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Mohapatra S, Panda AK, Bastia AK, Mukherjee AK, Sanghamitra P, Meher J, Mohanty SP, Pradhan SK. Development of Submergence-Tolerant, Bacterial Blight-Resistant, and High-Yielding Near Isogenic Lines of Popular Variety, 'Swarna' Through Marker-Assisted Breeding Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:672618. [PMID: 34386025 PMCID: PMC8353458 DOI: 10.3389/fpls.2021.672618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 05/13/2023]
Abstract
The rice variety 'Swarna' is highly popular in the eastern region of India. The farmers of eastern India cultivate mainly rainfed rice and face the adverse effects of climate change very frequently. Rice production in this region is not stable. Swarna variety is highly susceptible to bacterial blight (BB) disease and flash floods, which cause a heavy reduction in the yield. Transfer of five target genes/QTLs was targeted into the variety, Swarna by adopting marker-assisted backcross breeding approach. Direct markers for Sub1A, OsSPL14, and SCM2 QTLs and closely linked markers for xa5 and Xa21 BB resistance genes were screened in the backcross progenies. Swarna-Sub1, CR Dhan 800, and Swarna-Habataki near-isogenic lines (NILs) were used as donor parents in the breeding program. True multiple F1 plants were identified for backcrossing, and 796 BC1F1 seeds were generated. Foreground selection detected all the five target genes in six progenies in BC1F1 generation. The progeny containing all the target genes and more similar with the recipient parent was backcrossed, and a total of 446 BC2F1 seeds were produced. Foreground screening detected four BC2F1 plants carrying the five target genes. A total of 2,145 BC2F2 seeds were obtained from the best BC2F1 progeny. Screening of the progenies resulted in one plant with all five desirable genes, three plants with four, and another three progenies carrying three genes in homozygous conditions. The pyramided lines showed higher BB resistance and submergence tolerance than the recipient parent, Swarna. Culm strength of the pyramided lines showed higher breaking force than the recipient parent, Swarna. The pyramided line, SSBY-16-68-69 yielded the highest grain yield of 7.52 t/ha followed by the lines SSBY-16-68-511 (7.34 t/ha) and SSBY-16-68-1633 (7.02 t/ha). The best-pyramided line showed a yield advantage of 18% over the recipient parent and 6.8% over the yield component donor parent. Seven pyramided lines showed higher yield than the recipient parent, while five lines were better yielders than the yield component donor parent. The pyramided line SSBY-16-68-69 produced 365 grains/panicle, while the recipient had 152. The main morphologic and grain quality features of the recipient parent were retained in the pyramided lines.
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Affiliation(s)
| | - Alok Kumar Panda
- School of Applied Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | | | | | | | | | | | - Sharat Kumar Pradhan
- ICAR—National Rice Research Institute, Cuttack, India
- *Correspondence: Sharat Kumar Pradhan
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52
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Liu J, Fernie AR, Yan J. Crop breeding - From experience-based selection to precision design. JOURNAL OF PLANT PHYSIOLOGY 2021; 256:153313. [PMID: 33202375 DOI: 10.1016/j.jplph.2020.153313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Crops are the foundation of human society, not only by providing needed nutrition, but also by feeding livestock and serving as raw materials for industry. Cereal crops, which supply most of our calories, have been supporting humans for thousands of years. However food security is facing many challenges nowadays, including growing populations, water shortage, and increased incidence of biotic and abiotic stresses. According to statistical data from the Food and Agriculture Organization of the United Nations (FAO, http://www.fao.org/), the people suffering severe food insecurity increased from 7.9 % in 2015 to 9.7 % in 2019 and the number of people exposed to moderate or severe food insecurity have increased by 400 million over the same time period. Although there are many ways to cope with these challenges, crop breeding remains the most crucial and direct manner. With the development of molecular genetics, the speed of cloning genetic variations underlying corresponding phenotypes of agricultural importance is considerably more rapid. As a consequence breeding methods have evolved from phenotype-based to genome-based selection. In the future, knowledge-driven crop design, which integrates multi-omics data to reveal the connections between genotypes and phenotypes and to build selection models, will undoubtedly become the most efficient way to shape plants, to improve crops, and to ensure food security.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
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53
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Bernardo R. Reinventing quantitative genetics for plant breeding: something old, something new, something borrowed, something BLUE. Heredity (Edinb) 2020; 125:375-385. [PMID: 32296132 PMCID: PMC7784685 DOI: 10.1038/s41437-020-0312-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 01/19/2023] Open
Abstract
The goals of quantitative genetics differ according to its field of application. In plant breeding, the main focus of quantitative genetics is on identifying candidates with the best genotypic value for a target population of environments. Keeping quantitative genetics current requires keeping old concepts that remain useful, letting go of what has become archaic, and introducing new concepts and methods that support contemporary breeding. The core concept of continuous variation being due to multiple Mendelian loci remains unchanged. Because the entirety of germplasm available in a breeding program is not in Hardy-Weinberg equilibrium, classical concepts that assume random mating, such as the average effect of an allele and additive variance, need to be retired in plant breeding. Doing so is feasible because with molecular markers, mixed-model approaches that require minimal genetic assumptions can be used for best linear unbiased estimation (BLUE) and prediction. Plant breeding would benefit from borrowing approaches found useful in other disciplines. Examples include reliability as a new measure of the influence of genetic versus nongenetic effects, and operations research and simulation approaches for designing breeding programs. The genetic entities in such simulations should not be generic but should be represented by the pedigrees, marker data, and phenotypic data for the actual germplasm in a breeding program. Over the years, quantitative genetics in plant breeding has become increasingly empirical and computational and less grounded in theory. This trend will continue as the amount and types of data available in a breeding program increase.
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Affiliation(s)
- Rex Bernardo
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Buford Circle, Saint Paul, MN, 55108, USA.
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Bhaduri D, Chakraborty K, Nayak AK, Shahid M, Tripathi R, Behera R, Singh S, Srivastava AK. Alteration in plant spacing improves submergence tolerance in Sub1 and non-Sub1 rice (cv. IR64) by better light interception and effective carbohydrate utilisation under stress. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 47:891-903. [PMID: 32553088 DOI: 10.1071/fp19364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
Besides genetic improvement for developing stress-tolerant cultivars, agronomic management may also add considerable tolerance against different abiotic stresses in crop plants. In the present study, we evaluated the effect of six different spacing treatments (S1: 10 × 10 cm; S2: 15 × 10 cm; S3:15 × 15 cm; S4:20 × 10 cm; S5: 20 × 15 cm; S6: 20 × 20 cm (row-row × plant-plant)) for improving submergence tolerance in rice. A high yielding submergence intolerant rice cultivar IR64 was tested against its SUB1 QTL introgressed counterpart (IR64-Sub1) for 12 days of complete submergence for different spacing treatments in field tanks. Relatively wider spaced plants showed higher individual plant biomass and early seedling vigour, which was particularly helpful for IR64 in increasing plant survival (by 150% in S6 over S1) under 12 days of submergence, whereas the improvement was less in IR64-Sub1 (13%). Underwater radiation inside the plant canopy, particularly beyond 40 cm water depth, was significantly greater in wider spacing treatments. Leaf senescence pattern captured by SPAD chlorophyll meter reading and chlorophyll fluorescence imaging data (Fm, Fv/Fm) taken at different time intervals after stress imposition suggested that there was lesser light penetration inside the canopy of closer spaced plants, and that it might hasten leaf senescence and damage to the photosynthetic system. The initial content of total non-structural carbohydrate (NSC) was higher in wider spaced plants of IR64, and also the rate of depletion of NSC was lesser compared with closer spaced plants. In contrast, there was not much difference in NSC depletion rate under different spacing in IR64-Sub1. Further, higher antioxidant enzyme activities in wider spaced plants (both IR64 and IR64-Sub1) after de-submergence indicated better stress recovery and improved tolerance. Taken together we found that wider spacing (row-row: 20 cm and plant-plant: 15 cm and more) can significantly improve submergence tolerance ability in rice, particularly in submergence intolerant non-Sub1 cultivar like IR64, perhaps due to better underwater light penetration, delayed leaf senescence and slower depletion of NSC reserve.
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Affiliation(s)
- Debarati Bhaduri
- ICAR-National Rice Research Institute, Cuttack-753006, Odisha, India
| | | | - A K Nayak
- ICAR-National Rice Research Institute, Cuttack-753006, Odisha, India; and Corresponding author.
| | - Mohammad Shahid
- ICAR-National Rice Research Institute, Cuttack-753006, Odisha, India
| | - Rahul Tripathi
- ICAR-National Rice Research Institute, Cuttack-753006, Odisha, India
| | - Rashmita Behera
- ICAR-National Rice Research Institute, Cuttack-753006, Odisha, India
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55
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Babu PM, Neeraja CN, Rathod S, Suman K, Uttam GA, Chakravartty N, Lachagari VBR, Chaitanya U, Rao LVS, Voleti SR. Stable SNP Allele Associations With High Grain Zinc Content in Polished Rice ( Oryza sativa L.) Identified Based on ddRAD Sequencing. Front Genet 2020; 11:763. [PMID: 32849786 PMCID: PMC7432318 DOI: 10.3389/fgene.2020.00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Polished rice is widely consumed staple food across the globe, however, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising genotypes for grain Zn, a total of 40 genotypes consisting 20 rice landraces, and 20 released high yielding rice varieties were evaluated in three environments (wet seasons 2014, 2015 and 2016) for nine traits including days to 50% flowering (DFF), plant height (PH), panicle length (PL), total number of tillers (TNT), single plant yield (SPY), Fe and Zn in brown (IBR, ZBR) and polished rice (IPR, ZPR). Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) analyses identified genotypes G22 (Edavankudi Pokkali), G17 (Taraori Basmati), G27 (Chittimuthyalu) and G26 (Kalanamak) stable for ZPR and G8 (Savitri) stable for SPY across three environments. Significant negative correlation between yield and grain Zn was reaffirmed. Regression analysis indicated the contribution of traits toward ZPR and SPY and also desirable level of grain Zn in brown rice. A total of 39,137 polymorphic single nucleotide polymorphisms (SNPs) were obtained through double digest restriction site associated DNA (dd-RAD) sequencing of 40 genotypes. Association analyses with nine phenotypic traits revealed 188 stable SNPs with six traits across three environments. ZPR was associated with SNPs located in three putative candidate genes (LOC_Os03g47980, LOC_Os07g47950 and LOC_Os07g48050) on chromosomes 3 and 7. The genomic region of chromosome 7 co localized with reported genomic regions (rMQTL7.1) and OsNAS3 candidate gene. SPY was found to be associated with 12 stable SNPs located in 11 putative candidate genes on chromosome 1, 6, and 12. Characterization of rice landraces and varieties in terms of stability for their grain Zn and yield identified promising donors and recipients along with genomic regions in the present study to be deployed rice Zn biofortification breeding program.
