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Parween S, Anonuevo JJ, Butardo VM, Misra G, Anacleto R, Llorente C, Kosik O, Romero MV, Bandonill EH, Mendioro MS, Lovegrove A, Fernie AR, Brotman Y, Sreenivasulu N. Balancing the double-edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms. Plant Biotechnol J 2020; 18:1763-1777. [PMID: 31945237 PMCID: PMC7336377 DOI: 10.1111/pbi.13339] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/15/2019] [Accepted: 01/05/2020] [Indexed: 05/07/2023]
Abstract
Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome-wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low-to-intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non-starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water-insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia.
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Affiliation(s)
- Sabiha Parween
- International Rice Research InstituteMetro ManilaPhilippines
| | | | - Vito M. Butardo
- International Rice Research InstituteMetro ManilaPhilippines
- Present address:
Department of Chemistry and BiotechnologyFaculty of Science, Engineering and TechnologySwinburne University of TechnologyHawthornVictoriaAustralia
| | - Gopal Misra
- International Rice Research InstituteMetro ManilaPhilippines
| | - Roslen Anacleto
- International Rice Research InstituteMetro ManilaPhilippines
| | - Cindy Llorente
- International Rice Research InstituteMetro ManilaPhilippines
| | - Ondrej Kosik
- Department of Plant SciencesRothamsted ResearchHarpendenHertsUK
| | - Marissa V. Romero
- Philippine Rice Research InstituteMaligayaScience City of MuñozPhilippines
| | | | - Merlyn S. Mendioro
- Institute of Biological SciencesCollege of Arts and ScienceUniversity of PhilippinesLos BanosPhilippines
| | | | | | - Yariv Brotman
- Department of Life SciencesBen‐Gurion University of the NegevBeershebaIsrael
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Calayugan MIC, Formantes AK, Amparado A, Descalsota-Empleo GI, Nha CT, Inabangan-Asilo MA, Swe ZM, Hernandez JE, Borromeo TH, Lalusin AG, Mendioro MS, Diaz MGQ, Viña CBD, Reinke R, Swamy BPM. Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.). Sci Rep 2020; 10:2283. [PMID: 32042046 PMCID: PMC7010768 DOI: 10.1038/s41598-020-59184-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/24/2020] [Indexed: 12/28/2022] Open
Abstract
The development of micronutrient dense rice varieties with good agronomic traits is one of the sustainable and cost-effective approaches for reducing malnutrition. Identification of QTLs for high grain Fe and Zn, yield and yield components helps in precise and faster development of high Fe and Zn rice. We carried out a three-season evaluation using IR05F102 x IR69428 derived doubled-haploid population at IRRI. Inclusive composite interval mapping was carried out using SNP markers and Best Linear Unbiased Estimates of the phenotypic traits. A total of 23 QTLs were identified for eight agronomic traits and grain Fe and Zn concentration that explained 7.2 to 22.0% PV. A QTL by environment interaction analysis confirmed the stability of nine QTLs, including two QTLs for Zn on chromosomes 5 and 12. One epistatic interaction for plant height was significant with 28.4% PVE. Moreover, five QTLs were identified for Fe and Zn that harbor several candidate genes, e.g. OsZIP6 on QTL qZn5.1. A number of QTLs were associated with a combination of greater yield and increased grain Zn levels. These results are useful for development of new rice varieties with good agronomic traits and high grain Zn using MAS, and identification of genetic resources with the novel QTLs for grain Zn.
