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Le TD, Gathignol F, Vu HT, Nguyen KL, Tran LH, Vu HTT, Dinh TX, Lazennec F, Pham XH, Véry AA, Gantet P, Hoang GT. Genome-Wide Association Mapping of Salinity Tolerance at the Seedling Stage in a Panel of Vietnamese Landraces Reveals New Valuable QTLs for Salinity Stress Tolerance Breeding in Rice. PLANTS 2021; 10:plants10061088. [PMID: 34071570 PMCID: PMC8228224 DOI: 10.3390/plants10061088] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.
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Affiliation(s)
- Thao Duc Le
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Floran Gathignol
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
| | - Huong Thi Vu
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Khanh Le Nguyen
- Faculty of Agricultural Technology, University of Engineering and Technology, Hanoi 00000, Vietnam;
| | - Linh Hien Tran
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Hien Thi Thu Vu
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi 00000, Vietnam;
| | - Tu Xuan Dinh
- Incubation and Support Center for Technology and Science Enterprises, Hanoi 00000, Vietnam;
| | - Françoise Lazennec
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
| | - Xuan Hoi Pham
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
| | - Anne-Aliénor Véry
- UMR BPMP, Univ Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France;
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 34095 Montpellier, France; (F.G.); (F.L.)
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Correspondence: (P.G.); (G.T.H.); Tel.: +33-467-416-414 (P.G.); +84-397-600-496 (G.T.H.)
| | - Giang Thi Hoang
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, LMI RICE-2, Hanoi 00000, Vietnam; (T.D.L.); (H.T.V.); (L.H.T.); (X.H.P.)
- Correspondence: (P.G.); (G.T.H.); Tel.: +33-467-416-414 (P.G.); +84-397-600-496 (G.T.H.)
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Wang L, Wang HL, Yin L, Tian CY. Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination. BMC Genomics 2017; 18:806. [PMID: 29052505 PMCID: PMC5649071 DOI: 10.1186/s12864-017-4209-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages. RESULTS A total of 79,414 transcripts were assembled using Trinity, of which 57.67% were functionally annotated. KEGG enrichment unveiled that photosynthesis and flavonol biosynthesis pathways were activated earlier in brown seed compared with black seed. Gene expression analysis revealed that nine candidate unigenes in gibberellic acid and abscisic acid signal transduction and 23 unigenes in circadian rhythm-plant pathway showed distinct expression profiles to promote dimorphic seed germination. 194 conserved miRNAs comprising 40 families and 21 novel miRNAs belonging to 20 families in Suaeda aralocaspica were identified using miRDeep-P and Mfold. The expression of miRNAs in black seed was suppressed at imbibition stage. Among the identified miRNAs, 59 conserved and 13 novel miRNAs differentially expressed during seed germination. Of which, 43 conserved and nine novel miRNAs showed distinct expression patterns between black and brown seed. Using TAPIR, 208 unigenes were predicted as putative targets of 35 conserved miRNA families and 17 novel miRNA families. Among functionally annotated targets, genes participated in transcription regulation constituted the dominant category, followed by genes involved in signaling and stress response. Seven of the predicted targets were validated using 5' rapid amplification of cDNA ends or real-time quantitative reverse transcription-PCR. CONCLUSIONS Our results indicate that specific genes and miRNAs are regulated differently between black and brown seed during germination, which may contribute to the different germination behaviors of Suaeda aralocaspica dimorphic seeds in unpredictable variable environments. Our results lay a solid foundation for further studying the roles of candidate genes and miRNAs in Suaeda aralocaspica dimorphic seed germination.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Hong-Ling Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Lan Yin
- ABLife, Inc., Optics Valley International Biomedical Park, Building 18, East Lake High-Tech Development Zone, 858 Gaoxin Boulevard, Wuhan, 430075, China.
| | - Chang-Yan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Diray-Arce J, Clement M, Gul B, Khan MA, Nielsen BL. Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. BMC Genomics 2015; 16:353. [PMID: 25943316 PMCID: PMC4422317 DOI: 10.1186/s12864-015-1553-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 04/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of Suaeda fruticosa, a halophyte that has the ability to sequester salts in its leaves. Suaeda fruticosa is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores. This plant is an obligate halophyte that grows optimally from 200-400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. De novo assembly of the transcriptome and analysis has allowed identification of differentially expressed and unique genes present in this non-conventional crop. RESULTS Twelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of Suaeda fruticosa. The transcriptome was assembled de novo using Velvet and Oases k-45 and clustered using CDHIT-EST. There are 54,526 unigenes; among these 475 genes are downregulated and 44 are upregulated when samples from plants grown under optimal salt are compared with those grown without salt. BLAST analysis identified the differentially expressed genes, which were categorized in gene ontology terms and their pathways. CONCLUSIONS This work has identified potential genes involved in salt tolerance in Suaeda fruticosa, and has provided an outline of tools to use for de novo transcriptome analysis. The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression and identification of genes that may be involved in salt tolerance. The transcriptome may serve as a reference sequence for study of other succulent halophytes.