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Affiliation(s)
- P Madhu Babu
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - K Suman
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - G Anurag Uttam
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | | | - U Chaitanya
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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Shimoyama N, Johnson M, Beaumont A, Schläppi M. Multiple Cold Tolerance Trait Phenotyping Reveals Shared Quantitative Trait Loci in Oryza sativa. RICE (NEW YORK, N.Y.) 2020; 13:57. [PMID: 32797316 PMCID: PMC7427827 DOI: 10.1186/s12284-020-00414-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/29/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Developing chilling tolerant accessions of domesticated Asian rice is a potential source of significant crop improvement. The uniquely chilling sensitive nature of the tropically originating Oryza sativa make it the most important cereal crop that can gain significantly from improved tolerance to low temperatures. However, mechanisms underlying this complex trait are not fully understood. Oryza sativa has two subspecies with different levels of chilling tolerance, JAPONICA and INDICA, providing an ideal tool to investigate mechanistic differences in the chilling stress tolerance responses within this important crop species. RESULTS The Rice Diversity Panel 1 (RDP1) was used to investigate a core set of Oryza sativa accessions. The tools available for this panel allowed for a comprehensive analysis of two chilling tolerance traits at multiple temperatures across a 354-cultivar subset of the RDP1. Chilling tolerance trait values were distributed as mostly subpopulation specific clusters of Tolerant, Intermediate, and Sensitive accessions. Genome-wide association study (GWAS) mapping approaches using all 354 accessions yielded a total of 245 quantitative trait loci (QTL), containing 178 unique QTL covering 25% of the rice genome, while 40 QTL were identified by multiple traits. QTL mappings using subsets of rice accession clusters yielded another 255 QTL, for a total of 500 QTL. The genes within these multiple trait QTL were analyzed for Gene Ontology (GO) term and potential pathway enrichments. Terms related to "carbohydrate biosynthesis", "carbohydrate transmembrane transport", "small molecule protein modification", and "plasma membrane" were enriched from this list. Filtering was done to identify more likely candidate pathways involved in conferring chilling tolerance, resulting in enrichment of terms related to "Golgi apparatus", "stress response", "transmembrane transport", and "signal transduction". CONCLUSIONS Taken together, these GO term clusters revealed a likely involvement of Golgi-mediated subcellular and extracellular vesicle and intracellular carbohydrate transport as a general cold stress tolerance response mechanism to achieve cell and metabolic homeostasis under chilling stress.
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Affiliation(s)
- Naoki Shimoyama
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Melineeh Johnson
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - André Beaumont
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
| | - Michael Schläppi
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233 USA
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57
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Alam R, Hummel M, Yeung E, Locke AM, Ignacio JCI, Baltazar MD, Jia Z, Ismail AM, Septiningsih EM, Bailey‐Serres J. Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. PLANT DIRECT 2020; 4:e00240. [PMID: 32775950 PMCID: PMC7403837 DOI: 10.1002/pld3.240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/25/2020] [Accepted: 06/17/2020] [Indexed: 05/11/2023]
Abstract
Crops with resilience to multiple climatic stresses are essential for increased yield stability. Here, we evaluate the interaction between two loci associated with flooding survival in rice (Oryza sativa L.). ANAEROBIC GERMINATION 1 (AG1), encoding trehalose 6-phosphate phosphatase 7 (TPP7), promotes mobilization of endosperm reserves to enhance the elongation of a hollow coleoptile in seeds that are seeded directly into shallow paddies. SUBMERGENCE 1 (SUB1), encoding the ethylene-responsive transcription factor SUB1A-1, confers tolerance to complete submergence by dampening carbohydrate catabolism, to enhance recovery upon desubmergence. Interactions between AG1/TPP7 and SUB1/SUB1A-1 were investigated under three flooding scenarios using four near-isogenic lines by surveying growth and survival. Pyramiding of the two loci does not negatively affect anaerobic germination or vegetative-stage submergence tolerance. However, the pyramided AG1 SUB1 genotype displays reduced survival when seeds are planted underwater and maintained under submergence for 16 d. To better understand the roles of TPP7 and SUB1A-1 and their interaction, temporal changes in carbohydrates and shoot transcriptomes were monitored in the four genotypes varying at the two loci at four developmental timeponts, from day 2 after seeding through day 14 of complete submergence. TPP7 enhances early coleoptile elongation, whereas SUB1A-1 promotes precocious photoautotrophy and then restricts underwater elongation. By contrast, pyramiding of the AG1 and SUB1 slows elongation growth, the transition to photoautotrophy, and survival. mRNA-sequencing highlights time-dependent and genotype-specific regulation of mRNAs associated with DNA repair, cell cycle, chromatin modification, plastid biogenesis, carbohydrate catabolism and transport, elongation growth, and other processes. These results suggest that interactions between AG1/TPP7 and SUB1/SUB1A-1 could impact seedling establishment if paddy depth is not effectively managed after direct seeding.
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Affiliation(s)
- Rejbana Alam
- Department of Botany and Plant SciencesCenter for Plant Cell BiologyUniversity of California RiversideRiversideCAUSA
| | - Maureen Hummel
- Department of Botany and Plant SciencesCenter for Plant Cell BiologyUniversity of California RiversideRiversideCAUSA
| | - Elaine Yeung
- Department of Botany and Plant SciencesCenter for Plant Cell BiologyUniversity of California RiversideRiversideCAUSA
| | - Anna M. Locke
- Department of Botany and Plant SciencesCenter for Plant Cell BiologyUniversity of California RiversideRiversideCAUSA
- Present address:
Soybean and Nitrogen Fixation Research UnitUSDA‐ARSRaleighNCUSA
| | | | - Miriam D. Baltazar
- Department of Biological SciencesCavite State UniversityIndangPhilippines
| | - Zhenyu Jia
- Department of Botany and Plant SciencesCenter for Plant Cell BiologyUniversity of California RiversideRiversideCAUSA
| | | | - Endang M. Septiningsih
- International Rice Research InstituteMetro ManilaPhilippines
- Present address:
Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTXUSA
| | - Julia Bailey‐Serres
- Department of Botany and Plant SciencesCenter for Plant Cell BiologyUniversity of California RiversideRiversideCAUSA
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Singh A, Singh Y, Mahato AK, Jayaswal PK, Singh S, Singh R, Yadav N, Singh AK, Singh PK, Singh R, Kumar R, Septiningsih EM, Balyan HS, Singh NK, Rai V. Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance. Sci Rep 2020; 10:8621. [PMID: 32451398 PMCID: PMC7248102 DOI: 10.1038/s41598-020-65588-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/28/2020] [Indexed: 11/24/2022] Open
Abstract
Erratic rainfall leading to flash flooding causes huge yield losses in lowland rice. The traditional varieties and landraces of rice possess variable levels of tolerance to submergence stress, but gene discovery and utilization of these resources has been limited to the Sub1A-1 allele from variety FR13A. Therefore, we analysed the allelic sequence variation in three Sub1 genes in a panel of 179 rice genotypes and its association with submergence tolerance. Population structure and diversity analysis based on a 36-plex genome wide genic-SNP assay grouped these genotypes into two major categories representing Indica and Japonica cultivar groups with further sub-groupings into Indica, Aus, Deepwater and Aromatic-Japonica cultivars. Targetted re-sequencing of the Sub1A, Sub1B and Sub1C genes identfied 7, 7 and 38 SNPs making 8, 9 and 67 SNP haplotypes, respectively. Haplotype networks and phylogenic analysis revealed evolution of Sub1B and Sub1A genes by tandem duplication and divergence of the ancestral Sub1C gene in that order. The alleles of Sub1 genes in tolerant reference variety FR13A seem to have evolved most recently. However, no consistent association could be found between the Sub1 allelic variation and submergence tolerance probably due to low minor allele frequencies and presence of exceptions to the known Sub1A-1 association in the genotype panel. We identified 18 cultivars with non-Sub1A-1 source of submergence tolerance which after further mapping and validation in bi-parental populations will be useful for development of superior flood tolerant rice cultivars.
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Affiliation(s)
- Anuradha Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Yashi Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Ajay K Mahato
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Pawan K Jayaswal
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Sangeeta Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Renu Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Neera Yadav
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - A K Singh
- Department of Crop Physiology, Narendra Deo University of Agriculture & Technology, Ayodhya, UP, India
| | - P K Singh
- Department of Genetics and Plant Breeding, Banaras Hindu University, Varanasi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Rajesh Kumar
- Department of Genetics and Plant Breeding, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Endang M Septiningsih
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Department of Soil and Crop Sciences, Texas A & M University, TX, 77843, USA
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India.
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Submergence Tolerance in Rice: Review of Mechanism, Breeding and, Future Prospects. SUSTAINABILITY 2020. [DOI: 10.3390/su12041632] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Flooding or submergence is one of the major environmental stressors affecting many man-made and natural ecosystems worldwide. The increase in the frequency and duration of heavy rainfall due to climate change has negatively affected plant growth and development, which eventually causes the death of plants if it persists for days. Most crops, especially rice, being a semi-aquatic plant, are greatly affected by flooding, leading to yield losses each year. Genetic variability in the plant response to flooding includes the quiescence scheme, which allows underwater endurance of a prolonged period, escape strategy through stem elongation, and alterations in plant architecture and metabolism. Investigating the mechanism for flooding survival in wild species and modern rice has yielded significant insight into developmental, physiological, and molecular strategies for submergence and waterlogging survival. Significant progress in the breeding of submergence tolerant rice varieties has been made during the last decade following the successful identification and mapping of a quantitative trait locus for submergence tolerance, designated as SUBMERGENCE 1 (SUB1) from the FR13A landrace. Using marker-assisted backcrossing, the SUB1 QTL (quantitative trait locus) has been incorporated into many elite varieties within a short time and with high precision as compared with conventional breeding methods. Despite the advancement in submergence tolerance, for future studies, there is a need for practical approaches exploring genome-wide association studies (GWA) and QTL in combination with specific tolerance traits, such as drought, salinity, disease and insect resistance.