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Affiliation(s)
- Mark Ian C Calayugan
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Andrea Kariza Formantes
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines
| | - Amery Amparado
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Gwen Iris Descalsota-Empleo
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,University of the Philippines Los Baños, Laguna, 4031, Philippines.,University of the Southern Mindanao, Kabacan, Cotabato, 9407, Philippines
| | - Chau Thanh Nha
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,Cuu Long Delta Rice Research Institute (CLRRI), Cần Thơ, Vietnam
| | | | - Zin Mar Swe
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.,Department of Agriculture, Yezin, Myanmar
| | - Jose E Hernandez
- University of the Philippines Los Baños, Laguna, 4031, Philippines
| | | | | | | | | | | | - Russell Reinke
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Ghosal S, Quilloy FA, Casal C, Septiningsih EM, Mendioro MS, Dixit S. Trait-based mapping to identify the genetic factors underlying anaerobic germination of rice: Phenotyping, GXE, and QTL mapping. BMC Genet 2020; 21:6. [PMID: 31952473 PMCID: PMC6969419 DOI: 10.1186/s12863-020-0808-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 01/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anaerobic germination is one of the most important traits for rice under direct-seeded conditions. The trait reduces risk of crop failure due to waterlogged conditions after seeding and allows water to be used as a means of weed control. The identification of QTLs and causal genes for anaerobic germination will facilitate breeding for improved direct-seeded rice varieties. In this study, we explored a BC1F2:3 population developed from a cross between BJ1, an indica landrace, and NSIC Rc222, a high-yielding recurrent parent. The population was phenotyped under different screening methods (anaerobic screenhouse, anaerobic tray, and aerobic screenhouse) to establish the relationship among the methods and to identify the most suitable screening method, followed by bulk segregant analysis (BSA) to identify large-effect QTLs. RESULTS The study showed high heritability for survival (SUR) under all three phenotyping conditions. Although high correlation was observed within screening environments between survival at 14 and 21 days after seeding, the correlation across environments was low. Germination under aerobic and anaerobic conditions showed very low correlation, indicating the independence of their genetic control. The results were further confirmed through AMMI analysis. Four significant markers with an effect on anaerobic germination were identified through BSA. CIM analysis revealed qAG1-2, qAG6-2, qAG7-4, and qAG10-1 having significant effects on the trait. qAG6-2 and qAG10-1 were consistent across screening conditions and seedling age while qAG1-2 and qAG7-4 were specific to screening methods. All QTLs showed an effect when survival across all screening methods was analyzed. Together, the QTLs explained 39 to 55% of the phenotypic variation for survival under anaerobic conditions. No QTL effects were observed under aerobic conditions. CONCLUSIONS The study helped us understand the effect of phenotyping method on anaerobic germination, which will lead to better phenotyping for this trait in future studies. The QTLs identified through this study will allow the improvement of breeding lines for the trait through marker-assisted selection or through forward breeding approaches such as genomic selection. The high frequency of the BJ1 allele of these QTLs will enhance the robustness of germination under anaerobic conditions in inbred and hybrid rice varieties.
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Affiliation(s)
- Sharmistha Ghosal
- International Rice Research Institute, Los Baños, Laguna, Philippines.,University of the Philippines, Los Baños, Laguna, Philippines.,Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | | | - Carlos Casal
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | | | - Shalabh Dixit
- International Rice Research Institute, Los Baños, Laguna, Philippines.
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4
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Ghosal S, Casal C, Quilloy FA, Septiningsih EM, Mendioro MS, Dixit S. Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis. Rice (N Y) 2019; 12:50. [PMID: 31309351 PMCID: PMC6629739 DOI: 10.1186/s12284-019-0305-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/19/2019] [Indexed: 06/02/2023]
Abstract
Anaerobic germination (AG) is an important trait for direct-seeded rice (DSR) to be successful. Rice usually has low germination under anaerobic conditions, which leads to a poor crop stand in DSR when rain occurs after seeding. The ability of rice to germinate under water reduces the risk of poor crop stand. Further, this allows the use of water as a method of weed control. The identification of the genetic factors leading to high anaerobic germination is required to develop improved DSR varieties. In the present study, two BC1F2:3 mapping families involving a common parent with anaerobic germination potential, Kalarata, an indica landrace, and two recurrent parents, NSIC Rc222 and NSIC Rc238, were used. Phenotyping was done under two environmental conditions and genotyping was carried out through the KASP SNP genotyping platform. A total of 185 and 189 individuals genotyped with 170 and 179 polymorphic SNPs were used for QTL analysis for the two populations, Kalarata/NSIC Rc238 and Kalarata/NSIC Rc222, respectively. A total of five QTLs on chromosomes 3, 5, 6, 7, and 8 for survival (SUR) and four QTLs on chromosomes 1, 3 (two locations), and 7 for the trait seedling height (SH) across the populations and over the screening conditions were identified. Except for the QTLs on chromosomes 5 and 8, the parent with AG potential, Kalarata, contributed all the other QTLs. Among the five QTLs for SUR, the second-largest QTL (qSUR6-1) was novel for AG potential in rice, showing a stable expression in terms of genetic background and screening conditions explaining 11.96% to 16.01% of the phenotypic variation. The QTL for SH (qSH1-1) was also novel. Considering different genetic backgrounds and different screening conditions, the QTLs identified for the trait SUR explained phenotypic variation in the range of 57.60% to 73.09% while that for the trait SH ranged from 13.53% to 34.30%.
