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Singh S, Praveen A, Dudha N, Bhadrecha P. Integrating physiological and multi-omics methods to elucidate heat stress tolerance for sustainable rice production. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1185-1208. [PMID: 39100874 PMCID: PMC11291831 DOI: 10.1007/s12298-024-01480-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 08/06/2024]
Abstract
Heat stress presents unique challenges compared to other environmental stressors, as predicting crop responses and understanding the mechanisms for heat tolerance are complex tasks. The escalating impact of devastating climate changes heightens the frequency and intensity of heat stresses, posing a noteworthy threat to global agricultural productivity, especially in rice-dependent regions of the developing world. Humidity has been demonstrated to negatively affect rice yields worldwide. Plants have evolved intricate biochemical adaptations, involving intricate interactions among genes, proteins, and metabolites, to counter diverse external signals and ensure their survival. Modern-omics technologies, encompassing transcriptomics, metabolomics, and proteomics, have revolutionized our comprehension of the intricate biochemical and cellular shifts that occur in stressed agricultural plants. Integrating these multi-omics approaches offers a comprehensive view of cellular responses to heat stress and other challenges, surpassing the insights gained from multi-omics analyses. This integration becomes vital in developing heat-tolerant crop varieties, which is crucial in the face of increasingly unpredictable weather patterns. To expedite the development of heat-resistant rice varieties, aiming at sustainability in terms of food production and food security globally, this review consolidates the latest peer-reviewed research highlighting the application of multi-omics strategies.
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Affiliation(s)
- Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, U.P. 203201 India
| | - Afsana Praveen
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Namrata Dudha
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, U.P. 203201 India
| | - Pooja Bhadrecha
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab India
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Ramalingam AP, Mohanavel W, Kambale R, Rajagopalan VR, Marla SR, Prasad PVV, Muthurajan R, Perumal R. Pilot-scale genome-wide association mapping in diverse sorghum germplasms identified novel genetic loci linked to major agronomic, root and stomatal traits. Sci Rep 2023; 13:21917. [PMID: 38081914 PMCID: PMC10713643 DOI: 10.1038/s41598-023-48758-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
This genome-wide association studies (GWAS) used a subset of 96 diverse sorghum accessions, constructed from a large collection of 219 accessions for mining novel genetic loci linked to major agronomic, root morphological and physiological traits. The subset yielded 43,452 high quality single nucleotide polymorphic (SNP) markers exhibiting high allelic diversity. Population stratification showed distinct separation between caudatum and durra races. Linkage disequilibrium (LD) decay was rapidly declining with increasing physical distance across all chromosomes. The initial 50% LD decay was ~ 5 Kb and background level was within ~ 80 Kb. This study detected 42 significant quantitative trait nucleotide (QTNs) for different traits evaluated using FarmCPU, SUPER and 3VmrMLM which were in proximity with candidate genes related and were co-localized in already reported quantitative trait loci (QTL) and phenotypic variance (R2) of these QTNs ranged from 3 to 20%. Haplotype validation of the candidate genes from this study resulted nine genes showing significant phenotypic difference between different haplotypes. Three novel candidate genes associated with agronomic traits were validated including Sobic.001G499000, a potassium channel tetramerization domain protein for plant height, Sobic.010G186600, a nucleoporin-related gene for dry biomass, and Sobic.002G022600 encoding AP2-like ethylene-responsive transcription factor for plant yield. Several other candidate genes were validated and associated with different root and physiological traits including Sobic.005G104100, peroxidase 13-related gene with root length, Sobic.010G043300, homologous to Traes_5BL_8D494D60C, encoding inhibitor of apoptosis with iWUE, and Sobic.010G125500, encoding zinc finger, C3HC4 type domain with Abaxial stomatal density. In this study, 3VmrMLM was more powerful than FarmCPU and SUPER for detecting QTNs and having more breeding value indicating its reliable output for validation. This study justified that the constructed subset of diverse sorghums can be used as a panel for mapping other key traits to accelerate molecular breeding in sorghum.
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Affiliation(s)
- Ajay Prasanth Ramalingam
- Tamil Nadu Agricultural University, Coimbatore, India
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - Rohit Kambale
- Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Sandeep R Marla
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - P V Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, USA.
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Sinha D, Maurya AK, Abdi G, Majeed M, Agarwal R, Mukherjee R, Ganguly S, Aziz R, Bhatia M, Majgaonkar A, Seal S, Das M, Banerjee S, Chowdhury S, Adeyemi SB, Chen JT. Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals. Genes (Basel) 2023; 14:1484. [PMID: 37510388 PMCID: PMC10380062 DOI: 10.3390/genes14071484] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in environmental pollution such as water pollution and soil degradation as well as alterations in the composition and concentration of environmental gases. These changes are affecting not only biodiversity loss but also affecting the physio-biochemical processes of crop plants, resulting in a stress-induced decline in crop yield. To overcome such problems and ensure the supply of food material, consistent efforts are being made to develop strategies and techniques to increase crop yield and to enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication and initially remained dependent on phenotype-based selection for crop improvement. But it has grown through cytological and biochemical methods, and the newer contemporary methods are based on DNA-marker-based strategies that help in the selection of agronomically useful traits. These are now supported by high-end molecular biology tools like PCR, high-throughput genotyping and phenotyping, data from crop morpho-physiology, statistical tools, bioinformatics, and machine learning. After establishing its worth in animal breeding, genomic selection (GS), an improved variant of marker-assisted selection (MAS), has made its way into crop-breeding programs as a powerful selection tool. To develop novel breeding programs as well as innovative marker-based models for genetic evaluation, GS makes use of molecular genetic markers. GS can amend complex traits like yield as well as shorten the breeding period, making it advantageous over pedigree breeding and marker-assisted selection (MAS). It reduces the time and resources that are required for plant breeding while allowing for an increased genetic gain of complex attributes. It has been taken to new heights by integrating innovative and advanced technologies such as speed breeding, machine learning, and environmental/weather data to further harness the GS potential, an approach known as integrated genomic selection (IGS). This review highlights the IGS strategies, procedures, integrated approaches, and associated emerging issues, with a special emphasis on cereal crops. In this domain, efforts have been taken to highlight the potential of this cutting-edge innovation to develop climate-smart crops that can endure abiotic stresses with the motive of keeping production and quality at par with the global food demand.