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60
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Conversion of partial restorer Swarna into restorer by transferring fertility restorer Rf gene(s) through marker assisted back cross breeding (MABB) in rice. Sci Rep 2020; 10:1101. [PMID: 31980666 PMCID: PMC6981128 DOI: 10.1038/s41598-020-58019-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/24/2019] [Indexed: 11/20/2022] Open
Abstract
The major constraints in hybrid rice breeding are availability of limited number of parental lines with specific desirable traits and lower frequency of restorers among elite breeding lines. The popular, high-yielding mega-rice variety Swarna, has been identified to be a partial restorer (as it has only one of major fertility restorer genes, Rf4) and hence cannot be utilized directly in the hybrid rice breeding. To convert the partial restorer to complete restorer, a cross was made between Swarna and a stable restorer KMR3R possessing Rf3 and Rf4 genes and developed BC1F5 and BC2F4 populations by marker-assisted back cross breeding (MABB). The SSR marker DRRM-RF3-10 linked to Rf3 gene located on chromosome 1, clearly distinguished restorers from partial restorers. All the improved lines of Swarna possessing Rf3 and Rf4 genes showed complete fertility restoration in test crosses with higher grain yield heterosis. Few rice hybrids developed by using converted restorers were evaluated in multi location testing under the All India Co-ordinated Rice Improvement Project (AICRIP). The results indicated that new rice hybrids expressed higher heterosis with matching grain quality attributes like Swarna. This study provides significantly novel and relevant restorers to enhance and economize future hybrid rice breeding programs.
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61
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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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Kato Y, Collard BCY, Septiningsih EM, Ismail AM. Increasing flooding tolerance in rice: combining tolerance of submergence and of stagnant flooding. ANNALS OF BOTANY 2020; 124:1199-1210. [PMID: 31306479 PMCID: PMC6944782 DOI: 10.1093/aob/mcz118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Rice ecosystems in the tropical coastal areas are subject to two types of flooding stress: transient complete submergence and long-term water stagnation (stagnant flooding). Here, we aimed to dissect the mechanisms for stagnant flooding tolerance of rice genotypes carrying SUB1, a quantitative trait locus for submergence tolerance. METHODS We screened 80 elite genotypes under stagnant flooding stress in the lowland rice fields in the wet and dry seasons, and examined the tolerance mechanisms of promising genotypes for the two following seasons. KEY RESULTS Yield reduction under stagnant flooding averaged 48 % in the dry season and 89 % in the wet season. Elite genotypes carrying SUB1 showed 49 % lower yield than those without SUB1 under stagnant flooding, with no differences under shallow water conditions. However, we identified a few high-yielding Sub1 genotypes that were as tolerant of stagnant flooding as a reference genotype that lacked SUB1. These genotypes had intermediate stature with more shoot elongation in response to rising water than a moderately tolerant Sub1 reference variety, resulting in greater canopy expansion and higher yield. It was important to increase lodging resistance, since plant height >140 cm increased lodging under stagnant flooding. The culm diameter was closely associated with culm strength; reduced aerenchyma formation and increased lignin accumulation in the culm should increase lodging resistance. CONCLUSIONS The study demonstrated a successful combination of submergence and stagnant flooding tolerance in a rice breeding programme, and identified elite Sub1 genotypes that also tolerate stagnant flooding. Our results will support genetic improvement of Sub1 varieties for stagnant flooding tolerance.
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Affiliation(s)
- Yoichiro Kato
- International Rice Research Institute, Metro Manila, Philippines
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Bertrand C Y Collard
- International Rice Research Institute, Metro Manila, Philippines
- Yanco Agricultural Institute, Department of Primary Industries, New South Wales, Australia
| | - Endang M Septiningsih
- International Rice Research Institute, Metro Manila, Philippines
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
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Melandri G, Sikirou M, Arbelaez JD, Shittu A, Semwal VK, Konaté KA, Maji AT, Ngaujah SA, Akintayo I, Govindaraj V, Shi Y, Agosto-Peréz FJ, Greenberg AJ, Atlin G, Ramaiah V, McCouch SR. Multiple Small-Effect Alleles of Indica Origin Enhance High Iron-Associated Stress Tolerance in Rice Under Field Conditions in West Africa. FRONTIERS IN PLANT SCIENCE 2020; 11:604938. [PMID: 33584748 PMCID: PMC7874229 DOI: 10.3389/fpls.2020.604938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/15/2020] [Indexed: 05/03/2023]
Abstract
Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × O. sativa bi-parental rice populations and one O.sativa diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites. Mapping of these traits identified a large number of QTLs and single nucleotide polymorphisms (SNPs) associated with stress tolerance in the field. Favorable alleles associated with tolerance to high levels of iron in anaerobic rice soils were rare and almost exclusively derived from the indica subpopulation, including the most favorable alleles identified in NERICA varieties. These findings highlight the complex genetic architecture underlying rice response to HIA stress and suggest that a recurrent selection program focusing on an expanded indica genepool could be productively used in combination with genomic selection to increase the efficiency of selection in breeding programs designed to enhance tolerance to this prevalent abiotic stress in West Africa.
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Affiliation(s)
- Giovanni Melandri
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Mouritala Sikirou
- Africa Rice Center, Ibadan, Nigeria
- School of Horticulture and Green Landscaping, Kétou, Bénin
| | - Juan D. Arbelaez
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | | | | | | | - Inoussa Akintayo
- Central Agricultural Research Institute, Suakoko, Liberia
- Africa Rice Center, Suakoko, Liberia
| | - Vishnu Govindaraj
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | - Gary Atlin
- Bill & Melinda Gates Foundation, Seattle, WA, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Venuprasad Ramaiah,
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Emerick K, Ronald PC. Sub1 Rice: Engineering Rice for Climate Change. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034637. [PMID: 31182543 DOI: 10.1101/cshperspect.a034637] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
By the year 2100, the number of people on Earth is expected to increase by ∼50%, placing increasing demands on food production in a time when a changing climate is predicted to compromise crop yields. Feeding this future world requires scientifically informed innovations in agriculture. Here, we describe how a rice gene conferring tolerance to prolonged submergence has helped farmers in South and Southeast Asia mitigate rice crop failure during floods. We discuss how planting of this new variety benefited socially disadvantaged groups. This example indicates that investment in agricultural improvement can protect farmers from risks associated with a changing climate.
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Affiliation(s)
- Kyle Emerick
- Department of Economics, Tufts University, Medford, Massachusetts 02155-6722
| | - Pamela C Ronald
- Department of Plant Pathology, College of Agricultural and Environmental Sciences Genome Center, University of California, Davis, California 95616
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Arbelaez JD, Dwiyanti MS, Tandayu E, Llantada K, Jarana A, Ignacio JC, Platten JD, Cobb J, Rutkoski JE, Thomson MJ, Kretzschmar T. 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. RICE (NEW YORK, N.Y.) 2019; 12:55. [PMID: 31350673 PMCID: PMC6660535 DOI: 10.1186/s12284-019-0311-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/02/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. RESULTS Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. CONCLUSIONS This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | | | - Erwin Tandayu
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Krizzel Llantada
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Annalhea Jarana
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Carlos Ignacio
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Damien Platten
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Joshua Cobb
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Jessica Elaine Rutkoski
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Houston, TX 77843 USA
| | - Tobias Kretzschmar
- Southern Cross Plant Sciences, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
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Arbelaez JD, Tandayu E, Reveche MY, Jarana A, van Rogen P, Sandager L, Stolt P, Ng E, Varshney RK, Kretzschmar T, Cobb J. Methodology: ssb- MASS: a single seed-based sampling strategy for marker-assisted selection in rice. PLANT METHODS 2019; 15:78. [PMID: 31367224 PMCID: PMC6652012 DOI: 10.1186/s13007-019-0464-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers' nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. RESULTS Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7-8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost-benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. CONCLUSION This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Erwin Tandayu
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Maria Ymber Reveche
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Annalhea Jarana
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Petra van Rogen
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Line Sandager
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Patrik Stolt
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Enghwa Ng
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
| | - Joshua Cobb
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
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Donde R, Kumar J, Gouda G, Gupta MK, Mukherjee M, Baksh SY, Mahadani P, Sahoo KK, Behera L, Dash SK. Assessment of Genetic Diversity of Drought Tolerant and Susceptible Rice Genotypes Using Microsatellite Markers. RICE SCIENCE 2019; 26:239-247. [DOI: 10.1016/j.rsci.2019.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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Nghi KN, Tondelli A, Valè G, Tagliani A, Marè C, Perata P, Pucciariello C. Dissection of coleoptile elongation in japonica rice under submergence through integrated genome-wide association mapping and transcriptional analyses. PLANT, CELL & ENVIRONMENT 2019; 42:1832-1846. [PMID: 30802973 DOI: 10.1111/pce.13540] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Accepted: 02/10/2019] [Indexed: 05/23/2023]
Abstract
Rice is unique among cereals for its ability to germinate not only when submerged but also under anoxic conditions. Rice germination under submergence or anoxia is characterized by a longer coleoptile and delay in radicle emergence. A panel of temperate and tropical japonica rice accessions showing a large variability in coleoptile length was used to investigate genetic factors involved in this developmental process. The ability of the Khao Hlan On rice landrace to vigorously germinate when submerged has been previously associated with the presence of the trehalose 6 phosphate phosphatase 7 (TPP7) gene. In this study, we found that, in the presence of TPP7, polymorphisms and transcriptional variations of the gene in coleoptile tissue were not related to differences in the final coleoptile length under submergence. In order to find new chromosomal regions associated with the different ability of rice to elongate the coleoptile under submergence, we used genome-wide association study analysis on a panel of 273 japonica rice accessions. We discovered 11 significant marker-trait associations and identified candidate genes potentially involved in coleoptile length. Candidate gene expression analyses indicated that japonica rice genotypes possess complex genetic elements that control final coleoptile length under low oxygen.