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Affiliation(s)
- Sharmistha Ghosal
- International Rice Research Institute, Los Baños, Laguna Philippines
- University of the Philippines, Los Baños, Laguna Philippines
- Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - Carlos Casal
- International Rice Research Institute, Los Baños, Laguna Philippines
| | | | | | | | - Shalabh Dixit
- International Rice Research Institute, Los Baños, Laguna Philippines
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5
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Baltazar MD, Ignacio JCI, Thomson MJ, Ismail AM, Mendioro MS, Septiningsih EM. QTL mapping for tolerance to anaerobic germination in rice from IR64 and the aus landrace Kharsu 80A. Breed Sci 2019; 69:227-233. [PMID: 31481831 PMCID: PMC6711729 DOI: 10.1270/jsbbs.18159] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/17/2018] [Indexed: 05/06/2023]
Abstract
Direct seeding of rice often results in poor crop establishment due to unlevelled fields, unpredicted heavy rains after sowing, and weed and pest invasion. Thus, it is important to develop varieties able to tolerate flooding during germination, also known as anaerobic germination (AG), to address these constraints. A study was conducted to identify QTLs associated with AG tolerance from an IR64/Kharsu 80A F2:3 mapping population using 190 lines phenotyped for seedling survival under the stress. Genotyping was performed using a genomewide 384-plex Indica/Indica SNP set. Four QTLs derived from Kharsu 80A providing increased tolerance to anaerobic germination were identified: three on chromosome 7 (qAG7.1, qAG7.2 and qAG7.3) and one on chromosome 3 (qAG3), with LOD values ranging from 5.7 to 7.7, and phenotypic variance explained (R2) from 8.1% to 12.6%. The QTLs identified in this study can be further investigated to better understand the genetic bases of AG tolerance in rice, and used for marker-assisted selection to develop more robust direct-seeded rice varieties.
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Affiliation(s)
- Miriam D. Baltazar
- International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
- University of the Philippines,
Los Banos, Laguna 4031,
Philippines
- Department of Biological Sciences, Cavite State University,
4122 Indang, Cavite,
Philippines
| | | | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University,
College Station, TX 77483,
USA
| | - Abdelbagi M. Ismail
- International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | | | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University,
College Station, TX 77483,
USA
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Descalsota GIL, Swamy BPM, Zaw H, Inabangan-Asilo MA, Amparado A, Mauleon R, Chadha-Mohanty P, Arocena EC, Raghavan C, Leung H, Hernandez JE, Lalusin AB, Mendioro MS, Diaz MGQ, Reinke R. Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification. Front Plant Sci 2018; 9:1347. [PMID: 30294335 PMCID: PMC6158342 DOI: 10.3389/fpls.2018.01347] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 08/27/2018] [Indexed: 05/19/2023]
Abstract
The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH 1.1 and Zn 7.1 were consistently identified in all the four environments, ten QTLs qDF 3.1, qDF 6.2 qDF 9.1 qPH 5.1 qGL 3.1, qGW 3.1, qGW 11.1, and qZn 6.2 were detected in two environments, while two major loci qBLB 11.1 and qBLB 5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.
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Affiliation(s)
- Gwen Iris L. Descalsota
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
- University of Southern Mindanao, Kabacan, Philippines
| | | | - Hein Zaw
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | | | - Amery Amparado
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | - Ramil Mauleon
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | | | - Emily C. Arocena
- Philippine Rice Research Institute, Science City of Muñoz, Philippines
| | - Chitra Raghavan
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | - Hei Leung
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
| | | | | | | | | | - Russell Reinke
- Strategic Innovation Platform, International Rice Research Institute, Manila, Philippines
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7
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Kretzschmar T, Pelayo MAF, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih EM. A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. Nat Plants 2015. [PMID: 27250677 DOI: 10.3410/f.725735765.793509252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.
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Affiliation(s)
- Tobias Kretzschmar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Lourd Franz M Gabunada
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Rosario Jimenez
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Nese Sreenivasulu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J Mackill
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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8
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Kretzschmar T, Pelayo MAF, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih EM. A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. Nat Plants 2015; 1:15124. [PMID: 27250677 DOI: 10.1038/nplants.2015.124] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/24/2015] [Indexed: 05/04/2023]
Abstract
Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.