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Affiliation(s)
- Dwaipayan Sinha
- Department of Botany, Government General Degree College, Mohanpur 721436, India
| | - Arun Kumar Maurya
- Department of Botany, Multanimal Modi College, Modinagar, Ghaziabad 201204, India
| | - Gholamreza Abdi
- Department of Biotechnology, Persian Gulf Research Institute, Persian Gulf University, Bushehr 75169, Iran
| | - Muhammad Majeed
- Department of Botany, University of Gujrat, Punjab 50700, Pakistan
| | - Rachna Agarwal
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Rashmi Mukherjee
- Research Center for Natural and Applied Sciences, Department of Botany (UG & PG), Raja Narendralal Khan Women's College, Gope Palace, Midnapur 721102, India
| | - Sharmistha Ganguly
- Department of Dravyaguna, Institute of Post Graduate Ayurvedic Education and Research, Kolkata 700009, India
| | - Robina Aziz
- Department of Botany, Government, College Women University, Sialkot 51310, Pakistan
| | - Manika Bhatia
- TERI School of Advanced Studies, New Delhi 110070, India
| | - Aqsa Majgaonkar
- Department of Botany, St. Xavier's College (Autonomous), Mumbai 400001, India
| | - Sanchita Seal
- Department of Botany, Polba Mahavidyalaya, Polba 712148, India
| | - Moumita Das
- V. Sivaram Research Foundation, Bangalore 560040, India
| | - Swastika Banerjee
- Department of Botany, Kairali College of +3 Science, Champua, Keonjhar 758041, India
| | - Shahana Chowdhury
- Department of Biotechnology, Faculty of Engineering Sciences, German University Bangladesh, TNT Road, Telipara, Chandona Chowrasta, Gazipur 1702, Bangladesh
| | - Sherif Babatunde Adeyemi
- Ethnobotany/Phytomedicine Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin P.M.B 1515, Nigeria
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
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El-aty MSA, Abo-youssef MI, Bahgt MM. Genetic diversity Analysis using molecular markers of some rice varieties for Physiological, biochemical and yield Traits under water deficit condition.. [DOI: 10.21203/rs.3.rs-3111398/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Abstract
Rice is a major staple food crop all over the world. Recent climate change trends forecast an increase in drought severity, necessitating the creation of novel drought-tolerant rice cultivars in order to continue rice production in this ecosystem. This study was carried out at the experimental farm of the rice research and training center (RRTC) using the randomized complete block design (RCBD) to assess the impact of water scarcity on eight rice varieties by identifying differences in physiological and biochemical responses among drought-sensitive and resistant rice varieties, in addition applying two PCR-based molecular marker systems ISSR and SCoT to assess the genetic diversity among the studied rice varieties. The results revealed that, Water shortage stress significantly reduced relative water content, total chlorophyll content, grain yield, and yield characteristics. while, it significantly raised proline content and antioxidant enzyme activity (CAT, APX, and SOD). The combined analysis of variance demonstrated that the mean squares for environments, varieties, and their interaction were highly significant for all investigated traits, suggesting that the germplasm used in the study had significant genetic diversity from one environment (normal irrigation) to another (water deficit) and could rank differently in both of them. Mean performance data showed that, Puebla and Hispagran varieties were selected as the most favourable varieties for most physiological and biochemical parameters studied, as well as yield traits which recorded the highest desirable values under both irrigation treatments. They were recommended for use in rice hybrid breeding programmes for water scarcity tolerance. Genetic Similarity and Cluster Analysis revealed that, the both molecular markers exhibited comparable genetic diversity values but a higher level of polymorphism was represented by ISSR. This indicates the high efficiency of both markers in discriminating the tested varieties. The dendrogram generated by ISSR and SCoT markers combined data divided the varieties into two major clusters. Cluster I consisted of the genotype Sakha 106. Cluster II retained seven varieties, which were further divided into two sub-clusters; Sakha 101, Sakha 105, Sakha 106, Sakha 107 constituted the first subgroup, while Giza 177, Hispagran, and Puebla formed the second one.
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Gu Q, Kang J, Gao S, Zhao Y, Yi H, Zha X. Eukaryotic Translation Elongation Factor OsEF1A Positively Regulates Drought Tolerance and Yield in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:2593. [PMID: 37514208 PMCID: PMC10383209 DOI: 10.3390/plants12142593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/26/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023]
Abstract
Drought is one of the most serious stresses affecting rice growth. Drought stress causes accelerated senescence, reduced fertility, and subsequent reductions in crop yield. Eukaryotic translation elongation factor EF1A is an important multifunctional protein that plays an essential role in the translation of eukaryotic proteins. In this study, we localized and cloned the OsEF1A gene in rice (Oryza sativa) in order to clarify its role in drought tolerance and yield. Subcellular localization revealed that it was mainly localized to the cell membrane, cytoskeleton and nucleus. Compared with the wild-type, OsEF1A overexpressing transgenic plants had significantly more tillers and grains per plant, resulting in a significantly higher yield. Increases in the relative water content and proline content were also observed in the transgenic seedlings under drought stress, with a decrease in the malondialdehyde content, all of which are representative of drought tolerance. Taken together, these findings suggest that OsEF1A plays a positive regulatory role in rice nutritional development under drought stress. These findings will help support future studies aimed at improving yield and stress tolerance in rice at the molecular level, paving the way for a new green revolution.
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Affiliation(s)
- Qing Gu
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Junfang Kang
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Shuang Gao
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Yarui Zhao
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Huan Yi
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Xiaojun Zha
- College of Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
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Muthuramalingam P, Jeyasri R, Rakkammal K, Satish L, Shamili S, Karthikeyan A, Valliammai A, Priya A, Selvaraj A, Gowri P, Wu QS, Karutha Pandian S, Shin H, Chen JT, Baskar V, Thiruvengadam M, Akilan M, Ramesh M. Multi-Omics and Integrative Approach towards Understanding Salinity Tolerance in Rice: A Review. BIOLOGY 2022; 11:biology11071022. [PMID: 36101403 PMCID: PMC9312129 DOI: 10.3390/biology11071022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Rice (Oryza sativa L.) plants are simultaneously encountered by environmental stressors, most importantly salinity stress. Salinity is the major hurdle that can negatively impact growth and crop yield. Understanding the salt stress and its associated complex trait mechanisms for enhancing salt tolerance in rice plants would ensure future food security. The main aim of this review is to provide insights and impacts of molecular-physiological responses, biochemical alterations, and plant hormonal signal transduction pathways in rice under saline stress. Furthermore, the review highlights the emerging breakthrough in multi-omics and computational biology in identifying the saline stress-responsive candidate genes and transcription factors (TFs). In addition, the review also summarizes the biotechnological tools, genetic engineering, breeding, and agricultural practicing factors that can be implemented to realize the bottlenecks and opportunities to enhance salt tolerance and develop salinity tolerant rice varieties. Future studies pinpointed the augmentation of powerful tools to dissect the salinity stress-related novel players, reveal in-depth mechanisms and ways to incorporate the available literature, and recent advancements to throw more light on salinity responsive transduction pathways in plants. Particularly, this review unravels the whole picture of salinity stress tolerance in rice by expanding knowledge that focuses on molecular aspects.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Korea
| | - Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Lakkakula Satish
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Sasanala Shamili
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Adhimoolam Karthikeyan
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Korea;
| | - Alaguvel Valliammai
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Arumugam Priya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Anthonymuthu Selvaraj
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Pandiyan Gowri
- Department of Botany, Science Campus, Alagappa University, Karaikudi 630 003, India;
| | - Qiang-Sheng Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China;
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic
| | - Shunmugiah Karutha Pandian
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
| | - Hyunsuk Shin
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea
- Department of GreenBio Science, Gyeongsang National University, Jinju 52725, Korea
- Correspondence: (H.S.); (M.T.); (M.R.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan;
| | - Venkidasamy Baskar
- Department of Oral and Maxillofaciel Surgery, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai 602 105, India;
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Korea
- Correspondence: (H.S.); (M.T.); (M.R.)
| | - Manoharan Akilan
- Department of Plant Breeding and Genetics, Anbil Dharmalingam Agricultural College and Research Institute, Tamil Nadu Agricultural University, Trichy 620 027, India;
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 003, India; (P.M.); (R.J.); (K.R.); (A.V.); (A.P.); (A.S.); (S.K.P.)
- Correspondence: (H.S.); (M.T.); (M.R.)