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Affiliation(s)
- Khac Nhu Nghi
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Giampiero Valè
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Vercelli, Italy
| | - Andrea Tagliani
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Caterina Marè
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
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69
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Mori Y, Kurokawa Y, Koike M, Malik AI, Colmer TD, Ashikari M, Pedersen O, Nagai K. Diel O2 Dynamics in Partially and Completely Submerged Deepwater Rice: Leaf Gas Films Enhance Internodal O2 Status, Influence Gene Expression and Accelerate Stem Elongation for 'Snorkelling' during Submergence. PLANT & CELL PHYSIOLOGY 2019; 60:973-985. [PMID: 30668838 DOI: 10.1093/pcp/pcz009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Deepwater rice has a remarkable shoot elongation response to partial submergence. Shoot elongation to maintain air-contact enables 'snorkelling' of O2 to submerged organs. Previous research has focused on partial submergence of deepwater rice. We tested the hypothesis that leaf gas films enhance internode O2 status and stem elongation of deepwater rice when completely submerged. Diel patterns of O2 partial pressure (pO2) were measured in internodes of deepwater rice when partially or completely submerged, and with or without gas films on leaves, for the completely submerged plants. We also took measurements for paddy rice. Deepwater rice elongated during complete submergence and the shoot tops emerged. Leaf gas films improved O2 entry during the night, preventing anoxia in stems, which is of importance for elongation of the submerged shoots. Expressions of O2 deprivation inducible genes were upregulated in completely submerged plants during the night, and more so when gas films were removed from the leaves. Diel O2 dynamics showed similar patterns in paddy and deepwater rice. We demonstrated that shoot tops in air enabled 'snorkelling' and increased O2 in internodes of both rice ecotypes; however, 'snorkelling' was achieved only by rapid shoot elongation by deepwater rice, but not by paddy rice.
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Affiliation(s)
- Yoshinao Mori
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, Japan
| | - Yusuke Kurokawa
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, Japan
| | - Masaya Koike
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, Japan
| | - Al Imran Malik
- Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, Australia
| | - Timothy David Colmer
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, Australia
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, Japan
| | - Ole Pedersen
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, Australia
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3rd floor, DK, Copenhagen, Denmark
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi, Japan
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Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects. FRONTIERS IN PLANT SCIENCE 2019; 10:340. [PMID: 30967888 PMCID: PMC6439527 DOI: 10.3389/fpls.2019.00340] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.
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Affiliation(s)
- Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Piyada Juntawong
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Julián Mario Peña-Castro
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Mexico
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71
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Rameshkumar R, Karthikeyan A, Rathinapriya P, Ramesh M. Micropropagation of traditional deep water rice (Oryza sativa L.) cv. TNR1 for viable seed production and germplasm conservation. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.01.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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72
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Yadav S, Sandhu N, Majumder RR, Dixit S, Kumar S, Singh SP, Mandal NP, Das SP, Yadaw RB, Singh VK, Sinha P, Varshney RK, Kumar A. Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress. Sci Rep 2019; 9:2616. [PMID: 30796339 PMCID: PMC6385343 DOI: 10.1038/s41598-019-39084-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1-Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.
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Affiliation(s)
- Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ratna Rani Majumder
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - S P Singh
- Bihar Agricultural University, Sabour, Bihar, India
| | - N P Mandal
- Central Rainfed Upland Rice Research station, National Rice Research Institute, Hazaribagh, Jharkhand, India
| | - S P Das
- ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, Tripura, India
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-arid Tropics, Patancheru, Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-arid Tropics, Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Sandhu N, Dixit S, Swamy BPM, Raman A, Kumar S, Singh SP, Yadaw RB, Singh ON, Reddy JN, Anandan A, Yadav S, Venkataeshwarllu C, Henry A, Verulkar S, Mandal NP, Ram T, Badri J, Vikram P, Kumar A. Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas. RICE (NEW YORK, N.Y.) 2019; 12:8. [PMID: 30778782 PMCID: PMC6379507 DOI: 10.1186/s12284-019-0269-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/11/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY1.1, qDTY2.1, qDTY3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal. RESULTS Grain yield advantage of the NILs with qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 and qDTY2.1 + qDTY3.1 + Sub1 ranged from 76 to 2479 kg ha- 1 and 396 to 2376 kg ha- 1 under non-stress (NS) respectively and 292 to 1118 kg ha- 1 and 284 to 2086 kg ha- 1 under reproductive drought stress (RS), respectively. The NIL, IR96322-34-223-B-1-1-1-1 having qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321-1447-651-B-1-1-2 having qDTY1.1 + qDTY3.1 + Sub 1 and IR 94391-131-358-19-B-1-1-1 having qDTY3.1 + Sub1 have been released as varieties Bahuguni dhan-1' and 'Bahuguni dhan-2' respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322-34-223-B-1-1-1-1, IR 96321-1447-651-B-1-1-2 and IR 94391-131-358-19-B-1-1-1 respectively on 6 K SNP Infinium chip. CONCLUSION The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha- 1 under reproductive stage drought stress and 0.1 to 1.0 t ha- 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.
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Affiliation(s)
- Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, India
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Anitha Raman
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar India
| | - S. P. Singh
- Bihar Agricultural University, Sabour, Bihar India
| | - R. B. Yadaw
- National Rice Research Program Hardinath, Dhanusha, Nepal
| | - O. N. Singh
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - J. N. Reddy
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - A. Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Challa Venkataeshwarllu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Amelia Henry
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Satish Verulkar
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh India
| | - N. P. Mandal
- Central Rainfed Upland Rice Research station, National Rice Research Institute, Hazaribagh, Jharkhand India
| | - T. Ram
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jyothi Badri
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Prashant Vikram
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Analysis of the distribution of assimilation products and the characteristics of transcriptomes in rice by submergence during the ripening stage. BMC Genomics 2019; 20:18. [PMID: 30621581 PMCID: PMC6323827 DOI: 10.1186/s12864-018-5320-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 11/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Research on the submergence stress of rice has concentrated on the quiescence strategy to survive in long-term flooding conditions based on Submergence-1A (SUB1A). In the case of the ripening period, it is important that submergence stress can affect the quality as well as the survival of rice. Therefore, it is essential to understand the changes in the distribution of assimilation products in grain and ripening characteristics in submergence stress conditions. However, such studies have been insufficient at the physiological and molecular biological levels. Results We confirmed that the distribution rate of assimilation products in grain was decreased by submergence treatment. These results were caused by an increase in the distribution rate of assimilation products to the stem according to escape strategy. To understand this phenomenon at the molecular level, we analyzed the relative expression levels of genes related to sucrose metabolism, and found that the sucrose phosphate synthase gene (OsSPS), which induces the accumulation of sucrose in tissues, was decreased in the seeds and leaves, but not in the stems. Furthermore, the sucrose transporter gene (OsSUT) related to sucrose transport decreased in the seeds and leaves, but increased in stems. We also analyzed the biological metabolic processes related to starch and sucrose synthesis, carbon fixation, and glycolysis using the KEGG mapper with selected differentially expressed genes (DEGs) in seeds, stems, and leaves caused by submergence treatment. We found that the expression of genes for each step related to starch and D-glucose synthesis was down-regulated in the seeds and leaves but up-regulated in the stem. Conclusion The results of this study provide basic data for the development of varieties and corresponding technologies adapted to submergence conditions, through understanding the action network of the elements that change in the submergence condition, as well as information regarding useful DEGs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5320-7) contains supplementary material, which is available to authorized users.
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Kretzschmar T, Mbanjo EGN, Magalit GA, Dwiyanti MS, Habib MA, Diaz MG, Hernandez J, Huelgas Z, Malabayabas ML, Das SK, Yamano T. DNA fingerprinting at farm level maps rice biodiversity across Bangladesh and reveals regional varietal preferences. Sci Rep 2018; 8:14920. [PMID: 30297917 PMCID: PMC6175857 DOI: 10.1038/s41598-018-33080-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 09/19/2018] [Indexed: 11/26/2022] Open
Abstract
The development, dissemination, and adoption of improved rice varieties are imperative for global food and nutritional security. Knowledge of the crop's distribution across agro-ecologies is important for impact assessment studies, varietal replacement strategies, and the development and implementation of agricultural policies. Bangladesh is the world's 4th largest rice producer. Though traditional varieties (TVs) are abundant and valued throughout Bangladesh, population growth and vulnerability to climate change, necessitate efficient deployment of high-yielding stress-tolerant modern varieties (MVs). To aid agricultural policy and strategy this study aimed to accurately assess the distribution of MVs and TVs across Bangladesh during the rainfed rice-growing season. Information derived from a survey of rice production areas were compared and combined with DNA fingerprinting information from the same locations. Biodiversity of Bangladesh rice remained high. While TVs and first generation MVs of Bangladeshi and Indian origin were still commonly grown, recently released stress-tolerant MVs were adopted in large proportions in several districts. Although farmers successfully distinguished TVs from MVs grown in their fields, a considerable lack of authenticity among MVs was observed, pinpointing shortcomings in the seed supply chain. This study identifies focal points for extension work and validates DNA fingerprinting as reliable method for impact assessment studies.
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Affiliation(s)
- Tobias Kretzschmar
- International Rice Research Institute (IRRI), Pili Drive, Los Baños, 4031, Laguna, Philippines.
