shall help enhance grain yield under RS.
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Kulwal PL. Trait Mapping Approaches Through Linkage Mapping in Plants. PLANT GENETICS AND MOLECULAR BIOLOGY 2018; 164:53-82. [DOI: 10.1007/10_2017_49] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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40
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Dixit S, Singh A, Sandhu N, Bhandari A, Vikram P, Kumar A. Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:143. [PMID: 29151804 PMCID: PMC5670188 DOI: 10.1007/s11032-017-0737-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1 , qDTY6.1 , and qDTY6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.
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Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Anshuman Singh
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Rani Lakshmi Bai Central Agriculture University, Jhansi, India
| | - Nitika Sandhu
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Aditi Bhandari
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Prashant Vikram
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera México-Veracruz, El Batán, 56237 Texcoco, CP Mexico
| | - Arvind Kumar
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Catolos M, Sandhu N, Dixit S, Shamsudin NAA, Naredo MEB, McNally KL, Henry A, Diaz MG, Kumar A. Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:1763. [PMID: 29085383 PMCID: PMC5650699 DOI: 10.3389/fpls.2017.01763] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/26/2017] [Indexed: 05/21/2023]
Abstract
Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield (qDTY1.1, qDTY1.3 , and qDTY8.1 ) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits (qRT9.1 for root-growth angle and qRT5.1 for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus qDTY1.1 was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0-22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations qDTY1.3 +qDTY8.1 showed the highest mean grain yield advantage followed by lines having qDTY1.1 +qDTY8.1 and qDTY1.1 +qDTY8.1 +qDTY1.3 , across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.
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Affiliation(s)
- Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
- Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Noraziya A. A. Shamsudin
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
- School of Environmental and Natural Resource Sciences, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Ma E. B. Naredo
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Kenneth L. McNally
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Amelia Henry
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Ma G. Diaz
- Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
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Kadam NN, Tamilselvan A, Lawas LMF, Quinones C, Bahuguna RN, Thomson MJ, Dingkuhn M, Muthurajan R, Struik PC, Yin X, Jagadish SVK. Genetic Control of Plasticity in Root Morphology and Anatomy of Rice in Response to Water Deficit. PLANT PHYSIOLOGY 2017; 174:2302-2315. [PMID: 28600346 PMCID: PMC5543957 DOI: 10.1104/pp.17.00500] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 05/19/2023]
Abstract
Elucidating the genetic control of rooting behavior under water-deficit stress is essential to breed climate-robust rice (Oryza sativa) cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly related to root morphology and anatomy, involving 45,000 root-scanning images and nearly 25,000 cross sections from the root-shoot junction. The phenotypic plasticity of these traits was quantified as the relative change in trait value under water-deficit compared with control conditions. We then carried out a genome-wide association analysis on these traits and their plasticity, using 45,608 high-quality single-nucleotide polymorphisms. One hundred four significant loci were detected for these traits under control conditions, 106 were detected under water-deficit stress, and 76 were detected for trait plasticity. We predicted 296 (control), 284 (water-deficit stress), and 233 (plasticity) a priori candidate genes within linkage disequilibrium blocks for these loci. We identified key a priori candidate genes regulating root growth and development and relevant alleles that, upon validation, can help improve rice adaptation to water-deficit stress.
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Affiliation(s)
- Niteen N Kadam
- International Rice Research Institute, Metro Manila, The Philippines
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University and Research, 6700 AK Wageningen, The Netherlands
| | - Anandhan Tamilselvan
- International Rice Research Institute, Metro Manila, The Philippines
- Tamil Nadu Agricultural University, Coimbatore, 641003 Tamil Nadu, India
| | - Lovely M F Lawas
- International Rice Research Institute, Metro Manila, The Philippines
| | - Cherryl Quinones
- International Rice Research Institute, Metro Manila, The Philippines
| | - Rajeev N Bahuguna
- International Rice Research Institute, Metro Manila, The Philippines
| | - Michael J Thomson
- International Rice Research Institute, Metro Manila, The Philippines
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843
| | - Michael Dingkuhn
- International Rice Research Institute, Metro Manila, The Philippines
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | | | - Paul C Struik
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University and Research, 6700 AK Wageningen, The Netherlands
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Department of Plant Sciences, Wageningen University and Research, 6700 AK Wageningen, The Netherlands
| | - S V Krishna Jagadish
- International Rice Research Institute, Metro Manila, The Philippines
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
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Talukder SK, Saha MC. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses. FRONTIERS IN PLANT SCIENCE 2017; 8:1317. [PMID: 28798766 PMCID: PMC5526908 DOI: 10.3389/fpls.2017.01317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.