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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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Kaur H, Kohli SK, Khanna K, Bhardwaj R. Scrutinizing the impact of water deficit in plants: Transcriptional regulation, signaling, photosynthetic efficacy, and management. PHYSIOLOGIA PLANTARUM 2021; 172:935-962. [PMID: 33686690 DOI: 10.1111/ppl.13389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
Suboptimal availability of water limits plant growth, development, and performance. Drought is one of the leading factors responsible for worldwide crop yield reduction. In the future, owing to climate changes, more agricultural land will be affected by prolonged periods of water deficit. Thus, understanding the fundamental mechanism of drought response is a major scientific concern for improvement of crop production. To combat drought stress, plants deploy varied mechanistic strategies and alter their morphological, physiochemical, and molecular attributes. This helps plant to enhance water uptake and storage, reduce water loss and avoid wilting. Induction of several transcription factors and drought responsive genes leads to synthesis of stress proteins, regulation of water channels i.e. aquaporins and production of osmolytes that are essential for maintenance of osmotic balance at the cellular level. Self- and hormone-regulated signaling pathways are often stimulated by plants after receiving drought stress signals via secondary messengers, mitogen-activated protein kinases, and stress hormones. These signaling cascades often leads to stomatal closure and reduction in transpiration rates. Reduced carbon dioxide diffusion in chloroplast, lowered efficacy of photosystems, and other metabolic constraints limits the key regulatory photosynthetic process during water deficit. The impact of these stomatal and nonstomatal limitations varies with stress intensity, superimposed stresses and plant species. A clear understanding of the drought resistance process is thus important before adopting strategies for imparting drought tolerance in plants. These management practices at present include exogenous hormone application, breeding, and genetic engineering techniques for combating the water deficit issues.
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Affiliation(s)
- Harsimran Kaur
- PG Department of Agriculture, Plant Protection Division, Khalsa College, Amritsar, Punjab, India
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sukhmeen Kaur Kohli
- PG Department of Agriculture, Plant Protection Division, Khalsa College, Amritsar, Punjab, India
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
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Dowd T, McInturf S, Li M, Topp CN. Rated-M for mesocosm: allowing the multimodal analysis of mature root systems in 3D. Emerg Top Life Sci 2021; 5:249-260. [PMID: 33555320 PMCID: PMC8166344 DOI: 10.1042/etls20200278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 11/17/2022]
Abstract
A plants' water and nutrients are primarily absorbed through roots, which in a natural setting is highly dependent on the 3-dimensional configuration of the root system, collectively known as root system architecture (RSA). RSA is difficult to study due to a variety of factors, accordingly, an arsenal of methods have been developed to address the challenges of both growing root systems for imaging, and the imaging methods themselves, although there is no 'best' method as each has its own spectrum of trade-offs. Here, we describe several methods for plant growth or imaging. Then, we introduce the adaptation and integration of three complementary methods, root mesocosms, photogrammetry, and electrical resistance tomography (ERT). Mesocosms can allow for unconstrained root growth, excavation and preservation of 3-dimensional RSA, and modularity that facilitates the use of a variety of sensors. The recovered root system can be digitally reconstructed through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. Lastly, we demonstrate how 3-dimensional water availability can be measured using ERT inside of root mesocosms.
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Affiliation(s)
- Tyler Dowd
- Topp Lab, Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO, 63124 U.S.A
| | - Samuel McInturf
- Topp Lab, Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO, 63124 U.S.A
| | - Mao Li
- Topp Lab, Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO, 63124 U.S.A
| | - Christopher N Topp
- Topp Lab, Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, MO, 63124 U.S.A
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Singh BK, Ramkumar MK, Dalal M, Singh A, Solanke AU, Singh NK, Sevanthi AM. Allele mining for a drought responsive gene DRO1 determining root growth angle in donors of drought tolerance in rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:523-534. [PMID: 33854281 PMCID: PMC7981370 DOI: 10.1007/s12298-021-00950-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/05/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Deeper Rooting 1 (DRO1) gene identified from a major QTL on chromosome 9 increases the root growth angle (RGA) and thus facilitates survival under drought and hence is an excellent candidate for rice improvement. Twenty-four major Indian upland and lowland genotypes including the 'yield under drought' (DTY) QTL donors were subjected to allele mining of DRO1 (3058 bp) using four pairs of overlapping primers. A total of 216 and 52 SNPs were identified across all genotypes in the gene and coding region (756 bp) respectively with transversions 3.6 fold more common than transitions in the gene and 2.5 times in the CDS. In 251 amino acid long protein, substitutions were found in 19 positions, wherein change in position 92 was the most frequent. Based on allele mining, the 24 genotypes can be classified into 16 primary structure variants ranging from complete functional allele (Satti, IR36 and DTY 3.1 donor, IR81896-B-B-195) to truncated non-functional alleles in PMK2, IR64, IR20 and Swarna. All the DTY donors, other than IR81896-B-B-195, and most of the upland drought tolerant cultivars (Nagina 22, Vandana and Dhagaddeshi) had accumulated 6-19 SNPs and 4-8 amino acid substitutions resulting in substantial differences in their protein structure. The expression analysis revealed that all the genotypes showed upregulation under drought stress though the degree of upregulation varied among genotypes. The information on structural variations in DRO1 gene will be very useful for the breeders, especially in the light of recent breeding programmes on improving drought tolerance using several DTY donors and upland accessions. SUPPLEMENTARY INFORMATION The online version of this article (10.1007/s12298-021-00950-2).
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Affiliation(s)
- Bablee Kumari Singh
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - M. K. Ramkumar
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Monika Dalal
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Archana Singh
- Division of Biochemistry, Indian Agricultural Research Institute, Pusa campus, New Delhi, India
| | - Amolkumar U. Solanke
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Nagendra K. Singh
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
| | - Amitha Mithra Sevanthi
- Indian Council of Agricultural Research- National Institute for Plant Biotechnology, Pusa campus, New Delhi, India
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11
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Incorporating Drought and Submergence Tolerance QTL in Rice ( Oryza sativa L.)-The Effects under Reproductive Stage Drought and Vegetative Stage Submergence Stresses. PLANTS 2021; 10:plants10020225. [PMID: 33498963 PMCID: PMC7912027 DOI: 10.3390/plants10020225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = quantitative trait loci) viz. qDTY3.1 and qDTY12.1 using marker-assisted breeding. We report here the effect of different combinations of Sub1 and qDTY on morpho-physiological, agronomical traits and yield under reproductive stage drought stress (RS) and non-stress (NS) conditions. Lines with outstanding performance in RS and NS trials were also evaluated in vegetative stage submergence stress (VS) trial to assess the tolerance level. The QTL class analysis revealed Sub1 + qDTY3.1 as the best QTL combination affecting the measured traits in RS trial followed by Sub1 + qDTY12.1. The effects of single Sub1, qDTY3.1 and qDTY12.1 were not as superior as when the QTLs are combined, suggesting the positive interaction of Sub1 and qDTY. Best performing lines selected from the RS and NS trials recorded yield advantage up to 4453.69 kg ha−1 and 6954 kg ha−1 over the parents, respectively. The lines were also found having great tolerance to submergence ranging from 80% to 100%, contributed by a lower percentage of shoot elongation and reduction of chlorophyll content after 14 days of VS. These lines could provide yield sustainability to farmers in regions impacted with drought and submergence while serving as important genetic materials for future breeding programs.