- Southern Cross University, Military Road, East Limore, 2480, NSW, Australia.
| | | | - Grace Angelique Magalit
- International Rice Research Institute (IRRI), Pili Drive, Los Baños, 4031, Laguna, Philippines
| | - Maria Stefanie Dwiyanti
- International Rice Research Institute (IRRI), Pili Drive, Los Baños, 4031, Laguna, Philippines
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | | | - Maria Genaleen Diaz
- Institute of Crop Science, College of Agriculture and Food Science, UPLB, College, Laguna, Philippines
| | - Jose Hernandez
- Institute of Crop Science, College of Agriculture and Food Science, UPLB, College, Laguna, Philippines
| | - Zenaida Huelgas
- IRRI Bangladesh Office, 103, Block-F, Rd No 1, Dhaka, 1213, Bangladesh
| | - Maria Luz Malabayabas
- International Rice Research Institute (IRRI), Pili Drive, Los Baños, 4031, Laguna, Philippines
| | - Subrata Kumar Das
- IRRI Bangladesh Office, 103, Block-F, Rd No 1, Dhaka, 1213, Bangladesh
| | - Takashi Yamano
- International Rice Research Institute (IRRI), Pili Drive, Los Baños, 4031, Laguna, Philippines
- Asian Development Bank (ADB), 6 ADB Ave, Ortigas Center, Mandaluyong, 1550, Metro, Manila, Philippines
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Dar MH, Zaidi NW, Waza SA, Verulkar SB, Ahmed T, Singh PK, Roy SKB, Chaudhary B, Yadav R, Islam MM, Iftekharuddaula KM, Roy JK, Kathiresan RM, Singh BN, Singh US, Ismail AM. No yield penalty under favorable conditions paving the way for successful adoption of flood tolerant rice. Sci Rep 2018; 8:9245. [PMID: 29915310 PMCID: PMC6006260 DOI: 10.1038/s41598-018-27648-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/30/2018] [Indexed: 01/25/2023] Open
Abstract
Flooding is one of the major constraints for rice production in rainfed lowlands, especially in years and areas of high rainfall. Incorporating the Sub1 (Submergence1) gene into high yielding popular varieties has proven to be the most feasible approach to sustain rice production in submergence-prone areas. Introgression of this QTL into popular varieties has resulted in considerable improvement in yield after flooding. However, its impact under non-flooded conditions or years have not been thoroughly evaluated which is important for the farmers to accept and adopt any new version of their popular varieties. The present study was carried out to evaluate the effect of Sub1 on grain yield of rice in different genetic backgrounds, under non-submergence conditions, over years and locations. The study was carried out using head to head trials in farmer’s fields, which enable the farmers to more accurately compare the performance of Sub1 varieties with their recurrent parents under own management. The data generated from different head to head trials revealed that the grain yield of Sub1 varieties was either statistically similar or higher than their non-Sub1 counterparts under non-submergence conditions. Thus, Sub1 rice varieties show no instance of yield penalty of the introgressed gene.
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Affiliation(s)
- Manzoor H Dar
- International Rice Research Institute (IRRI-India), NASC Complex, New Delhi, India.
| | - Najam W Zaidi
- International Rice Research Institute (IRRI-India), NASC Complex, New Delhi, India
| | - Showkat A Waza
- Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir (J&K), Kashmir, India
| | | | - T Ahmed
- Assam Agricultural University, Jorhat, Assam, India
| | - P K Singh
- Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | | | | | - Rambaran Yadav
- Regional Agriculture Research Station, NARC, Bara, Nepal
| | | | | | - J K Roy
- Association for Integrated Development (AID), Bhubaneswar, Odisha, India
| | | | - B N Singh
- Centre for Research and Development (CRD), Gorakhpur, UP, India
| | - Uma S Singh
- International Rice Research Institute (IRRI-India), NASC Complex, New Delhi, India
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77
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Kumar A, Sandhu N, Dixit S, Yadav S, Swamy BPM, Shamsudin NAA. Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought. RICE (NEW YORK, N.Y.) 2018; 11:35. [PMID: 29845495 PMCID: PMC5975061 DOI: 10.1186/s12284-018-0227-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/21/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies. RESULTS Based on class analysis of the QTL combinations, the identified superior QTL classes in F3/BC1F3/BC2F3 generations with positive QTL x QTL and QTL x background interactions that were captured through phenotyping maintained its superiority in yield under non-stress (NS) and reproductive-stage drought stress (RS) across advanced generations in all five studies. The marker-assisted selection breeding strategy combining both genotyping and phenotyping in early generation significantly reduced the number of genotypes to be carried forward. The strategy presented in this study providing genotyping and phenotyping cost savings of 25-68% compared with the traditional marker-assisted selection approach. The QTL classes, Sub1 + qDTY 1.1 + qDTY 2.1 + qDTY 3.1 and Sub1 + qDTY 2.1 + qDTY 3.1 in Swarna-Sub1, Sub1 + qDTY 1.1 + qDTY 1.2 , Sub1 + qDTY 1.1 + qDTY 2.2 and Sub1 + qDTY 2.2 + qDTY 12.1 in IR64-Sub1, qDTY 2.2 + qDTY 4.1 in Samba Mahsuri, Sub1 + qDTY 3.1 + qDTY 6.1 + qDTY 6.2 and Sub1 + qDTY 6.1 + qDTY 6.2 in TDK1-Sub1 and qDTY 12.1 + qDTY 3.1 and qDTY 2.2 + qDTY 3.1 in MR219 had shown better and consistent performance under NS and RS across generations over other QTL classes. CONCLUSION "Deployment of this procedure will save time and resources and will allow breeders to focus and advance only germplasm with high probability of improved performance. The identification of superior QTL classes and capture of positive QTL x QTL and QTL x background interactions in early generation and their consistent performance in subsequent generations across five backgrounds supports the efficacy of a combined MAS breeding strategy".
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Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Current address: Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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78
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Anis GB, Zhang Y, Wang H, Li Z, Wu W, Sun L, Riaz A, Cao L, Cheng S. Genomic Regions Analysis of Seedling Root Traits and Their Regulation in Responses to Phosphorus Deficiency Tolerance in CSSL Population of Elite Super Hybrid Rice. Int J Mol Sci 2018; 19:ijms19051460. [PMID: 29757987 PMCID: PMC5983790 DOI: 10.3390/ijms19051460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/28/2018] [Accepted: 05/02/2018] [Indexed: 11/28/2022] Open
Abstract
Phosphorus (P) is the essential macro-element supporting rice productivity. Quantitative trait loci (QTL) underlying related traits at the seedling stage under two different phosphorus levels was investigated in rice using a population of 76 Chromosomal Sequence Substitution Lines (CSSLs) derived from a cross between the maintainer variety XieqingzaoB (P stress tolerant) and the restorer variety Zhonghui9308 (P stress sensitive); the parents of super hybrid rice Xieyou9308. A genetic linkage map with 120 DNA marker loci was constructed. At logarithmic odd (LOD) value of 2.0, a total of seven QTLs were detected for studied traits under two P levels and their relative ratio. The LOD values ranged from 2.00 to 3.32 and explaining 10.82% to 18.46% of phenotypic variation. Three QTLs were detected under low phosphorus (P−), one under normal (P+) and three under their relative ratio (P−/P+) on the rice chromosomes 3, 5, 6, 8 and 10. No significant QTLs were found for shoot dry weight (SDW) and total dry weight (TDW). The pleiotropic QTLs influencing root number (qRN5) and root dry weight (qRDW5) as novel QTLs under P− level were detected near marker RM3638 on chromosome 5, which considered to directly contributing to phosphorus deficiency tolerance in rice. These QTLs need further analysis, including the fine mapping and cloning, which may use in molecular marker assisted breeding.
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Affiliation(s)
- Galal Bakr Anis
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
- Rice Research and Training Center, Field Crops Research Institute, Agriculture Research Center, Kafr Elsheikh 33717, Egypt.
| | - Yingxin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
| | - Huimin Wang
- Jiangxi Academy of Agricultural Sciences, Nanchang 210014, China.
| | - Zihe Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
| | - Weixun Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
| | - Lianping Sun
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
| | - Liyong Cao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
| | - Shihua Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, Zhejiang, China.
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79
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Zhao N, Li C, Yan Y, Cao W, Song A, Wang H, Chen S, Jiang J, Chen F. Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions. Int J Mol Sci 2018; 19:E1455. [PMID: 29757964 PMCID: PMC5983694 DOI: 10.3390/ijms19051455] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 01/04/2023] Open
Abstract
Waterlogging stress is among the most severe abiotic stressors in the breeding and the production of Chrysanthemum morifolium. However, the mechanism underlying the response to waterlogging and post-waterlogging reoxygenation in C. morifolium remains unknown. In this study, we compared the differences between the transcriptomes of two chrysanthemum cultivars, i.e., the waterlogging-tolerant cultivar "Nannongxuefeng" and the waterlogging-sensitive cultivar "Qinglu", by performing RNA-seq to elucidate the possible mechanism of waterlogging and reoxygenation in C. morifolium. "Nannongxuefeng" had a higher ethylene production under the waterlogging and reoxygenation conditions. Furthermore, the expression of transcription factors and genes that are involved in the hormone response, N-end rule pathway and ROS signaling significantly differed between the two cultivars. "Nannongxuefeng" and "Qinglu" significantly differed in their response to waterlogging and reoxygenation, providing a deeper understanding of the mechanism underlying the response to waterlogging and guidance for the breeding of C. morifolium.
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Affiliation(s)
- Nan Zhao
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chuanwei Li
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yajun Yan
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wen Cao
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Aiping Song
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Haibin Wang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiafu Jiang
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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80
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Mackill DJ, Khush GS. IR64: a high-quality and high-yielding mega variety. RICE (NEW YORK, N.Y.) 2018; 11:18. [PMID: 29629479 PMCID: PMC5890005 DOI: 10.1186/s12284-018-0208-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/14/2018] [Indexed: 05/05/2023]
Abstract
High-yielding varieties developed in the 1960s and 1970s at the International Rice Research Institute (IRRI) and elsewhere benefited farmers and the public, ultimately increasing yields and reducing the cost of rice to consumers. Most of these varieties, however, did not have the optimum cooking quality that was possessed by many of the traditional varieties they replaced. In 1985, the IRRI-developed indica variety IR64 was released in the Philippines. In addition to its high yield, early maturity and disease resistance, it had excellent cooking quality, matching that of the best varieties available. These merits resulted in its rapid spread and cultivation on over 10 million ha in the two decades after it was released. It has intermediate amylose content and gelatinization temperature, and good taste. It is resistant to blast and bacterial blight diseases, and to brown planthopper. Because of its success as a variety, it has been used extensively in scientific studies and has been well-characterized genetically. Many valuable genes have been introduced into IR64 through backcross breeding and it has been used in thousands of crosses. Its area of cultivation has declined in the past 10 years, but it has been replaced by a new generation of high-quality varieties that are mostly its progeny or relatives. Continued basic studies on IR64 and related varieties should help in unraveling the complex genetic control of yield and other desirable traits that are prized by rice farmers and consumers.
