Abstract
Salinity tolerance plays an important role in direct seeding cultivation since tolerance to salinity at the bud burst stage of rice directly affects seedling formation and yield. However, information on the quantitative trait loci (QTL) associated with salinity tolerance at the bud burst stage is limited. Here, a recombinant inbred line (RIL) population, derived from a cross between Kongyu131 (salinity-sensitive) and Xiaobaijingzi (salinity-tolerant), was used to identify QTLs for salinity tolerance at the bud burst stage using a high-density genetic map. Four QTLs were identified. The threshold LOD score for QTL identification was 3.0. Among the four QTLs detected, two QTLs namely qRSL3 (PVE, 22.59%) and qRRL3 (PVE, 21.21%) were considered to be one QTL, named qST3, which was the major QTL related to salinity tolerance on chromosome 3. This major QTL was located within an interval of 2.55 Mb and contained 253 candidate genes. Using RNA-seq data, 51 differentially expressed genes (DEGs) were detected among the candidate region. According to Rice Annotation Project and quantitative real-time PCR (qRT-PCR) analysis, Os03g0664800 was accepted as the most likely candidate gene for qST3. These results will be useful for improving salinity tolerance of rice and for developing rice cultivars suitable for direct seeding in salinized soil.
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References
Bimpong IK, Manneh B, Diop B, Ghislain K, Sow A, Amoah NKA, Gregorio G, Singh RK, Ortiz R, Wopereis M (2014) New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage. Euphytica 200(1):45–60
Chen T, Zhu Y, Chen K, Shen C, Zhao X, Shabala S, Shabala L, Meinke H, Venkataraman G, Chen ZH (2020) Identification of new QTL for salt tolerance from rice variety Pokkali. J Agron Crop Sci 206(2):202–213
Dingkuhn M, De Datta S, Pamplona R, Javellana C, Schnier H (1992) Effect of late-season N fertilization on photosynthesis and yield of transplanted and direct-seeded tropical flooded rice. II. a canopy stratification study. Field Crops Res 28(3):235–249
Hossain H, Rahman M, Alam M, Singh R (2015) Mapping of quantitative trait loci associated with reproductive-stage salt tolerance in rice. J Agron Crop Sci 201(1):17–31
Huang X-Y, Chao D-Y, Gao J-P, Zhu M-Z, Shi M, Lin H-X (2009) A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev 23(15):1805–1817
Kong W, Zhong H, Gong Z, Fang X, Sun T, Deng X, Li Y (2019) Meta-analysis of salt stress transcriptome responses in different rice genotypes at the seedling stage. Plants 8(3):64
Lei L, Zheng H, Bi Y, Yang L, Liu H, Wang J, Sun J, Zhao H, Li X, Li J (2020) Identification of a Major QTL and candidate gene analysis of salt tolerance at the bud burst stage in rice (Oryza sativa L.) using QTL-Seq and RNA-Seq. Rice 13(1):1–14
Li X, Zheng H, Wu W, Liu H, Wang J, Jia Y, Li J, Yang L, Lei L, Zou D (2020) QTL Mapping and candidate gene analysis for Alkali tolerance in japonica rice at the bud stage based on linkage mapping and Genome-wide association study. Rice 13(1):1–11
Liang W, Cui W, Ma X, Wang G, Huang Z (2014) Function of wheat Ta-UnP gene in enhancing salt tolerance in transgenic Arabidopsis and rice. Biochem Biophys Res Commun 450(1):794–801
Liao Y-D, Lin K-H, Chen C-C, Chiang C-M (2016) Oryza sativa protein phosphatase 1a (OsPP1a) involved in salt stress tolerance in transgenic rice. Mol Breeding 36(3):22
Liu H, Hussain S, Zheng M, Peng S, Huang J, Cui K, Nie L (2015) Dry direct-seeded rice as an alternative to transplanted-flooded rice in Central China. Agron Sustain Dev 35(1):285–294
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. Methods 25(4):402–408
Ma X, Chen X, Zhao J, Wang S, Tan L, Sun C, Liu F (2019) Identification of QTLs related to cadmium tolerance from wild rice (Oryza nivara) using a high-density genetic map for a set of introgression lines. Euphytica 215(12):1–12
Mardani Z, Rabiei B, Sabouri H, Sabouri A (2014) Identification of molecular markers linked to salt-tolerant genes at germination stage of rice. Plant Breed 133(2):196–202
McCouch S (1997) Report on QTL nomenclature. Rice Genet Newsl 14:11–13
Mohammadi R, Mendioro MS, Diaz GQ, Gregorio GB, Singh RK (2013) Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.). J Genet 92(3):433–443
Niones JM (2004) Fine mapping of the salinity tolerance gene on chromosome 1 of rice (Oryza sativa L.) using near-isogenic lines. MS, Dissertation, University of the Philippines Los Banos, Laguna