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12
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Zhou X, Chen Y, Zhao Y, Gao F, Liu H. The application of exogenous PopW increases the tolerance of Solanum lycopersicum L. to drought stress through multiple mechanisms. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2521-2535. [PMID: 33424162 PMCID: PMC7772130 DOI: 10.1007/s12298-020-00918-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 05/25/2023]
Abstract
Tomato is a major cultivated vegetable species of great economic importance throughout the world, but its fruit yield is severely impaired by drought stress. PopW, a harpin protein from Ralstonia solanacearum ZJ3721, plays vital roles in various plant defence responses and growth. In this study, we observed that the foliar application of PopW increased tomato drought tolerance. Our results showed that compared with water-treated plants, PopW-treated plants presented a significantly higher recovery rate and leaf relative water content under drought-stress conditions. PopW decreased the malondialdehyde content and relative electrical conductivity by 40.2% and 21%, respectively. Drought disrupts redox homeostasis through the excessive accumulation of reactive oxygen species (ROS). PopW-treated plants displayed an obvious reduction in ROS accumulation due to enhanced activities of the antioxidant enzyme catalase, superoxide dismutase and peroxidase. Moreover, PopW promoted early stomatal closure, thereby minimizing the water loss rate of plants under drought stress. Further investigation revealed that endogenous abscisic acid (ABA) levels and the transcript levels of drought-responsive genes involved in ABA signal transduction pathways increased in response to PopW. These results confirm that PopW increases drought tolerance through multiple mechanisms involving an enhanced water-retention capacity, balanced redox homeostasis, increased osmotic adjustment, reduced membrane damage and decreased stomatal aperture, suggesting that the application of exogenous PopW may be a potential method to enhance tomato drought tolerance.
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Affiliation(s)
- Xiaosi Zhou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, People’s Republic of China
| | - Yu Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, People’s Republic of China
| | - Yangyang Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 People’s Republic of China
| | - Fangyuan Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, People’s Republic of China
| | - Hongxia Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, People’s Republic of China
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13
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Muthu V, Abbai R, Nallathambi J, Rahman H, Ramasamy S, Kambale R, Thulasinathan T, Ayyenar B, Muthurajan R. Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding. PLoS One 2020; 15:e0227421. [PMID: 31910435 PMCID: PMC6946594 DOI: 10.1371/journal.pone.0227421] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/18/2019] [Indexed: 01/13/2023] Open
Abstract
Increases in rice productivity are significantly hampered because of the increase in the occurrence of abiotic stresses, including drought, salinity, and submergence. Developing a rice variety with inherent tolerance against these major abiotic stresses will help achieve a sustained increase in rice production under unfavorable conditions. The present study was conducted to develop abiotic stress-tolerant rice genotypes in the genetic background of the popular rice variety Improved White Ponni (IWP) by introgressing major effect quantitative trait loci (QTLs) conferring tolerance against drought (qDTY1.1, qDTY2.1), salinity (Saltol), and submergence (Sub1) through a marker assisted backcross breeding approach. Genotyping of early generation backcrossed inbred lines (BILs) resulted in the identification of three progenies, 3-11-9-2, 3-11-11-1, and 3-11-11-2, possessing all four target QTLs and maximum recovery of the recurrent parent genome (88.46%). BILs exhibited consistent agronomic and grain quality characters compared to those of IWP and enhanced performance against dehydration, salinity, and submergence stress compared with the recurrent parent IWP. BILs exhibited enhanced tolerance against salinity during germination and increased shoot length, root length, and vigor index compared to those of IWP. All three BILs exhibited reduced symptoms of injury because of salinity (NaCl) and dehydration (PEG) than did IWP. At 12 days of submergence stress, BILs exhibited enhanced survival and greater recovery, whereas IWP failed completely. BILs were found to exhibit on par grain and cooking quality characteristics with their parents. Results of this study clearly demonstrated the effects of the target QTLs in reducing damage caused by drought, salinity, and submergence and lead to the development of a triple stress tolerant version of IWP.
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Affiliation(s)
- Valarmathi Muthu
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Ragavendran Abbai
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Hifzur Rahman
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Sasikala Ramasamy
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Rohit Kambale
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Thiyagarajan Thulasinathan
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Bharathi Ayyenar
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology Tamil Nadu Agricultural University, Coimbatore, India
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14
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Sharma E, Jain M, Khurana JP. Differential quantitative regulation of specific gene groups and pathways under drought stress in rice. Genomics 2019; 111:1699-1712. [DOI: 10.1016/j.ygeno.2018.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 11/21/2018] [Indexed: 10/27/2022]
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15
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Mohd Ikmal A, Nurasyikin Z, Tuan Nur Aqlili Riana TA, Puteri Dinie Ellina Z, Wickneswari R, Noraziyah AAS. Drought Yield QTL ( qDTY) with Consistent Effects on Morphological and Agronomical Traits of Two Populations of New Rice ( Oryza sativa) Lines. PLANTS (BASEL, SWITZERLAND) 2019; 8:E186. [PMID: 31238548 PMCID: PMC6630983 DOI: 10.3390/plants8060186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/03/2022]
Abstract
Drought has been a major limiting factor for rice production. Drought yield QTLs (qDTYs; QTLs = quantitative trait loci) were pyramided into MRQ74 and MR219 to produce drought tolerant lines. In this study, new drought tolerant MRQ74 and MR219 pyramided lines (PLs) were evaluated under drought stress (RS) and non-stress (NS) conditions to evaluate the effects of different qDTYs combinations on morphological and agronomical traits. MRQ74 PLs having qDTY12.1 possessed the best root length (RL) under both RS and NS but the effect was only significant for MR219 PLs under RS. Some qDTYs combinations also found to have consistent effect on the same trait of both populations. PLs with only qDTY12.1 showed the highest grain yield (GY) under RS in both populations which means qDTY12.1 controlled RL and caused higher GY under drought condition. The interaction of major-effect qDTY12.1 with qDTY2.2 also shows significant effect on leaf rolling (LR) of both PL populations. These qDTYs proved to be beneficial in improving traits related to drought tolerance. Selected PLs with qDTY12.1 combinations also found to have better RL and root weight (RW) under RS. Improvement of morphological and agronomical traits led to higher GY of PLs. Therefore, qDTY12.1 either is present singly or in combination with other qDTYs was the best qDTY due to its consistent effect on morphological and agronomical traits and GY across populations under RS and NS.
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Affiliation(s)
- Asmuni Mohd Ikmal
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
| | - Zainuddin Nurasyikin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
| | | | | | - Ratnam Wickneswari
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
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16
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Barnaby JY, Rohila JS, Henry CG, Sicher RC, Reddy VR, McClung AM. Physiological and Metabolic Responses of Rice to Reduced Soil Moisture: Relationship of Water Stress Tolerance and Grain Production. Int J Mol Sci 2019; 20:ijms20081846. [PMID: 30991628 PMCID: PMC6514846 DOI: 10.3390/ijms20081846] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 12/17/2022] Open
Abstract
Access to adequate irrigation resources is critical for sustained agricultural production, and rice, a staple cereal grain for half of the world population, is one of the biggest users of irrigation. To reduce water use, several water saving irrigation systems have been developed for rice production, but a reliable system to evaluate cultivars for water stress tolerance is still lacking. Here, seven rice cultivars that have diverse yield potential under water stress were evaluated in a field study using four continuous irrigation regimes varying from saturation to wilting point. To understand the relationship between water stress and yield potential, the physiological and leaf metabolic responses were investigated at the critical transition between vegetative and reproductive growth stages. Twenty-nine metabolite markers including carbohydrates, amino acids and organic acids were found to significantly differ among the seven cultivars in response to increasing water stress levels with amino acids increasing but organic acids and carbohydrates showing mixed responses. Overall, our data suggest that, in response to increasing water stress, rice cultivars that do not show a significant yield loss accumulate carbohydrates (fructose, glucose, and myo-inositol), and this is associated with a moderate reduction in stomatal conductance (gs), particularly under milder stress conditions. In contrast, cultivars that had significant yield loss due to water stress had the greatest reduction in gs, relatively lower accumulation of carbohydrates, and relatively high increases in relative chlorophyll content (SPAD) and leaf temperature (Tm). These data demonstrate the existence of genetic variation in yield under different water stress levels which results from a suite of physiological and biochemical responses to water stress. Our study, therefore, suggests that in rice there are different physiological and metabolic strategies that result in tolerance to water stress that should be considered in developing new cultivars for deficit irrigation production systems that use less water.