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Calingacion M, Mumm R, Tan K, Quiatchon-Baeza L, Concepcion JCT, Hageman JA, Prakash S, Fitzgerald M, Hall RD. A Multidisciplinary Phenotyping and Genotyping Analysis of a Mapping Population Enables Quality to Be Combined with Yield in Rice. Front Mol Biosci 2017; 4:32. [PMID: 28589124 PMCID: PMC5438996 DOI: 10.3389/fmolb.2017.00032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/04/2017] [Indexed: 12/21/2022] Open
Abstract
In this study a mapping population (F8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography—Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and commercial spectral libraries. These data were used to predict the potential role of these metabolites in determining differences in aroma between genotypes. A number of QTLs for yield and for individual metabolites have been identified. Following these combined multi-disciplinary analyses, it proved possible to identify a number of lines which appeared to combine the favourable aroma attributes of IR64 with the favourable (higher) yield potential of Apo. As such, these lines are excellent candidates to assess further as potential genotypes to work up into a new variety of rice which has both good yield and good quality, thus meeting the needs of both farmer and consumer alike.
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Affiliation(s)
- Mariafe Calingacion
- Grain Quality and Nutrition Centre, International Rice Research InstituteLaguna, Philippines.,Laboratory of Plant Physiology, Wageningen University and ResearchWageningen, Netherlands
| | - Roland Mumm
- Wageningen Plant Research, Wageningen University and ResearchWageningen, Netherlands.,Netherlands Metabolomics CentreLeiden, Netherlands
| | - Kevin Tan
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Lenie Quiatchon-Baeza
- Grain Quality and Nutrition Centre, International Rice Research InstituteLaguna, Philippines
| | - Jeanaflor C T Concepcion
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Jos A Hageman
- Biometris, Wageningen University and ResearchWageningen, Netherlands
| | - Sangeeta Prakash
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Melissa Fitzgerald
- Department of Food Science and Technology, School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Robert D Hall
- Laboratory of Plant Physiology, Wageningen University and ResearchWageningen, Netherlands.,Wageningen Plant Research, Wageningen University and ResearchWageningen, Netherlands.,Netherlands Metabolomics CentreLeiden, Netherlands
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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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46
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Dixit S, Yadaw RB, Mishra KK, Kumar A. Marker-assisted breeding to develop the drought-tolerant version of Sabitri, a popular variety from Nepal. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2017; 213:184. [PMID: 33364630 PMCID: PMC7734194 DOI: 10.1007/s10681-017-1976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/20/2017] [Indexed: 05/03/2023]
Abstract
Sabitri is a rice variety grown in a large part of the rainfed areas of Nepal. It was originally developed for irrigated condition; hence, this variety suffers high yield decline under drought. Two QTLs, qDTY3.2 and qDTY12.1 , with large effects on grain yield under drought were identified in the Sabitri background in separate QTL mapping studies. The present study reports the development of Sabitri near isogenic lines (NILs) with combinations of these two QTLs and their characterization under drought. To do so, marker-assisted backcross breeding (MABB) was combined with phenotypic selection to develop high-yielding drought-tolerant NILs with Sabitri grain type. Apart from this, drought-tolerant variants for grain type with high yield under non-stress were identified among the developed NILs. Early days to flowering of up to 13 days and reduction in plant height of up to 13 cm as compared to Sabitri were observed in the developed NILs. Some of these NILs showed higher yield compared to Sabitri and relatively higher tolerance to drought, indicating the capture of positive alleles and interactions during the course of selection. The developed NILs possessed high yield potential which make them suitable materials for the testing of water-saving technologies in irrigated areas. Based on their performance, these NILs can be deployed in rainfed areas in Nepal and other countries of South Asia to increase yield stability.
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Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ram Baran Yadaw
- Nepal Agricultural Research Council, National Rice Research Project, Hardinath, Nepal
| | - Krishna Kumar Mishra
- Nepal Agricultural Research Council, National Rice Research Project, Hardinath, Nepal
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- e-mail:
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47
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Gimhani DR, Gregorio GB, Kottearachchi NS, Samarasinghe WLG. SNP-based discovery of salinity-tolerant QTLs in a bi-parental population of rice (Oryza sativa). Mol Genet Genomics 2016; 291:2081-2099. [PMID: 27535768 DOI: 10.1007/s00438-016-1241-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 08/10/2016] [Indexed: 02/02/2023]
Abstract
Breeding for salt tolerance is the most promising approach to enhance the productivity of saline prone areas. However, polygenic inheritance of salt tolerance in rice acts as a bottleneck in conventional breeding for salt tolerance. Hence, we set our goals to construct a single nucleotide polymorphism (SNP)-based molecular map employing high-throughput SNP marker technology and to investigate salinity tolerant QTLs with closest flanking markers using an elite rice background. Seedling stage salinity responses were assessed in a population of 281 recombinant inbred lines (RILs) derived from the cross between At354 (salt tolerant) and Bg352 (salt susceptible), by 11 morpho-physiological indices under a hydroponic system. Selected extreme 94 RILs were genotyped using Illumina Infinium rice 6K SNP array and densely saturated molecular map spanning 1460.81 cM of the rice genome with an average interval of 1.29 cM between marker loci was constructed using 1135 polymorphic SNP markers. The results revealed 83 significant QTLs for 11 salt responsive traits explaining 12.5-46.7 % of phenotypic variation in respective traits. Of them, 72 QTLs responsible for 10 traits were co-localized together forming 14 QTL hotspots at 14 different genomic regions. The all QTL hotspots were flanked less than 1 Mb intervals and therefore the SNP loci associated with these QTL hotspots would be important in candidate gene discovery for salt tolerance.