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Affiliation(s)
- Joann Diray-Arce
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA.
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, 84602, USA.
| | - Bilquees Gul
- Institute of Sustainable Halophyte Utilization, University of Karachi, Karachi, Pakistan.
| | - M Ajmal Khan
- College of Arts and Sciences, Qatar University, Doha, Qatar.
| | - Brent L Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, 84602, USA.
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Aprile A, Havlickova L, Panna R, Marè C, Borrelli GM, Marone D, Perrotta C, Rampino P, De Bellis L, Curn V, Mastrangelo AM, Rizza F, Cattivelli L. Different stress responsive strategies to drought and heat in two durum wheat cultivars with contrasting water use efficiency. BMC Genomics 2013; 14:821. [PMID: 24267539 PMCID: PMC4046701 DOI: 10.1186/1471-2164-14-821] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 11/18/2013] [Indexed: 12/21/2022] Open
Abstract
Background Durum wheat often faces water scarcity and high temperatures, two events that usually occur simultaneously in the fields. Here we report on the stress responsive strategy of two durum wheat cultivars, characterized by different water use efficiency, subjected to drought, heat and a combination of both stresses. Results The cv Ofanto (lower water use efficiency) activated a large set of well-known drought-related genes after drought treatment, while Cappelli (higher water use efficiency) showed the constitutive expression of several genes induced by drought in Ofanto and a modulation of a limited number of genes in response to stress. At molecular level the two cvs differed for the activation of molecular messengers, genes involved in the regulation of chromatin condensation, nuclear speckles and stomatal closure. Noteworthy, the heat response in Cappelli involved also the up-regulation of genes belonging to fatty acid β-oxidation pathway, glyoxylate cycle and senescence, suggesting an early activation of senescence in this cv. A gene of unknown function having the greatest expression difference between the two cultivars was selected and used for expression QTL analysis, the corresponding QTL was mapped on chromosome 6B. Conclusion Ofanto and Cappelli are characterized by two opposite stress-responsive strategies. In Ofanto the combination of drought and heat stress led to an increased number of modulated genes, exceeding the simple cumulative effects of the two single stresses, whereas in Cappelli the same treatment triggered a number of differentially expressed genes lower than those altered in response to heat stress alone. This work provides clear evidences that the genetic system based on Cappelli and Ofanto represents an ideal tool for the genetic dissection of the molecular response to drought and other abiotic stresses. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-821) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov,le Lecce Monteroni, I-73100 Lecce, Italy.
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Délano-Frier JP, Avilés-Arnaut H, Casarrubias-Castillo K, Casique-Arroyo G, Castrillón-Arbeláez PA, Herrera-Estrella L, Massange-Sánchez J, Martínez-Gallardo NA, Parra-Cota FI, Vargas-Ortiz E, Estrada-Hernández MG. Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress. BMC Genomics 2011; 12:363. [PMID: 21752295 PMCID: PMC3146458 DOI: 10.1186/1471-2164-12-363] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/13/2011] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a rich source of health-promoting peptides. Although several recent studies, mostly involving subtractive hybridization strategies, have contributed to increase the relatively low number of grain amaranth expressed sequence tags (ESTs), transcriptomic information of this species remains limited, particularly regarding tissue-specific and biotic stress-related genes. Thus, a large scale transcriptome analysis was performed to generate stem- and (a)biotic stress-responsive gene expression profiles in grain amaranth. RESULTS A total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa). CONCLUSIONS This study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture.
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Affiliation(s)
- John P Délano-Frier
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Hamlet Avilés-Arnaut
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Kena Casarrubias-Castillo
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Gabriela Casique-Arroyo
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Paula A Castrillón-Arbeláez
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Génomica para la Biodiversidad, Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Julio Massange-Sánchez
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Norma A Martínez-Gallardo
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Fannie I Parra-Cota
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - Erandi Vargas-Ortiz
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
| | - María G Estrada-Hernández
- Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León. Apartado Postal 629, C.P. 36821, Irapuato, Gto., México
- Department of Entomology, College of Agricultural Sciences. Penn State University, University Park, PA 16802, USA
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Thomson MJ, de Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK, Gregorio GB, Ismail AM. Characterizing the Saltol Quantitative Trait Locus for Salinity Tolerance in Rice. RICE 2010; 3:148-160. [PMID: 0 DOI: 10.1007/s12284-010-9053-8] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 09/02/2010] [Indexed: 05/26/2023]
Abstract
Abstract
This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na+/K+ homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for marker-assisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress.
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