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Affiliation(s)
- Jinyoung Y Barnaby
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
| | - Jai S Rohila
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
| | - Chris G Henry
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Richard C Sicher
- USDA-ARS Adaptive Cropping Systems Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705, USA.
| | - Vagimalla R Reddy
- USDA-ARS Adaptive Cropping Systems Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Beltsville, MD 20705, USA.
| | - Anna M McClung
- USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA.
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17
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Sengupta D, Kariyat D, Marriboina S, Reddy AR. Pod-wall proteomics provide novel insights into soybean seed-filling process under chemical-induced terminal drought stress. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2481-2493. [PMID: 30370933 DOI: 10.1002/jsfa.9457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/25/2018] [Accepted: 10/25/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Drought is very detrimental when it occurs during the reproductive phase of soybeans, leading to considerable yield loss due to the disproportionate allocation of photo-assimilates to competing sinks. As pod walls are known to play a crucial role in regulating carbon partitioning during seed filling under stress conditions, the present study aims to analyze the stage-specific carbon allocation pattern during potassium iodide (KI)-simulated terminal drought, and to provide an insight into the pod-wall proteome responses during drought onset. RESULTS A comparative proteomics approach was adopted to visualize the differential protein expression in soybean pod-wall at stage R5 (seed initiation). Sugar status was analyzed using high-performance liquid chromatography (HPLC) and biochemical methods. Potassium iodide-simulated terminal drought during reproductive stages 4, 5 and 6 (R4, R5, and R6) caused a significant decline in starch, total carbohydrate, and reducing sugar in the leaves; however, the pod-wall and seeds showed a reduction only in the total carbohydrate content, whereas starch and reducing sugar levels remained unchanged. A pod-wall proteome at stage R5 showed immediate induction of proteins belonging to stress signaling / regulation, protein folding / stabilization, redox-homeostasis, cellular energy, and carbon utilization and down-regulation of negative regulators of drought stress and protein degradation-related proteins. CONCLUSIONS A KI spray effectively simulated terminal drought stress and caused around 50% yield loss when compared to controls. Our results indicate that, at the very onset of desiccation stress, the pod wall (stage R5) activates strong protective responses to maintain the carbon allocation to the surviving seeds. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Hyderabad, India
| | - Divya Kariyat
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Hyderabad, India
| | - Sureshbabu Marriboina
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Hyderabad, India
| | - Attipalli R Reddy
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. CR Rao Road, Hyderabad, India
- Yogi Vemana University, Kadapa, Andhra Pradesh, India
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18
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Okporie E, Onyishi G, Utobo E, Ekwu L, Swaray S, Jalloh M. Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1584054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Yussuf Oladosu
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emmanuel Okporie
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Godwin Onyishi
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emeka Utobo
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Lynda Ekwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Senesie Swaray
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Momodu Jalloh
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
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Abreu FRM, Dedicova B, Vianello RP, Lanna AC, de Oliveira JAV, Vieira AF, Morais OP, Mendonça JA, Brondani C. Overexpression of a phospholipase (OsPLDα1) for drought tolerance in upland rice (Oryza sativa L.). PROTOPLASMA 2018; 255:1751-1761. [PMID: 29846801 DOI: 10.1007/s00709-018-1265-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
This work aimed to evaluate the drought tolerance of transformed plants of the cultivar BRSMG Curinga that overexpress the rice phospholipase D α1 (OsPLDα1) gene. The productivity of independent transformation event plants of the OsPLDα1 gene was evaluated in an experiment where 19 days of water deficit were applied at the reproductive stage, a very strict growing condition for upland rice. The non-genetically modified cultivar (NGM) under drought treatment reduced productivity by 89% compared with that under irrigated treatment, whereas transformed plants (PLDα1_E2) reduced productivity by only 41%. After the drought treatment, the PLDα1_E2 plants productivity was five times greater than that of the NGM plant. Moreover, no adverse effects on growth and development of the transgenic plants were observed. Seven days after the resumption of irrigation, PLDα1_E2 plants had higher stomatal conductance, greater photosynthetic rate, and transpiration rate than did NGM plants, as well as a higher expression level of the OsPLDα1 gene. A delay in the senescence process was observed in these PLDα1_E2 plants, and this was determined for the recovery of photosynthesis, with greater expression of the Rubisco and lower expression of the SOD. This finding was suggestive of decreased oxidative stress, probably due to gas exchange by the partial closure of the stomata of these transformed plants, which prevented the formation of reactive oxygen species. OsPLDα1 gene overexpression resulted in a reduction in production loss under severe water deficit and revealed a possibility for the development of upland rice cultivars that are more tolerant to extreme drought conditions.
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Affiliation(s)
| | - Beata Dedicova
- International Center for Tropical Agriculture A.A. 6713, Cali, Colombia
| | | | - Anna Cristina Lanna
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil
| | | | - Ariadna Faria Vieira
- Escola de Agronomia, Universidade Federal de Goiás, Santo Antônio de Goiás, Goiás, Brazil
| | - Odilon Peixoto Morais
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil
| | - João Antônio Mendonça
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil
| | - Claudio Brondani
- Embrapa Arroz e Feijão, Rodovia GO-462, Km 12, Santo Antônio de Goiás, Goiás, Brazil.