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Affiliation(s)
- D R Gimhani
- Department of Biotechnology, Faculty of Agriculture and Plantation Management, Wayamba Univesity of Sri Lanka, Makandura, Gonawila (NWP), 60170, Sri Lanka.
| | - Glenn B Gregorio
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- East-West Seed Company (EWS), Km. 54 Cagayan Valley Road, Sampaloc, San Rafael, 3008, Bulacan, Philippines
| | - N S Kottearachchi
- Department of Biotechnology, Faculty of Agriculture and Plantation Management, Wayamba Univesity of Sri Lanka, Makandura, Gonawila (NWP), 60170, Sri Lanka
| | - W L G Samarasinghe
- Rice Research and Development Institute, Batalagoda, Ibbagamuwa, Sri Lanka
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Sandhu N, Raman KA, Torres RO, Audebert A, Dardou A, Kumar A, Henry A. Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions. PLANT PHYSIOLOGY 2016; 171:2562-76. [PMID: 27342311 PMCID: PMC4972292 DOI: 10.1104/pp.16.00705] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/21/2016] [Indexed: 05/02/2023]
Abstract
Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.
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Affiliation(s)
- Nitika Sandhu
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - K Anitha Raman
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Rolando O Torres
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Alain Audebert
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Audrey Dardou
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Arvind Kumar
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
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Vilayheuang K, Machida-Hirano R, Bounphanousay C, Watanabe KN. Genetic diversity and population structure of 'Khao Kai Noi', a Lao rice (Oryza sativa L.) landrace, revealed by microsatellite DNA markers. BREEDING SCIENCE 2016; 66:204-212. [PMID: 27162492 PMCID: PMC4784998 DOI: 10.1270/jsbbs.66.204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 11/03/2015] [Indexed: 06/05/2023]
Abstract
Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. 'Khao Kai Noi', a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of 'Khao Kai Noi' for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all 'Khao Kai Noi' accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population.
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Affiliation(s)
- Koukham Vilayheuang
- Graduate School of Life and Environmental Sciences, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
- Agriculture Research Center, National Agriculture and Forestry Research Institute (NAFRI),
Vientiane,
Lao P.D.R
| | - Ryoko Machida-Hirano
- Gene Research Center, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
| | - Chay Bounphanousay
- Agriculture Research Center, National Agriculture and Forestry Research Institute (NAFRI),
Vientiane,
Lao P.D.R
| | - Kazuo N. Watanabe
- Gene Research Center, University of Tsukuba,
Tennodai 1-1-1, Tsukuba, Ibaraki 305-8572,
Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba,
Tsukuba, Ibaraki 305-8572,
Japan
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Henry A, Swamy BPM, Dixit S, Torres RD, Batoto TC, Manalili M, Anantha MS, Mandal NP, Kumar A. Physiological mechanisms contributing to the QTL-combination effects on improved performance of IR64 rice NILs under drought. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1787-99. [PMID: 25680791 PMCID: PMC4378621 DOI: 10.1093/jxb/eru506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 05/04/2023]
Abstract
Characterizing the physiological mechanisms behind major-effect drought-yield quantitative trait loci (QTLs) can provide an understanding of the function of the QTLs-as well as plant responses to drought in general. In this study, we characterized rice (Oryza sativa L.) genotypes with QTLs derived from drought-tolerant traditional variety AdaySel that were introgressed into drought-susceptible high-yielding variety IR64, one of the most popular megavarieties in South Asian rainfed lowland systems. Of the different combinations of the four QTLs evaluated, genotypes with two QTLs (qDTY 2.2 + qDTY 4.1 ) showed the greatest degree of improvement under drought compared with IR64 in terms of yield, canopy temperature, and normalized difference vegetation index (NDVI). Furthermore, qDTY 2.2 and qDTY 4.1 showed a potential for complementarity in that they were each most effective under different severities of drought stress. Multiple drought-response mechanisms were observed to be conferred in the genotypes with the two-QTL combination: higher root hydraulic conductivity and in some cases greater root growth at depth. As evidenced by multiple leaf water status and plant growth indicators, these traits affected transpiration but not transpiration efficiency or harvest index. The results from this study highlight the complex interactions among major-effect drought-yield QTLs and the drought-response traits they confer, and the need to evaluate the optimal combinations of QTLs that complement each other when present in a common genetic background.
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Affiliation(s)
- Amelia Henry
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | | | - Shalabh Dixit
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Rolando D Torres
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Tristram C Batoto
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Mervin Manalili
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - M S Anantha
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand 825 301, India
| | - N P Mandal
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand 825 301, India
| | - Arvind Kumar
- Central Rainfed Upland Rice Research Station, Hazaribag, Jharkand 825 301, India
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