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Goto I, Neang S, Kuroki R, Reyes VP, Doi K, Skoulding NS, Taniguchi M, Yamauchi A, Mitsuya S. QTL analysis for sodium removal ability in rice leaf sheaths under salinity using an IR-44595/318 F 2 population. Front Plant Sci 2022; 13:1002605. [PMID: 36304401 PMCID: PMC9592983 DOI: 10.3389/fpls.2022.1002605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Over-accumulation of salt in rice plants is an effect of salt stress which decreases growth and grain yield. Salt removal ability in leaf sheaths is a tolerance mechanism to decrease salt entry and accumulation in leaf blades and maintain photosynthesis under salinity. In this study, a QTL analysis of removal ability of sodium ions (Na+) in leaf sheaths and Na+ accumulation-related traits, was conducted using F2 population between two rice varieties, IR-44595 with superior Na+ removal ability, and 318 with contrasting Na+ removal ability in leaf sheaths under salinity. Suggestive QTLs for Na+ removal ability in leaf sheaths were found on chromosomes 4 and 11. The suggestive QTL on chromosome 11 overlapped with other significant QTLs for Na+ concentration in shoots, leaf blades and leaf sheaths, and Na+/K+ ratio in leaf blades. Correlation analysis indicated that Na+ removal ability in leaf sheaths is important in reducing Na+ accumulation in leaf blades. The varietal difference of Na+ removal ability in leaf sheaths at the whole plant level was greater at lower NaCl concentrations and became smaller as the treatment NaCl concentration increased. Although the Na+ removal ability in leaf sheath was comparable between IR-44595 and 318 under high salinity at the whole plant level, the younger leaves of IR-44595 still showed a higher Na+ sheath-blade ratio than 318, which implied the Na+ removal ability functions in the younger leaves in IR-44595 to reduce Na+ entry in young leaf blades even under high salinity.
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Affiliation(s)
- Itsuki Goto
- Laboratory of Plant Physiology and Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Sarin Neang
- Laboratory of Crop Stress Regulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Ministory of Agriculture, Forestry and Fishery, Phnom Penh, Cambodia
| | - Ryuichi Kuroki
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Vincent Pamugas Reyes
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuyuki Doi
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Mitsutaka Taniguchi
- Laboratory of Plant Physiology and Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Akira Yamauchi
- Laboratory of Crop Stress Regulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shiro Mitsuya
- Laboratory of Plant Physiology and Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Laboratory of Crop Stress Regulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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de Ocampo MP, Ho VT, Thomson MJ, Mitsuya S, Yamauchi A, Ismail AM. QTL mapping under salt stress in rice using a Kalarata-Azucena population. Euphytica 2022; 218:74. [PMID: 36060537 PMCID: PMC9427886 DOI: 10.1007/s10681-022-03026-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 04/19/2022] [Indexed: 05/24/2023]
Abstract
UNLABELLED Salt stress is a major constraint across large rice production areas in Asia, because of the high sensitivity of modern rice varieties. To identify quantitative trait loci (QTL) associated with salt tolerance in rice, we developed an F2 population from a cross between the salt-tolerant landrace, Kalarata, and the salt-sensitive parent, Azucena. F3 families from this population were screened and scored for salt tolerance using IRRI's Standard evaluation system (SES). Growth, biomass, Na+ and K+ concentrations in leaf tissues, and chlorophyll concentration were determined. A genetic linkage map was constructed with 151 SSRs and InDel markers, which cover 1463 cM with an average distance of 9.69 cM between loci. A total of 13 QTL were identified using Composite Interval Mapping for 16 traits. Several novel QTL were identified in this study, the largest is for root sodium concentration (LOD = 11.0, R2 = 25.0) on chromosome 3, which also co-localize with a QTL for SES. Several QTL on the short arm of chromosome 1 coincide with the Saltol locus identified before. The novel QTL identified in this study constitute future targets for molecular breeding, to combine them with other QTL identified before, for higher tolerance and stable performance of rice varieties in salt affected soils. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10681-022-03026-8.
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Affiliation(s)
- Marjorie P. de Ocampo
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Viet The Ho
- Faculty of Biology and Environment, Ho Chi Minh City University of Food Industry, Ho Chi Minh City, Vietnam
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, 343C Heep Center, Texas A&M University, College Station, TX USA
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601 Japan
| | - Abdelbagi M. Ismail
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Neang S, de Ocampo M, Egdane JA, Platten JD, Ismail AM, Seki M, Suzuki Y, Skoulding NS, Kano-Nakata M, Yamauchi A, Mitsuya S. A GWAS approach to find SNPs associated with salt removal in rice leaf sheath. Ann Bot 2020; 126:1193-1202. [PMID: 33009812 PMCID: PMC7684702 DOI: 10.1093/aob/mcaa139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/20/2020] [Accepted: 10/02/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.