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Affiliation(s)
- David J Mackill
- Mars, Inc. and Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Gurdev S Khush
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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81
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Xuan TD, Khang DT. Effects of Exogenous Application of Protocatechuic Acid and Vanillic Acid to Chlorophylls, Phenolics and Antioxidant Enzymes of Rice (Oryza sativa L.) in Submergence. Molecules 2018; 23:E620. [PMID: 29522438 PMCID: PMC6017597 DOI: 10.3390/molecules23030620] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/04/2018] [Accepted: 03/06/2018] [Indexed: 11/16/2022] Open
Abstract
In this study, effects from application of protocatechuic acid (PA) and vanillic acid (VA) and their mixture on the submergence tolerance of rice were examined. The treatment of 0.01 mM PA and VA did not show significant increase of rice growth as compared to the controls. However, at higher concentrations (0.1-1.0 mM), rice shoot was elevated in submergence by 20.8-22.4%. The survival percentage of rice seedlings at any dose of PA, VA and their mixture was significantly higher than the controls. In general, the mixture of PA and VA was more active to promote shoot elongation and survival in submergence than sole treatment of either PA or VA. The amount of chlorophyll b by PA was significantly increased, while no change in chlorophyll a content was observed. VA remarkably reduced malondialdehyde quantity at three days of submergence, while no significant difference among treatment was observed in PA, the mixture, and respective controls. The two phenolic acids promoted contents of phenolics and flavonoids in rice leaves and roots, however the quantities of endogenous PA and VA in rice were not markedly differed after PA and VA treated on roots of rice seedlings. The ascorbate peroxidase and superoxide dismutase activities were enhanced, while the expression of genes encoding antioxidant enzymes was favored. VA increased the expression level of ascorbate peroxidase genes in higher levels than PA and their mixture, while no significant difference was observed in the other genes including superoxide dismutase, catalase, glutathione reductase, and peroxidase. Findings of this study showed that PA and VA increased the submergence tolerance of rice by promoting the photosynthetic and anti-oxidative processes in rice seedlings. The treatment of PA and VA mixture on seedling roots was potent to promote the submergence tolerance in rice.
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Affiliation(s)
- Tran Dang Xuan
- Graduate School of International Development and Cooperation, Hiroshima University, Higashi-Hiroshima City 739-8529, Japan.
| | - Do Tan Khang
- Biotechnology Research and Development Institute, Can Tho University, Can Tho City 902070, Vietnam.
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82
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Khan GH, Shikari AB, Vaishnavi R, Najeeb S, Padder BA, Bhat ZA, Parray GA, Bhat MA, Kumar R, Singh NK. Marker-assisted introgression of three dominant blast resistance genes into an aromatic rice cultivar Mushk Budji. Sci Rep 2018; 8:4091. [PMID: 29511225 PMCID: PMC5840290 DOI: 10.1038/s41598-018-22246-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/19/2018] [Indexed: 11/09/2022] Open
Abstract
Modern high yielding rice varieties have replaced most of the traditional cultivars in recent past. Mushk Budji, is one such short grained landrace known for its aroma and exquisite quality, however, is highly susceptible to blast disease that has led to considerable decline in its area. Mushk Budji was crossed to a triple-gene donor line, DHMAS 70Q 164-1b and followed through marker-assisted foreground and background selection in first and second backcross generations that helped to incorporate blast resistance genes Pi54, Pi1 and Pita. Marker-assisted background selection was carried out using 78 SSR and STS markers that helped to reduce linkage drag around the genes Pi54, Pi1 and Pita to 2.74, 4.60 and 2.03 Mb, respectively. The three-gene lines in BC2F2:3 were genotyped using 50 K SNP chip and revealed more than 92% genome similarity to the RP. 2-D gel assay detected differentially expressing 171 protein spots among a set of backcross derived lines, of which 38 spots showing match score of 4 helped us to calculate the proteome recovery. MALDI-TOF analysis helped to detect four significant proteins that were linked to quality and disease resistance. The improved lines expressed resistance to blast under artificial and natural field conditions.
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Affiliation(s)
- Gazala Hassan Khan
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, J & K, India
| | - Asif Bashir Shikari
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, J & K, India.
| | - Rakesh Vaishnavi
- DARS, Old Airport Road, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Budgam, J & K, India
| | - Sofi Najeeb
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, J & K, India
| | - Bilal A Padder
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, J & K, India
| | - Zahoor A Bhat
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, J & K, India
| | - Ghulam A Parray
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, J & K, India
| | - Mohammad Ashraf Bhat
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, FOA, Wadura, Sopore, Baramullah, J & K, India
| | - Ram Kumar
- ICAR- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, India
| | - Nagendra K Singh
- ICAR- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, India
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Das G, Rao GJN, Varier M, Prakash A, Prasad D. Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice. Sci Rep 2018; 8:2413. [PMID: 29402905 PMCID: PMC5799378 DOI: 10.1038/s41598-018-20495-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 01/19/2018] [Indexed: 12/31/2022] Open
Abstract
Rice, a major food crop, is grown in a wide range of ecological conditions and suffers significant yield losses as it is constantly exposed to a wide range of environmental and biotic stresses. The prevalence of different biotypes/strains has necessitated assembling of numerous resistance genes/QTLs into elite genotypes to confer a broader scale of resistance. The current study reports successful pyramiding of genes/QTLs that confer tolerance/resistance to submergence (Sub1), salinity (Saltol), blast (Pi2, Pi9) and gall midge (Gm1, Gm4) to supplement the four bacterial blight resistance genes (Xa 4, xa5, xa13, Xa21) present in Improved Tapaswini, an elite cultivar. The precise transfer of genes/QTLs was accomplished through effective foreground selection and suitable gene pyramids were identified. Background selection was practiced using morphological and grain quality traits to enhance the recovery of the recurrent parental genome. In the bioassays, the pyramids exhibited higher levels of resistance/ tolerance against the target stresses. The novel feature of the study was successful pyramidization and demonstration of the function of ten genes/QTLs in a new genotype. This success can stimulate several such studies to realize the full potential of molecular plant breeding as the foundation for rice improvement.
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Affiliation(s)
- Gitishree Das
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
- Research Institute of Biotechnology & Medical Converged Science, Dongguk University-Seoul, Ilsandong-gu, Gyeonggi-do, 10326, Republic of Korea.
| | - Gundimeda J N Rao
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
- Department of Bio Sciences and Bio Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
| | - M Varier
- NRRI-Central Rainfed Upland Rice Research Station, Hazaribagh, Jharkhand, 825301, India
| | - A Prakash
- Crop Protection Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Dokku Prasad
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
- Kaveri Seeds, Secunderabad, Telangana, 500003, India
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84
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Afrin W, Nafis MH, Hossain MA, Islam MM, Hossain MA. Responses of rice (Oryza sativa L.) genotypes to different levels of submergence. C R Biol 2018; 341:85-96. [PMID: 29398646 DOI: 10.1016/j.crvi.2018.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 01/08/2018] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
The study aims at identifying some submergence-tolerant rice genotypes through morphological and molecular characterization and their genetic variability analysis. Ten rice genotypes including two submergence-tolerant checks, two susceptible varieties and six advanced lines were evaluated for submergence tolerance in the laboratory and in the field during January-December 2015. The experiment was conducted in the field following randomized complete block design in a two-factor arrangement using five replications. Ten characters, viz. days to flowering, plant height, tiller number plant-1, effective tiller plant-1, and yield plant-1 etc. were studied for four treatments. A significant genotype×environment interaction was observed for all traits studied in this experiment. The yield was reduced for all genotypes at a different level of submergence stress compared to control. Binadhan-11, Binadhan-12, RC 249 and RC 251 showed tolerance, whereas RC 192, RC 193 and RC 225 showed moderate tolerance in submerged condition. The phenotypic coefficient of variance (PCV) was higher than the genotypic coefficient of variance (GCV) in all the studies traits. High heritability (75-97%) was found for all traits. High heritability along with high genetic advance was found for days to flowering (45.55) and plant height (40.05). Molecular characterization of the used genotypes was done with three SSR markers viz. RM 24, and submergence specific SC3 and SUB1. SC3 was found reliable for detection of submergence tolerant genotypes due to the highest gene diversity (0.840) compared to others. The banding pattern of the submergence specific markers SC3 and SUB1 identified in Binadhan-11, Binadhan-12, RC 192, RC 193, RC 225, RC 227, RC 249, and RC 251, which possess the SUB1 gene. Finally, clustering also separates the tolerant genotypes from the susceptible by dividing them into different clusters. The identified genotypes might be useful for the breeding programme for the development of submergence tolerant as well as resistant rice variety in Bangladesh.
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Affiliation(s)
- Wazifa Afrin
- Department of Genetics & Plant Breeding, Bangladesh Agricultural University, 2202 Mymensingh, Bangladesh; Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Mahmudul Hassan Nafis
- Department of Genetics & Plant Breeding, Bangladesh Agricultural University, 2202 Mymensingh, Bangladesh
| | - Muhammed Ali Hossain
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Md Amir Hossain
- Department of Genetics & Plant Breeding, Bangladesh Agricultural University, 2202 Mymensingh, Bangladesh.
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85
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Sharma N, Dang TM, Singh N, Ruzicic S, Mueller-Roeber B, Baumann U, Heuer S. Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice. RICE (NEW YORK, N.Y.) 2018; 11:2. [PMID: 29313187 PMCID: PMC5758481 DOI: 10.1186/s12284-017-0192-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/12/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. RESULTS Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. CONCLUSION This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance.
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Affiliation(s)
- Niharika Sharma
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Trang Minh Dang
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Intrexon Corp, California, USA
| | - Namrata Singh
- International Rice Research Institute (IRRI), Los Banos, Philippines
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | | | | | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia
| | - Sigrid Heuer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, Adelaide, South Australia, 5064, Australia.
- International Rice Research Institute (IRRI), Los Banos, Philippines.
- Rothamsted Research, Plant Science Department, Hertfordshire, Harpenden, AL5 2JQ, UK.