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Affiliation(s)
- Tobias Kretzschmar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Lourd Franz M Gabunada
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Rosario Jimenez
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Nese Sreenivasulu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J Mackill
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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9
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Kretzschmar T, Pelayo MAF, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS, Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih EM. A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice. Nat Plants 2015. [PMID: 27250677 DOI: 10.1038/nplant.2015.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.
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Affiliation(s)
- Tobias Kretzschmar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Lourd Franz M Gabunada
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- University of the Philippines, Los Banos, Laguna 4031, Philippines
| | - Rejbana Alam
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Rosario Jimenez
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | | | | | - Nese Sreenivasulu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, USA
| | - Abdelbagi M Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - David J Mackill
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Toledo AMU, Ignacio JCI, Casal C, Gonzaga ZJ, Mendioro MS, Septiningsih EM. Development of Improved Ciherang-Sub1 Having Tolerance to Anaerobic Germination Conditions. ACTA ACUST UNITED AC 2015. [DOI: 10.9787/pbb.2015.3.2.077] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Hirabayashi H, Sasaki K, Kambe T, Gannaban RB, Miras MA, Mendioro MS, Simon EV, Lumanglas PD, Fujita D, Takemoto-Kuno Y, Takeuchi Y, Kaji R, Kondo M, Kobayashi N, Ogawa T, Ando I, Jagadish KSV, Ishimaru T. qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa. J Exp Bot 2015; 66:1227-36. [PMID: 25534925 PMCID: PMC4339588 DOI: 10.1093/jxb/eru474] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5-2.0 h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource.
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Affiliation(s)
- Hideyuki Hirabayashi
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiro Sasaki
- Japan International Research Centre for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines The University of Tokyo, Graduate School of Agricultural and Life Sciences, Institute of Sustainable Agro-ecosystem Services (ISAS), 1-1-1 Midoricho, Nishitokyo, Tokyo 188-0002, Japan
| | - Takashi Kambe
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ritchel B Gannaban
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Monaliza A Miras
- University of the Philippines, Los Baños, Laguna, The Philippines
| | | | - Eliza V Simon
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Patrick D Lumanglas
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Daisuke Fujita
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Yoko Takemoto-Kuno
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yoshinobu Takeuchi
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ryota Kaji
- NARO Tohoku Agricultural Research Centre (TARC), NARO, Shimo Furumichi, Daisen, Akita 014-0102, Japan
| | - Motohiko Kondo
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Nobuya Kobayashi
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan Japan International Research Centre for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Tsugufumi Ogawa
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen kihanadai nishi, Miyazaki, Miyazaki 889-2192, Japan
| | - Ikuo Ando
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Krishna S V Jagadish
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
| | - Tsutomu Ishimaru
- NARO Institute of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan Japan International Research Centre for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, The Philippines
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Mohammadi R, Mendioro MS, Diaz GQ, Gregorio GB, Singh RK. Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.). J Genet 2014; 92:433-43. [PMID: 24371165 DOI: 10.1007/s12041-013-0285-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Salinity tolerance in rice is critical at reproductive stage because it ultimately determines grain yield. An F2 mapping population derived from a Sadri/FL478 cross was exposed to saline field conditions (6-8 dS m(-1)) after the active tillering stage to identify reproductive stage specific QTLs for salinity tolerance. Genetic linkage map was constructed using 123 microsatellite markers on 232 F2 progenies. Totally 35 QTLs for 11 traits under salinity stress were detected with LOD > 3, out of which 28 QTLs that explained from 5.9 to 30.0% phenotypic variation were found to be significant based on permutation test. Three major QTL clusters were found on chromosomes 2 (RM423-RM174), 4 (RM551-RM518) and 6 (RM20224-RM528) for multiple traits under salinity stress. Both parental lines contributed additively for QTLs identified for the yield components. A majority of the QTLs detected in our study are reported for the first time for reproductive stage salinity stress. Fine-mapping of selected putative QTLs will be the next step to facilitate marker-assisted backcrossing and to detect useful genes for salinity tolerance at the reproductive stage in rice.
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Affiliation(s)
- Reza Mohammadi
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO, Box 7777, Metro Manila, Philippines.
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