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Affiliation(s)
- Sarin Neang
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | | | - James A Egdane
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | | | - Masahide Seki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | | | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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Neang S, Goto I, Skoulding NS, Cartagena JA, Kano-Nakata M, Yamauchi A, Mitsuya S. Tissue-specific expression analysis of Na + and Cl - transporter genes associated with salt removal ability in rice leaf sheath. BMC Plant Biol 2020; 20:502. [PMID: 33143652 PMCID: PMC7607675 DOI: 10.1186/s12870-020-02718-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/25/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND A significant mechanism of salt-tolerance in rice is the ability to remove Na+ and Cl- in the leaf sheath, which limits the entry of these toxic ions into the leaf blade. The leaf sheath removes Na+ mainly in the basal parts, and Cl- mainly in the apical parts. These ions are unloaded from the xylem vessels in the peripheral part and sequestered into the fundamental parenchyma cells at the central part of the leaf sheath. RESULTS This study aimed to identify associated Na+ and Cl- transporter genes with this salt removal ability in the leaf sheath of rice variety FL 478. From 21 known candidate Na+ and Cl- transporter rice genes, we determined the salt responsiveness of the expression of these genes in the basal and apical parts, where Na+ or Cl- ions were highly accumulated under salinity. We also compared the expression levels of these transporter genes between the peripheral and central parts of leaf sheaths. The expression of 8 Na+ transporter genes and 3 Cl- transporter genes was up-regulated in the basal and apical parts of leaf sheaths under salinity. Within these genes, OsHKT1;5 and OsSLAH1 were expressed highly in the peripheral part, indicating the involvement of these genes in Na+ and Cl- unloading from xylem vessels. OsNHX2, OsNHX3, OsNPF2.4 were expressed highly in the central part, which suggests that these genes may function in sequestration of Na+ and Cl- in fundamental parenchyma cells in the central part of leaf sheaths under salinity. Furthermore, high expression levels of 4 candidate genes under salinity were associated with the genotypic variation of salt removal ability in the leaf sheath. CONCLUSIONS These results indicate that the salt removal ability in rice leaf sheath may be regulated by expressing various Na+ or Cl- transporter genes tissue-specifically in peripheral and central parts. Moreover, some genes were identified as candidates whose expression levels were associated with the genotypic variation of salt removal ability in the leaf sheath. These findings will enhance the understanding of the molecular mechanism of salt removal ability in rice leaf sheath, which is useful for breeding salt-tolerant rice varieties.
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Affiliation(s)
- Sarin Neang
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Itsuki Goto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | | | - Joyce A Cartagena
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
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Sadok W, Lopez JR, Zhang Y, Tamang BG, Muehlbauer GJ. Sheathing the blade: Significant contribution of sheaths to daytime and nighttime gas exchange in a grass crop. Plant Cell Environ 2020; 43:1844-1861. [PMID: 32459028 DOI: 10.1111/pce.13808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/31/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Despite representing a sizeable fraction of the canopy, very little is known about leaf sheath gas exchange in grasses. Specifically, estimates of sheath stomatal conductance, transpiration and photosynthesis along with their responses to light, CO2 and vapour pressure deficit (VPD) are unknown. Furthermore, the anatomical basis of these responses is poorly documented. Here, using barley as a model system, and combining leaf-level gas exchange, whole-plant gravimetric measurements, transpiration inhibitors, anatomical observations, and biophysical modelling, we found that sheath and blade stomatal conductance and transpiration were similar, especially at low light, in addition to being genotypically variable. Thanks to high abaxial stomata densities and surface areas nearly half those of the blades, sheaths accounted for up to 17% of the daily whole-plant water use, which -surprisingly- increased to 45% during the nighttime. Sheath photosynthesis was on average 17-25% that of the blade and was associated with lower water use efficiency. Finally, sheaths responded differently to the environment, exhibiting a lack of response to CO2 but a strong sensitivity to VPD. Overall, these results suggest a key involvement of sheaths in feedback loops between canopy architecture and gas exchange with potentially significant implications on adaptation to current and future climates in grasses.
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Affiliation(s)
- Walid Sadok
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA
| | - Jose R Lopez
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA
| | - Yangyang Zhang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA
- Department of Grassland Science, China Agricultural University, Beijing, China
| | - Bishal G Tamang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA
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