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20
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Sahebi M, Hanafi MM, Rafii MY, Mahmud TMM, Azizi P, Osman M, Abiri R, Taheri S, Kalhori N, Shabanimofrad M, Miah G, Atabaki N. Improvement of Drought Tolerance in Rice ( Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3158474. [PMID: 30175125 PMCID: PMC6106855 DOI: 10.1155/2018/3158474] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/14/2018] [Accepted: 07/05/2018] [Indexed: 11/17/2022]
Abstract
Drought tolerance is an important quantitative trait with multipart phenotypes that are often further complicated by plant phenology. Different types of environmental stresses, such as high irradiance, high temperatures, nutrient deficiencies, and toxicities, may challenge crops simultaneously; therefore, breeding for drought tolerance is very complicated. Interdisciplinary researchers have been attempting to dissect and comprehend the mechanisms of plant tolerance to drought stress using various methods; however, the limited success of molecular breeding and physiological approaches suggests that we rethink our strategies. Recent genetic techniques and genomics tools coupled with advances in breeding methodologies and precise phenotyping will likely reveal candidate genes and metabolic pathways underlying drought tolerance in crops. The WRKY transcription factors are involved in different biological processes in plant development. This zinc (Zn) finger protein family, particularly members that respond to and mediate stress responses, is exclusively found in plants. A total of 89 WRKY genes in japonica and 97 WRKY genes in O. nivara (OnWRKY) have been identified and mapped onto individual chromosomes. To increase the drought tolerance of rice (Oryza sativa L.), research programs should address the problem using a multidisciplinary strategy, including the interaction of plant phenology and multiple stresses, and the combination of drought tolerance traits with different genetic and genomics approaches, such as microarrays, quantitative trait loci (QTLs), WRKY gene family members with roles in drought tolerance, and transgenic crops. This review discusses the newest advances in plant physiology for the exact phenotyping of plant responses to drought to update methods of analysing drought tolerance in rice. Finally, based on the physiological/morphological and molecular mechanisms found in resistant parent lines, a strategy is suggested to select a particular environment and adapt suitable germplasm to that environment.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamed M. Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - M. Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - T. M. M. Mahmud
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamad Osman
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Rambod Abiri
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nahid Kalhori
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - M. Shabanimofrad
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Gous Miah
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Narges Atabaki
- Iran Azad University of Tehran Science & Reserach Branch, Hesarak, Tehran 1477893855, Iran
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Mohd Ikmal A, Nurasyikin Z, Kumar A, Noraziyah AAS. Evaluation of morpho-physiological traits of MRQ74 pyramided lines with drought yield QTLs. EUPHYTICA 2018; 214:98. [DOI: 10.1007/s10681-018-2178-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/13/2018] [Indexed: 09/02/2023]
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22
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Uda M, Gopinath SC, Hasfalina C, Faridah S, Bunawan S, Sabrina WN, Parmin N, Hashim U, Afnan Uda M, Mazidah M. Production and purification of antibody by immunizing rabbit with rice tungro bacilliform and rice tungro spherical viruses. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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23
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta. Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017; 10:21. [PMID: 28523639 PMCID: PMC5436998 DOI: 10.1186/s12284-017-0161-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ma. Teressa Sta. Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
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24
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Reddy PS, Tharanya M, Sivasakthi K, Srikanth M, Hash CT, Kholova J, Sharma KK, Vadez V. Molecular cloning and expression analysis of Aquaporin genes in pearl millet [Pennisetum glaucum (L) R. Br.] genotypes contrasting in their transpiration response to high vapour pressure deficits. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:167-176. [PMID: 29223338 DOI: 10.1016/j.plantsci.2017.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 05/24/2023]
Abstract
Pearl millet is a crop of the semi-arid tropics having high degree of genetic diversity and variable tolerance to drought stress. To investigate drought tolerance mechanism that possibly accounts for differences in drought tolerance, four recombinant inbred lines from a high resolution cross (HRC) were selected for variability in their transpiration rate (Tr) response to vapour pressure deficit (VPD) conditions. The differential Tr response of the genotypes to increased VPD conditions was used to classify the genotypes as sensitive or insensitive to high VPD. Aquaporin (AQP) genes PgPIP1;1, PgPIP1;2, PgPIP2;1, PgPIP2;3, PgPIP2;6, PgTIP1;1 and PgTIP2;2 were cloned. Phylogenetic analysis revealed that the cloned PgAQPs were evolutionarily closer to maize AQPs than to rice. PgAQP genes, including PgPIP1;1 and PgPIP2;6 in root tissue showed a significant expression pattern with higher expression in VPD-insensitive genotypes than VPD-sensitive genotypes under low VPD conditions (1.2kPa) i.e when there is no high evaporative demand from the atmosphere. PgAQP genes (PgPIP2;1 in leaf and root tissues; PgPIP1;2 and PgTIP2;2 in leaf and PgPIP2;6 in root) followed a diurnal rhythm in leaves and roots that have either higher or lower expression levels at different time intervals. Under high VPD conditions (4.21kPa), PgPIP2;3 showed higher transcript abundance in VPD-insensitive genotypes, and PgPIP2;1 in VPD-sensitive genotypes, while rest of the PgAQPs showed differential expression. Our current hypothesis is that these differences in the expression of AQP genes under different VPDs suggests a role of the AQPs in tuning the water transport pathways with variation between genotypes.
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Affiliation(s)
- Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India
| | - Murugesan Tharanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India; Department of Industrial Biotechnology, Bharathidasan University, Tiruchirappalli, India
| | - Kaliamoorthy Sivasakthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India; Department of Industrial Biotechnology, Bharathidasan University, Tiruchirappalli, India
| | - Mallayee Srikanth
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India
| | - C Tom Hash
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India
| | - Jana Kholova
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India
| | - Kiran K Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, Telangana, India.
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25
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017. [PMID: 28523639 DOI: 10.1186/s12284-017-0161-6©] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B P Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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26
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Pang Y, Chen K, Wang X, Xu J, Ali J, Li Z. Recurrent selection breeding by dominant male sterility for multiple abiotic stresses tolerant rice cultivars. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2017; 213:268. [PMID: 31997828 PMCID: PMC6956909 DOI: 10.1007/s10681-017-2055-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/30/2017] [Indexed: 06/08/2023]
Abstract
Recurrent selection has not been extensively applied in rice breeding practices due to lack of male sterility genes. Recently, a male sterile line (named as 'Jiabuyu') controlled by a novel single dominant gene was found, which provides an ideal tool for rice recurrent selection breeding. Here, two different kinds of recurrent selection populations facilitated for outcrossing by the dominant male sterile line 'Jiabuyu' were developed, that included one population using 31 abiotic stress tolerance introgression lines with common recipient parent as founders, and the other one using 25 popular restorers lines applied in hybrid breeding as founders. After two cycles of recurrent selection through natural outcrossing, the seeds from male fertile progeny plants were screened for higher grain yield under normal irrigated, drought, and salt-stressed natural field conditions. Finally, we identified 11 promising high-yielding lines under irrigated conditions, 12 drought-tolerant and 12 salt-tolerant lines. Among them, one line gave higher grain yield across all three conditions, three lines yielded high in both irrigated and drought conditions and another three lines gave high yields in both drought and salt-stressed conditions. The present study was a commendable attempt at utilizing recurrent selection population facilitated by dominant male sterile line to improve rice complex traits, which provided valuable lessons for other rice breeders. The developed lines are promising to be rice varieties with high yield, drought and/or salinity tolerances.
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Affiliation(s)
- Yunlong Pang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 China
| | - Kai Chen
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Xiaoqian Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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27
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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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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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29
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Li X, Han H, Chen M, Yang W, Liu L, Li N, Ding X, Chu Z. Overexpression of OsDT11, which encodes a novel cysteine-rich peptide, enhances drought tolerance and increases ABA concentration in rice. PLANT MOLECULAR BIOLOGY 2017; 93:21-34. [PMID: 27718117 DOI: 10.1007/s11103-016-0544-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/14/2016] [Indexed: 05/25/2023]
Abstract
Short-chain peptides play important roles in plant development and responses to abiotic and biotic stresses. Here, we characterized a gene of unknown function termed OsDT11, which encodes an 88 amino acid short-chain peptide and belongs to the cysteine-rich peptide family. It was found that the expression of OsDT11 can be activated by polyethylene glycol (PEG) treatment. Compared with wild-type lines, the OsDT11-overexpression lines displayed dramatically enhanced tolerance to drought and had reduced water loss, reduced stomatal density, and an increased the concentration of abscisic acid (ABA). The suppression of OsDT11 expression resulted in an increased sensitivity to drought compared to wild-type expression. Several drought-related genes, including genes encoding abscisic acid (ABA) signaling markers, were also strongly induced in the OsDT11-overexpressing lines. Moreover, the expression of OsDT11 was repressed in ABA-insensitive mutant Osbzip23 and Os2H16 RNAi lines. These results suggest that OsDT11-mediated drought tolerance may be dependent on the ABA signaling pathway.
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Affiliation(s)
- Xiaoming Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China
| | - Huipei Han
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China
| | - Ming Chen
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China
| | - Wei Yang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China
| | - Li Liu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People's Republic of China
| | - Ning Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai an, 271018, Shandong, People's Republic of China.