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86
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Chamara BS, Marambe B, Kumar V, Ismail AM, Septiningsih EM, Chauhan BS. Optimizing Sowing and Flooding Depth for Anaerobic Germination-Tolerant Genotypes to Enhance Crop Establishment, Early Growth, and Weed Management in Dry-Seeded Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1654. [PMID: 30532759 PMCID: PMC6265439 DOI: 10.3389/fpls.2018.01654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/25/2018] [Indexed: 05/21/2023]
Abstract
Poor crop establishment, high weed infestation, and consequent yield loss are major concerns for dry-seeded rice (DSR). Flooding after seeding helps in managing weeds but reduces seed germination and crop stand. Anaerobic germination (AG)-tolerant rice genotypes could overcome these problems in DSR. Screenhouse experiments were established to evaluate the effect of seed sowing depth (SD) (0.5 cm, 1 cm, and 2 cm) and flooding depth (FD) (saturated, 2 cm, and 5 cm) on crop establishment, early growth, and weed competitiveness in DSR using AG-tolerant genotypes (Khao Hlan On, Ma-Zhan Red, IR64+AG1, and IR64). Echinochloa crus-galli, Ludwigia hyssopifolia, and Cyperus difformis were used in the weedy treatment. Rice plants reached maximum emergence 9-13 days later under flooding compared with saturated conditions. Crop emergence decreased by 12-22% at 0.5 and 1 cm SD and by 48-60% at 2 cm SD, when combined with 2 or 5 cm FD compared with saturated conditions. The 2 cm SD reduced seedling emergence by 23-42% in Khao Hlan On and Ma-Zhan Red, by 62-70% in IR64+AG1, and by 90-92% in IR64 under flooding. Initial growth in rice plant height was slow under flooding but increased progressively after the seedlings emerged from water and the final height was not affected by FD. Leaf area, total shoot biomass, tiller density, and leaf number per pot of rice were higher at 1 cm SD (P< 0.05), but decreased drastically at 2 cm SD under flooding. The emergence of E. crus-galli and L. hyssopifolia decreased by 53-65% and 89-95%, respectively, but increased by 49-68% in C. difformis under 2 and 5 cm FD, respectively, compared with saturated conditions. The shoot biomass of the weeds followed the same trend. Khao Hlan On showed the highest weed-competitive ability under all FD while the biomass of IR64+AG1 and IR64 decreased by 10-14% due to weed competition under 2 cm FD. The 1 cm SD showed better growth for all genotypes under different FD. The 2 cm FD is sufficient to have a significant control of problematic weed species. The tolerance of AG of rice genotypes should be further enhanced to increase their weed-competitive ability.
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Affiliation(s)
- Buddhika Sampath Chamara
- Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños, Philippines
- Postgraduate Institute of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
- *Correspondence: Buddhika Sampath Chamara, ; Virender Kumar,
| | - Buddhi Marambe
- Department of Crop Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Virender Kumar
- Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños, Philippines
- *Correspondence: Buddhika Sampath Chamara, ; Virender Kumar,
| | | | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Bhagirath Singh Chauhan
- The Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Gatton, QLD, Australia
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87
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Singh A, Carandang J, Gonzaga ZJC, Collard BCY, Ismail AM, Septiningsih EM. Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions. RICE (NEW YORK, N.Y.) 2017; 10:15. [PMID: 28429297 PMCID: PMC5398972 DOI: 10.1186/s12284-017-0154-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/11/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Stagnant flooding, where water of 25-50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of the Sub1 varieties, which can withstand around 2 weeks of complete submergence, perform poorly in these conditions. Hence, varieties tolerant of stagnant flooding are essential. RESULTS This paper presents the first study to map QTLs associated with tolerance to stagnant flooding, along with a parallel study under normal irrigation, using an F7 mapping population consisting of 148 RILs derived from a cross of Ciherang-Sub1 and the stagnant-flooding tolerant line IR10F365. Phenotypic data was collected for 15 key traits under both environments. Additionally, survival rate was measured under stress conditions. Genotyping was performed using the Illumina Infinium genotyping platform with a 6 K SNP chip, resulting in 469 polymorphic SNPs. Under stress and irrigated conditions, 38 and 46 QTLs were identified, respectively. Clusters of QTLs were detected in both stress and normal conditions, especially on chromosomes 3 and 5. CONCLUSIONS Unique and common QTLs were identified and their physiological consequences are discussed. These beneficial QTLs can be used as targets for molecular breeding and can be further investigated to understand the underlying molecular mechanisms involved in stagnant flooding tolerance in rice.
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Affiliation(s)
- Anshuman Singh
- Present address: Rani Lakshmi Bai Central Agricultural University, Jhansi, 284003 India
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Jerome Carandang
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | | | - Bertrand C. Y. Collard
- Present address: Sugar Research Australia, 71378 Bruce Highway, Meringa, PO Box122, Gordonvale, QLD 4865 Australia
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | | | - Endang M. Septiningsih
- Present address: Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
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dos Santos RS, Farias DDR, Pegoraro C, Rombaldi CV, Fukao T, Wing RA, de Oliveira AC. Evolutionary analysis of the SUB1 locus across the Oryza genomes. RICE (NEW YORK, N.Y.) 2017; 10:4. [PMID: 28176282 PMCID: PMC5296262 DOI: 10.1186/s12284-016-0140-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 12/20/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Tolerance to complete submergence is recognized in a limited number of Asian rice (Oryza sativa L.) varieties, most of which contain submergence-inducible SUB1A on the polygenic SUBMERGENCE-1 (SUB1) locus. It has been shown that the SUB1 locus encodes two Ethylene-Responsive Factor (ERF) genes, SUB1B and SUB1C, in all O. sativa varieties. These genes were also found in O rufipogon and O nivara, wild relatives of O. sativa. However, detailed analysis of the polygenic locus in other Oryza species has not yet been made. FINDINGS Chromosomal location, phylogenetic, and gene structure analyses have revealed that the SUB1 locus is conserved in the long arm of chromosome 9 in most Oryza species. We also show that the SUB1A-like gene of O. nivara is on chromosome 1 and that Leersia perrieri, a grass-tolerant to deep-flooding, presents three ERF genes in the SUB1 locus. CONCLUSION We provide here a deeper insight into the evolutionary origin and variation of the SUB1 locus and raise the possibility that an association of these genes with flooding tolerance in L. perrieri may exist.
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Affiliation(s)
- Railson Schreinert dos Santos
- Technology Development Center (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Daniel da Rosa Farias
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Camila Pegoraro
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Cesar Valmor Rombaldi
- Technology Development Center (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Takeshi Fukao
- Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, USA
| | - Rod A. Wing
- The School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, USA
| | - Antonio Costa de Oliveira
- Technology Development Center (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
- Plant Genomics and Breeding Center (CGF), Universidade Federal de Pelotas, Pelotas, Brazil
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90
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Thomson MJ, Singh N, Dwiyanti MS, Wang DR, Wright MH, Perez FA, DeClerck G, Chin JH, Malitic-Layaoen GA, Juanillas VM, Dilla-Ermita CJ, Mauleon R, Kretzschmar T, McCouch SR. Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications. RICE (NEW YORK, N.Y.) 2017; 10:40. [PMID: 28856618 PMCID: PMC5577349 DOI: 10.1186/s12284-017-0181-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/25/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit "sweet spot" for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice. RESULTS Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina's production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material. CONCLUSIONS The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.
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Affiliation(s)
- Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Houston, TX, 77843, USA.
| | - Namrata Singh
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
| | - Maria S Dwiyanti
- International Rice Research Institute, Los Baños, Philippines
- Present address: Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Diane R Wang
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
| | - Mark H Wright
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
- Department of Genetics, Stanford School of Medicine, Stanford, California, 94305, USA
| | - Francisco Agosto Perez
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
| | - Genevieve DeClerck
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA
- Present address: DeClerck Design, LLC, Freeville, NY, USA
| | - Joong Hyoun Chin
- International Rice Research Institute, Los Baños, Philippines
- Present address: Graduate School of Integrated Bioindustry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, South Korea
| | | | | | - Christine J Dilla-Ermita
- International Rice Research Institute, Los Baños, Philippines
- Present address: Department of Plant Pathology, Washington State University, Pullman, Washington, 99164, USA
| | - Ramil Mauleon
- International Rice Research Institute, Los Baños, Philippines
| | | | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, 14853, USA.
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Chen R, Cheng Y, Han S, Van Handel B, Dong L, Li X, Xie X. Whole genome sequencing and comparative transcriptome analysis of a novel seawater adapted, salt-resistant rice cultivar - sea rice 86. BMC Genomics 2017; 18:655. [PMID: 28835208 PMCID: PMC5569538 DOI: 10.1186/s12864-017-4037-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 08/08/2017] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Rice (Oryza sativa) is critical for human nutrition worldwide. Due to a growing population, cultivars that produce high yields in high salinity soil are of major importance. Here we describe the discovery and molecular characterization of a novel sea water adapted rice strain, Sea Rice 86 (SR86). RESULTS SR86 can produce nutritious grains when grown in high salinity soil. Compared to a salt resistant rice cultivar, Yanfen 47 (YF47), SR86 grows in environments with up to 3X the salt content, and produces grains with significantly higher nutrient content in 12 measured components, including 2.9X calcium and 20X dietary fiber. Whole genome sequencing demonstrated that SR86 is a relatively ancient indica subspecies, phylogenetically close to the divergence point of the major rice varietals. SR86 has 12 chromosomes with a total genome size of 373,130,791 bps, slightly smaller than other sequenced rice genomes. Via comparison with 3000 rice genomes, we identified 42,359 putative unique, high impact variants in SR86. Transcriptome analysis of SR86 grown under normal and high saline conditions identified a large number of differentially expressed and salt-induced genes. Many of those genes fall into several gene families that have established or suggested roles in salt tolerance, while others represent potentially novel mediators of salt adaptation. CONCLUSIONS Whole genome sequencing and transcriptome analysis of SR86 has laid a foundation for further molecular characterization of several desirable traits in this novel rice cultivar. A number of candidate genes related to salt adaptation identified in this study will be valuable for further functional investigation.