Puram VRR, Ontoy J, Linscombe S, Subudhi PK (2017) Genetic dissection of seedling stage salinity tolerance in rice using introgression lines of a salt tolerant landrace Nona Bokra. J Hered 108(6):658–670
Qadir M, Quillérou E, Nangia V, Murtaza G, Singh M, Thomas RJ, Drechsel P, Noble AD (2014) Economics of salt-induced land degradation and restoration. In: Natural resources forum, vol 4. Wiley, pp 282–295
Ren Z-H, Gao J-P, Li L-G, Cai X-L, Huang W, Chao D-Y, Zhu M-Z, Wang Z-Y, Luan S, Lin H-X (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37(10):1141–1146
Sabouri H, Sabouri A (2008) New evidence of QTLs attributed to salinity tolerance in rice. Afr J Biotechnol 7(24):4376–4388
Sabouri H, Biabani A (2009) Toward the mapping of agronomic characters on a rice genetic map: quantitative trait loci analysis under saline condition. Biotechnology 8(1):144–149
Setter TL, Laureles EV (1996) The beneficial effect of reduced elongation growth on submergence tolerance of rice. J Exp Bot 47(10):1551–1559
Singh K, Khanna CR (2010) Physiology and QTL analysis of coleoptile length, a trait for drought tolerance in wheat. J Plant Biol 37(2):1–9
Takehisa H, Shimodate T, Fukuta Y, Ueda T, Yano M, Yamaya T, Kameya T, Sato T (2004) Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crop Res 89(1):85–95
Thomson MJ, de Ocampo M, Egdane J, Rahman MA, Sajise AG, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3(2–3):148–160
Vignols F, Wigger M, Garcia-Garrido JM, Grellet F, Kader J-C, Delseny M (1997) Rice lipid transfer protein (LTP) genes belong to a complex multigene family and are differentially regulated. Gene 195(2):177–186
Wang F, Duan D, Duan P, Wang B (2007) Coleoptile elongation response of different salt-tolerant wheat cultivars to NaCl stress. Acta Agron Sin 33(12):2053
Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63
Wang Z, Wang J, Bao Y, Wu Y, Zhang H (2011) Quantitative trait loci controlling rice seed germination under salt stress. Euphytica 178(3):297–307
Wang Z, Chen Z, Cheng J, Lai Y, Wang J, Bao Y, Huang J, Zhang H (2012a) QTL analysis of Na+ and K+ concentrations in roots and shoots under different levels of NaCl stress in rice (Oryza sativa L.). PLoS One 7(12):e51202
Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J, Zhang H (2012b) Identification of QTLs with main, epistatic and QTL× environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125(4):807–815
Yang T, Zhang S, Zhao J, Liu Q, Huang Z, Mao X, Dong J, Wang X, Zhang G, Liu B (2016) Identification and pyramiding of QTLs for cold tolerance at the bud bursting and the seedling stages by use of single segment substitution lines in rice (Oryza sativa L.). Mol Breed 36(7):1–10
Yang J, Sun K, Li D, Luo L, Liu Y, Huang M, Yang G, Liu H, Wang H, Chen Z (2019) Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq. BMC Genomics 20(1):1–15
Yu H, Xie W, Li J, Zhou F, Zhang Q (2014) A whole-genome SNP array (RICE 6 K) for genomic breeding in rice. Plant Biotechnol J 12(1):28–37
Yu J, Zao W, He Q, Kim T-S, Park Y-J (2017) Genome-wide association study and gene set analysis for understanding candidate genes involved in salt tolerance at the rice seedling stage. Mol Genet Genom 292(6):1391–1403
Zeng L, Shannon MC, Lesch SM (2001) Timing of salinity stress affects rice growth and yield components. Agric Water Manag 48(3):191–206
Zhang J-S, Xie C, Li Z-Y, Chen S-Y (1999) Expression of the plasma membrane H+-ATPase gene in response to salt stress in a rice salt-tolerant mutant and its original variety. Theor Appl Genet 99(6):1006–1011
Zhang M, Ye J, Xu Q, Feng Y, Yuan X, Yu H, Wang Y, Wei X, Yang Y (2018) Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage. Plant Cell Rep 37(3):529–539
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This work was supported by the National Natural Science Foundation of China (U20A2025) the Natural Science Foundation Joint Guide Project of Heilongjiang (LH2019C035).
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Lei, L., Han, Z., Cui, B. et al. Mapping of a major QTL for salinity tolerance at the bud burst stage in rice (Oryza sativa L) using a high-density genetic map. Euphytica 217, 167 (2021). https://doi.org/10.1007/s10681-021-02901-0
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DOI: https://doi.org/10.1007/s10681-021-02901-0