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30
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Mahender A, Anandan A, Pradhan SK, Pandit E. Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches. SPRINGERPLUS 2016; 5:2086. [PMID: 28018794 PMCID: PMC5148756 DOI: 10.1186/s40064-016-3744-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 11/25/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. RESULTS Genes and QTLs are recently known for the nutritional quality of rice. By comprehensive literature survey and public domain database, we provided a critical review on nutritional aspects like grain protein and amino acid content, vitamins and minerals, glycemic index value, phenolic and flavonoid compounds, phytic acid, zinc and iron content along with QTLs linked to these traits. In addition, achievements through transgenic and advanced genomic approaches have been discussed. The information available on genes and/or QTLs involved in enhancement of micronutrient element and amino acids are summarized with graphical representation. CONCLUSION Compatible QTLs/genes may be combined together to design a desirable genotype with superior in multiple grain quality traits. The comprehensive review will be helpful to develop nutrient dense rice cultivars by integrating molecular markers and transgenic assisted breeding approaches with classical breeding.
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Affiliation(s)
- Anumalla Mahender
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Annamalai Anandan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
| | - Elssa Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute (Formerly, Central Rice Research Institute), Cuttack, Odisha 753006 India
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31
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Shamsudin NAA, Swamy BPM, Ratnam W, Sta Cruz MT, Sandhu N, Raman AK, Kumar A. Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought. RICE (NEW YORK, N.Y.) 2016; 9:21. [PMID: 27164982 PMCID: PMC4864745 DOI: 10.1186/s12284-016-0093-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/22/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI. RESULTS The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background. CONCLUSION Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.
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Affiliation(s)
- Noraziyah Abd Aziz Shamsudin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B P Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Anitha K Raman
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Swamy BPM, Rahman MA, Inabangan-Asilo MA, Amparado A, Manito C, Chadha-Mohanty P, Reinke R, Slamet-Loedin IH. Advances in breeding for high grain Zinc in Rice. RICE (NEW YORK, N.Y.) 2016; 9:49. [PMID: 27671163 PMCID: PMC5037106 DOI: 10.1186/s12284-016-0122-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 09/16/2016] [Indexed: 05/18/2023]
Abstract
Zinc (Zn) is one of the most essential micronutrients required for the growth and development of human beings. More than one billion people, particularly children and pregnant women suffer from Zn deficiency related health problems in Asia. Rice is the major staple food for Asians, but the presently grown popular high yielding rice varieties are poor supplier of Zn in their polished form. Breeding rice varieties with high grain Zn has been suggested to be a sustainable, targeted, food-based and cost effective approach in alleviating Zn deficiency. The physiological, genetic and molecular mechanisms of Zn homeostasis have been well studied, but these mechanisms need to be characterized from a biofortification perspective and should be well integrated with the breeding processes. There is a significant variation for grain Zn in rice germplasm and efforts are being directed at exploiting this variation through breeding to develop high Zn rice varieties. Several QTLs and gene specific markers have been identified for grain Zn and there is a great potential to use them in Marker-Assisted Breeding. A thorough characterization of genotype and environmental interactions is essential to identify key environmental factors influencing grain Zn. Agronomic biofortification has shown inconsistent results, but a combination of genetic and agronomic biofortification strategies may be more effective. Significant progress has been made in developing high Zn rice lines for release in target countries. A holistic breeding approach involving high Zn trait development, high Zn product development, product testing and release, including bioefficacy and bioavailability studies is essential for successful Zn biofortification.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Mohammad Akhlasur Rahman
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Mary Ann Inabangan-Asilo
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Amery Amparado
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Christine Manito
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Prabhjit Chadha-Mohanty
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Russell Reinke
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Inez H. Slamet-Loedin
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Jonas E, de Koning DJ. Goals and hurdles for a successful implementation of genomic selection in breeding programme for selected annual and perennial crops. Biotechnol Genet Eng Rev 2016; 32:18-42. [DOI: 10.1080/02648725.2016.1177377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Elisabeth Jonas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 75007 Uppsala, Sweden
| | - Dirk Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 75007 Uppsala, Sweden
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Guo C, Luo C, Guo L, Li M, Guo X, Zhang Y, Wang L, Chen L. OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:492-502. [PMID: 26172270 DOI: 10.1111/jipb.12376] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 05/26/2023]
Abstract
Domain of unknown function 1644 (DUF1644) is a highly conserved amino acid sequence motif present only in plants. Analysis of expression data of the family of DUF1644-containing genes indicated that they may regulate responses to abiotic stress in rice. Here we present our discovery of the role of OsSIDP366, a member of the DUF1644 gene family, in response to drought and salinity stresses in rice. Transgenic rice plants overexpressing OsSIDP366 showed enhanced drought and salinity tolerance and reduced water loss as compared to that in the control, whereas plants with downregulated OsSIDP366 expression levels using RNA interference (RNAi) were more sensitive to salinity and drought treatments. The sensitivity to abscisic acid (ABA) treatment was not changed in OsSIDP366-overexpressing plants, and OsSIDP366 expression was not affected in ABA-deficient mutants. Subcellular localization analysis revealed that OsSIDP366 is presented in the cytoplasmic foci that colocalized with protein markers for both processing bodies (PBs) and stress granules (SGs) in rice protoplasts. Digital gene expression (DGE) profile analysis indicated that stress-related genes such as SNAC1, OsHAK5 and PRs were upregulated in OsSIDP366-overexpressing plants. These results suggest that OsSIDP366 may function as a regulator of the PBs/SGs and positively regulate salt and drought resistance in rice.
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Affiliation(s)
- Chiming Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Chengke Luo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Lijia Guo
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Min Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaoling Guo
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Yuxia Zhang
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, 29634, USA
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361102, China
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Samara Shekar Reddy S, Singh B, Peter A, Venkateswar Rao T. Production of transgenic local rice cultivars ( Oryza sativa L.) for improved drought tolerance using Agrobacterium mediated transformation. Saudi J Biol Sci 2016; 25:1535-1545. [PMID: 30581315 PMCID: PMC6302895 DOI: 10.1016/j.sjbs.2016.01.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 02/01/2023] Open
Abstract
Rice being the staple food of middle and south India, there is an extensive research undertaken in protecting the species and improving the quality and yield. Several recombinations have been made to the rice genome to impart various qualities which lack in the pure breed. Oryza faces various natural stress, like temperature variance, high salinity, etc., drought is one of the major parameters affecting the growth and yield of the plant. Transgenic rice cultivars can be generated for drought tolerance using the Agrobacterium mediated transformations. The current work aims to impart the gene for drought tolerance in Oryza sativa L. using Agrobacterium mediated transformation. The gene targeted in this context is dehydration response element binding factors (DREB). DREB plays a major role in response to drought mediated stress. Sambha mahsuri (Indica type) and Cotton dora sannalu (Indica type) the two local cultivars have been transformed for the gene AtDREB1A under 35s CaMV promoters (pBIH binary vector) for which the vector used was Agrobacterium. The target plant tissue being used was calli. Optimization of the parameters was performed for a lethal dose of hygromycin, cefotaxime level, and acetosyringone level. PCR amplification was used for the confirmation of the transgenic (T 0) species in which 23% and 18% for Sambha mahsuri and Cotton dora sannalu, respectively. Southern blotting was performed for the genomic DNA. Normal growth was shown by the T 1 transgenic plants whose expression was confirmed by RT-PCR. The T 1 transgenic plants showed good tolerance to drought mediated stress for a total period of one and a half week under greenhouse condition. The study can be concluded by producing a potentially successful drought resistance T 1 species produced using Agrobacterium mediated transformation.