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Affiliation(s)
- Risheng Chen
- Wuhan Oceanrice International Biotech Co.,Ltd, 30 Rongzhong International building, High-tech Development Zone, No.889 Luoyu Road, Wuhan, FL 430074 China
| | - Yunfeng Cheng
- Wuhan Oceanrice International Biotech Co.,Ltd, 30 Rongzhong International building, High-tech Development Zone, No.889 Luoyu Road, Wuhan, FL 430074 China
| | - Suying Han
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People’s Republic of China
| | - Ben Van Handel
- Owachomo Consulting, LLC, 1101 Laveta Terrace, Ste. 19, Los Angeles, CA 90026 USA
| | - Ling Dong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angels, 650 Charles Young Dr, Los Angeles, CA 90095 USA
| | - Xinmin Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angels, 650 Charles Young Dr, Los Angeles, CA 90095 USA
| | - Xiaoqing Xie
- Wuhan Oceanrice International Biotech Co.,Ltd, 30 Rongzhong International building, High-tech Development Zone, No.889 Luoyu Road, Wuhan, FL 430074 China
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92
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Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
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93
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Transforming rice cultivation in flood prone coastal Odisha to ensure food and economic security. Food Secur 2017. [DOI: 10.1007/s12571-017-0696-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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94
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Gilliham M, Able JA, Roy SJ. Translating knowledge about abiotic stress tolerance to breeding programmes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:898-917. [PMID: 27987327 DOI: 10.1111/tpj.13456] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 05/20/2023]
Abstract
Plant breeding and improvements in agronomic practice are making a consistent contribution to increasing global crop production year upon year. However, the rate of yield improvement currently lags behind the targets set to produce enough food to meet the demands of the predicted global population in 2050. Furthermore, crops that are exposed to harmful abiotic environmental factors (abiotic stresses, e.g. water limitation, salinity, extreme temperature) are prone to reduced yields. Here, we briefly describe the processes undertaken in conventional breeding programmes, which are usually designed to improve yields in near-optimal conditions rather than specifically breeding for improved crop yield stability under stressed conditions. While there is extensive fundamental research activity that examines mechanisms of plant stress tolerance, there are few examples that apply this research to improving commercial crop yields. There are notable exceptions, and we highlight some of these to demonstrate the magnitude of yield gains that could be made by translating agronomic, phenological and genetic solutions focused on improving or mitigating the effect of abiotic stress in the field; in particular, we focus on improvements in crop water-use efficiency and salinity tolerance. We speculate upon the reasons for the disconnect between research and research translation. We conclude that to realise untapped rapid gains towards food security targets new funding structures need to be embraced. Such funding needs to serve both the core and collaborative activities of the fundamental, pre-breeding and breeding research communities in order to expedite the translation of innovative research into the fields of primary producers.
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Affiliation(s)
- Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Stuart J Roy
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Australian Centre for Plant Functional Genomics, Glen Osmond, SA, 5064, Australia
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95
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Valliyodan B, Ye H, Song L, Murphy M, Shannon JG, Nguyen HT. Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1835-1849. [PMID: 27927997 DOI: 10.1093/jxb/erw433] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought and its interaction with high temperature are the major abiotic stress factors affecting soybean yield and production stability. Ongoing climate changes are anticipated to intensify drought events, which will further impact crop production and food security. However, excessive water also limits soybean production. The success of soybean breeding programmes for crop improvement is dependent on the extent of genetic variation present in the germplasm base. Screening for natural genetic variation in drought- and flooding tolerance-related traits, including root system architecture, water and nitrogen-fixation efficiency, and yield performance indices, has helped to identify the best resources for genetic studies in soybean. Genomic resources, including whole-genome sequences of diverse germplasms, millions of single-nucleotide polymorphisms, and high-throughput marker genotyping platforms, have expedited gene and marker discovery for translational genomics in soybean. This review highlights the current knowledge of the genetic diversity and quantitative trait loci associated with root system architecture, canopy wilting, nitrogen-fixation ability, and flooding tolerance that contributes to the understanding of drought- and flooding-tolerance mechanisms in soybean. Next-generation mapping approaches and high-throughput phenotyping will facilitate a better understanding of phenotype-genotype associations and help to formulate genomic-assisted breeding strategies, including genomic selection, in soybean for tolerance to drought and flooding stress.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Li Song
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - MacKensie Murphy
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO 63873, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
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96
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Zeng D, Tian Z, Rao Y, Dong G, Yang Y, Huang L, Leng Y, Xu J, Sun C, Zhang G, Hu J, Zhu L, Gao Z, Hu X, Guo L, Xiong G, Wang Y, Li J, Qian Q. Rational design of high-yield and superior-quality rice. NATURE PLANTS 2017; 3:17031. [PMID: 28319055 DOI: 10.1038/nplants.2017.31] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/14/2017] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa L.) is a staple food for more than half of the world's population. To meet the ever-increasing demand for food, because of population growth and improved living standards, world rice production needs to double by 20301. The development of new elite rice varieties with high yield and superior quality is challenging for traditional breeding approaches, and new strategies need to be developed. Here, we report the successful development of new elite varieties by pyramiding major genes that significantly contribute to grain quality and yield from three parents over five years. The new varieties exhibit higher yield potential and better grain quality than their parental varieties and the China's leading super-hybrid rice, Liang-you-pai-jiu (LYP9 or Pei-ai 64S/93-11). Our results demonstrate that rational design is a powerful strategy for meeting the challenges of future crop breeding, particularly in pyramiding multiple complex traits.
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Affiliation(s)
- Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuchun Rao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Lichao Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yujia Leng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jie Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Chuan Sun
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Guosheng Xiong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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97
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Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A, Singh DP, Prabha R, Sahu PK, Gupta VK, Singh HB, Krishanani KK, Minhas PS. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies. FRONTIERS IN PLANT SCIENCE 2017; 8:172. [PMID: 28232845 PMCID: PMC5299014 DOI: 10.3389/fpls.2017.00172] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.
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Affiliation(s)
- Kamlesh K. Meena
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Ajay M. Sorty
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Utkarsh M. Bitla
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Khushboo Choudhary
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Dhananjaya P. Singh
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Ratna Prabha
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Pramod K. Sahu
- Department of Biotechnology, National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural ResearchKushmaur, India
| | - Vijai K. Gupta
- Molecular Glyco-Biotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland GalwayGalway, Ireland
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of TechnologyTallinn, Estonia
| | - Harikesh B. Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu UniversityVaranasi, India
| | - Kishor K. Krishanani
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
| | - Paramjit S. Minhas
- Department of Microbiology, School of Edaphic Stress Management, National Institute of Abiotic Stress Management, Indian Council of Agricultural ResearchBaramati, India
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98
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Singh A, Septiningsih EM, Balyan HS, Singh NK, Rai V. Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice (Oryza sativa L.). PLANT & CELL PHYSIOLOGY 2017; 58:185-197. [PMID: 28069894 DOI: 10.1093/pcp/pcw206] [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: 05/10/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Flooding of rice fields is a serious problem in the river basins of South and South-East Asia where about 15 Mha of lowland rice cultivation is regularly affected. Flooding creates hypoxic conditions resulting in poor germination and seedling establishment. Flash flooding, where rice plants are completely submerged for 10-15 d during their vegetative stage, causes huge losses. Water stagnation for weeks to months also leads to substantial yield losses when large parts of rice aerial tissues are inundated. The low-yielding traditional varieties and landraces of rice adapted to these flooding conditions have been replaced by flood-sensitive high-yielding rice varieties. The 'FR13A' rice variety and the Submergence 1A (SUB1A) gene were identified for flash flooding and subsequently introgressed to high-yielding rice varieties. The challenge is to find superior alleles of the SUB1A gene, or even new genes that may confer greater tolerance to submergence. Similarly, genes have been identified in tolerant landraces of rice for their ability to survive by rapid stem elongation (SNORKEL1 and SNORKEL2) during deep-water flooding, and for anaerobic germination ability (TPP7). Research on rice genotypes and novel genes that are tolerant to prolonged water stagnation is in progress. These studies will greatly assist in devising more efficient and precise molecular breeding strategies for developing climate-resilient high-yielding rice varieties for flood-prone regions. Here we review the state of our knowledge of flooding tolerance in rice and its application in varietal improvement.
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Affiliation(s)
- Anuradha Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Endang M Septiningsih
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Harendra S Balyan
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
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99
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Das G, Patra JK, Baek KH. Insight into MAS: A Molecular Tool for Development of Stress Resistant and Quality of Rice through Gene Stacking. FRONTIERS IN PLANT SCIENCE 2017; 8:985. [PMID: 28659941 PMCID: PMC5469070 DOI: 10.3389/fpls.2017.00985] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 05/24/2017] [Indexed: 05/21/2023]
Abstract
Rice yield is subjected to severe losses due to adverse effect of a number of stress factors. The most effective method of controlling reduced crop production is utilization of host resistance. Recent technological advances have led to the improvement of DNA based molecular markers closely linked to genes or QTLs in rice chromosome that bestow tolerance to various types of abiotic stresses and resistance to biotic stress factors. Transfer of several genes with potential characteristics into a single genotype is possible through the process of marker assisted selection (MAS), which can quicken the advancement of tolerant/resistant cultivars in the lowest number of generations with the utmost precision through the process of gene pyramiding. Overall, this review presented various types of molecular tools including MAS that can be reasonable and environmental friendly approach for the improvement of abiotic and biotic stress resistant rice with enhanced quality.
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Affiliation(s)
- Gitishree Das
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University SeoulGoyang-si, South Korea
| | - Jayanta Kumar Patra
- Research Institute of Biotechnology and Medical Converged Science, Dongguk University SeoulGoyang-si, South Korea
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam UniversityGyeongsan, South Korea
- *Correspondence: Kwang-Hyun Baek
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100
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Dixit S, Yadaw RB, Mishra KK, Kumar A. Marker-assisted breeding to develop the drought-tolerant version of Sabitri, a popular variety from Nepal. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2017; 213:184. [PMID: 33364630 PMCID: PMC7734194 DOI: 10.1007/s10681-017-1976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/20/2017] [Indexed: 05/03/2023]
Abstract
Sabitri is a rice variety grown in a large part of the rainfed areas of Nepal. It was originally developed for irrigated condition; hence, this variety suffers high yield decline under drought. Two QTLs, qDTY3.2 and qDTY12.1 , with large effects on grain yield under drought were identified in the Sabitri background in separate QTL mapping studies. The present study reports the development of Sabitri near isogenic lines (NILs) with combinations of these two QTLs and their characterization under drought. To do so, marker-assisted backcross breeding (MABB) was combined with phenotypic selection to develop high-yielding drought-tolerant NILs with Sabitri grain type. Apart from this, drought-tolerant variants for grain type with high yield under non-stress were identified among the developed NILs. Early days to flowering of up to 13 days and reduction in plant height of up to 13 cm as compared to Sabitri were observed in the developed NILs. Some of these NILs showed higher yield compared to Sabitri and relatively higher tolerance to drought, indicating the capture of positive alleles and interactions during the course of selection. The developed NILs possessed high yield potential which make them suitable materials for the testing of water-saving technologies in irrigated areas. Based on their performance, these NILs can be deployed in rainfed areas in Nepal and other countries of South Asia to increase yield stability.
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Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ram Baran Yadaw
- Nepal Agricultural Research Council, National Rice Research Project, Hardinath, Nepal
| | - Krishna Kumar Mishra
- Nepal Agricultural Research Council, National Rice Research Project, Hardinath, Nepal
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- e-mail:
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