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Affiliation(s)
- S. Samara Shekar Reddy
- Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
- Corresponding author. Tel.: +91 9985574076.
| | - Bharat Singh
- Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - A.J. Peter
- Prof. TNA Innovation Centre, Varsha Bioscience and Technology India Private Limited, Sy.No253/A, Jiblakpally (V), Donthigudem (G.P), Pochampally (M), Nalgonda (D), Telangana 508284, India
| | - T. Venkateswar Rao
- Prof. TNA Innovation Centre, Varsha Bioscience and Technology India Private Limited, Sy.No253/A, Jiblakpally (V), Donthigudem (G.P), Pochampally (M), Nalgonda (D), Telangana 508284, India
- Department of Biotechnology, K L University, Greenfields, Vaddeswaram (V), Guntur (D), Andhra Pradesh 522502, India
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Shamsudin NAA, Swamy BPM, Ratnam W, Sta Cruz MT, Raman A, Kumar A. Marker assisted pyramiding of drought yield QTLs into a popular Malaysian rice cultivar, MR219. BMC Genet 2016; 17:30. [PMID: 26818269 PMCID: PMC4729146 DOI: 10.1186/s12863-016-0334-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/14/2016] [Indexed: 11/15/2022] Open
Abstract
Background Three drought yield QTLs, qDTY2.2, qDTY3.1, and qDTY12.1 with consistent effect on grain yield under reproductive stage drought stress were pyramided through marker assisted breeding with the objective of improving the grain yield of the elite Malaysian rice cultivar MR219 under reproductive stage drought stress. Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selection were performed. BC1F3-derived lines with different combinations of qDTY2.2, qDTY3.1, and qDTY12.1 were evaluated under both reproductive stage drought stress and non-stress during the dry seasons of 2013 and 2014 at IRRI. Results The grain yield reductions in the stress trials compared to non-stress trials ranged from 79 to 93 %. In the stress trials, delay in days to flowering and reduction in plant height were observed. In both seasons, MR219 did not produce any yield under stress, however it produced a yield of 5917 kg ha−1 during the 2013 dry season and 8319 kg ha−1 during the 2014 dry season under non-stress. Selected introgressed lines gave a yield advantage of 903 to 2500 kg ha−1 over MR219 under reproductive stage drought stress and a yield of more than 6900 kg ha−1 under non-stress during the 2014 dry season. Among lines with single qDTY, lines carrying qDTY2.2 provided a higher yield advantage under reproductive stage drought stress in the MR219 background. Two-qDTY combinations (qDTY3.1+qDTY2.2 and qDTY3.1+qDTY12.1) performed better than lines with three qDTY combinations, indicating the absence of positive interactions between the three qDTYs. Conclusion We successfully developed drought-tolerant MR219 pyramided lines with a yield advantage of more than 1500 kg ha−1. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs. This is the first report on the successful effect of qDTYs in increasing the yield under drought in genetic backgrounds other than those in which the qDTYs were earlier identified.
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Affiliation(s)
- Noraziyah Abd Aziz Shamsudin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. .,International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - B P Mallikarjuna Swamy
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Ma Teressa Sta Cruz
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - Anitha Raman
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
| | - Arvind Kumar
- International Rice Research Institute, Los Banos, DAPO BOX 7777, Metro Manila, Philippines.
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Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice. Sci Rep 2016; 6:19349. [PMID: 26777777 PMCID: PMC4726002 DOI: 10.1038/srep19349] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022] Open
Abstract
Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice.
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Zhang F, Luo X, Zhou Y, Xie J. Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.). Biotechnol Lett 2015; 38:711-21. [PMID: 26667133 DOI: 10.1007/s10529-015-2012-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/02/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress. RESULTS 505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants. CONCLUSION These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.
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Affiliation(s)
- Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiangdong Luo
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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Global Reprogramming of Transcription in Chinese Fir (Cunninghamia lanceolata) during Progressive Drought Stress and after Rewatering. Int J Mol Sci 2015; 16:15194-219. [PMID: 26154763 PMCID: PMC4519895 DOI: 10.3390/ijms160715194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/21/2015] [Accepted: 06/30/2015] [Indexed: 12/02/2022] Open
Abstract
Chinese fir (Cunninghamia lanceolata), an evergreen conifer, is the most commonly grown afforestation species in southeast China due to its rapid growth and good wood qualities. To gain a better understanding of the drought-signalling pathway and the molecular metabolic reactions involved in the drought response, we performed a genome-wide transcription analysis using RNA sequence data. In this study, Chinese fir plantlets were subjected to progressively prolonged drought stress, up to 15 d, followed by rewatering under controlled environmental conditions. Based on observed morphological changes, plantlets experienced mild, moderate, or severe water stress before rehydration. Transcriptome analysis of plantlets, representing control and mild, moderate, and severe drought-stress treatments, and the rewatered plantlets, identified several thousand genes whose expression was altered in response to drought stress. Many genes whose expression was tightly coupled to the levels of drought stress were identified, suggesting involvement in Chinese fir drought adaptation responses. These genes were associated with transcription factors, signal transport, stress kinases, phytohormone signalling, and defence/stress response. The present study provides the most comprehensive transcriptome resource and the first dynamic transcriptome profiles of Chinese fir under drought stress. The drought-responsive genes identified in this study could provide further information for understanding the mechanisms of drought tolerance in Chinese fir.
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Abstract
The Intergovernmental Panel on Climate Change and other international agencies have concluded that global crop production is at risk due to climate change, population growth, and changing food preferences. Society expects that the agricultural sciences will innovate solutions to these problems and provide food security for the foreseeable future. My thesis is that an integrated research plan merging agronomic and genetic approaches has the greatest probability of success. I present a template for a research plan based on the lessons we have learned from the Green Revolution and from the development of genetically engineered crops that may guide us to meet this expectation. The plan starts with a vision of how the crop management system could change, and I give a few examples of innovations that are very much in their infancy but have significant potential. The opportunities need to be conceptualized on a regional basis for each crop to provide a target for change. The plan gives an overview of how the tools of plant biotechnology can be used to create the genetic diversity needed to implement the envisioned changes in the crop management system, using the development of drought tolerance in maize (Zea mays L.) as an example that has led recently to the commercial release of new hybrids in the USA. The plan requires an interdisciplinary approach that integrates and coordinates research on plant biotechnology, genetics, physiology, breeding, agronomy, and cropping systems to be successful.
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Coleman-Derr D, Tringe SG. Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 2014; 5:283. [PMID: 24936202 PMCID: PMC4047557 DOI: 10.3389/fmicb.2014.00283] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/22/2014] [Indexed: 01/24/2023] Open
Abstract
The exponential growth in world population is feeding a steadily increasing global need for arable farmland, a resource that is already in high demand. This trend has led to increased farming on subprime arid and semi-arid lands, where limited availability of water and a host of environmental stresses often severely reduce crop productivity. The conventional approach to mitigating the abiotic stresses associated with arid climes is to breed for stress-tolerant cultivars, a time and labor intensive venture that often neglects the complex ecological context of the soil environment in which the crop is grown. In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. Here, we highlight many of the advantages of these symbiont-based approaches and argue in favor of the broader recognition of crop species as ecological niches for a diverse community of microorganisms that function in concert with their plant hosts and each other to thrive under fluctuating environmental conditions.
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Boyer J, Byrne P, Cassman K, Cooper M, Delmer D, Greene T, Gruis F, Habben J, Hausmann N, Kenny N, Lafitte R, Paszkiewicz S, Porter D, Schlegel A, Schussler J, Setter T, Shanahan J, Sharp R, Vyn T, Warner D, Gaffney J. The U.S. drought of 2012 in perspective: A call to action. GLOBAL FOOD SECURITY-AGRICULTURE POLICY ECONOMICS AND ENVIRONMENT 2013. [DOI: 10.1016/j.gfs.2013.08.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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