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Comparative alternative splicing analysis of two contrasting rice cultivars under drought stress and association of differential splicing genes with drought response QTLs

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Abstract

Alternative splicing (AS) of precursor mRNA is often regulated by different developmental stages, environments, and genotypes. Little is known about how AS is regulated between different rice cultivars with distinctive response to certain abiotic stress. This study aimed to elucidate the AS patterns in contrasting rice (Oryza sativa L.) cultivars and examine its role during rice adaptation to drought environment. By comparing AS patterns between IRAT109 and ZS97 rice cultivars under drought stress, drought tolerant and susceptible respectively, 8034 shared, 11,086 ZS97-specific, and 12,057 IRAT109-specific AS events were observed where intron retention is the predominant AS pattern. Gene ontology (GO) as well as Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses suggested that the spliceosome and DNA repair represented the most significant functional categories among the genes with genotype-specific AS patterns. Other categories include basal transcription factors, environmental information, adaptation related pathways, oxidative phosphorylation, etc. Through integrating the drought-response related quantitative trait locus (QTLs) from 2006 to 2016 manually and mapping spliceosome and DNA repair genes with different AS patterns on chromosomes, we identified 14 out of 31 genes involved in splicesome and 4 out of 14 genes in DNA repair co-localized in drought stress related QTLs. We therefore propose that during long domestication, genes responsive to drought stress evolved specific AS patterns in upland rice, and spliceosome and DNA repair genes play potential roles in rice tolerance to drought stress. Genes with diversity AS patterns and co-localized with drought QTLs will serve as important resources for genetic improvement of rice adaptation to drought stress.

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References

  • Barbazuk WB, Fu Y, McGinnis KM (2008) Genome-wide analyses of alternative splicing in plants: opportunities and challenges. Genome Res 18(9):1381–1392

    Article  CAS  PubMed  Google Scholar 

  • Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72:291–336

    Article  CAS  PubMed  Google Scholar 

  • Boudsocq M, Willmann MR, McCormack M, Lee H, Shan L, He P et al (2010) Differential innate immune signalling via Ca(2+) sensor protein kinases. Nature 464(7287):418–422

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boyer JS (1982) Plant productivity and environment. Science (New York, NY) 218(4571):443–448

    Article  CAS  Google Scholar 

  • Busch A, Hertel KJ (2012) Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Genome Biol 13(2):2012–2013

    Article  Google Scholar 

  • Carvalho RF, Szakonyi D, Simpson CG, Barbosa IC, Brown JW, Baena-Gonzalez E et al (2016) The Arabidopsis SR45 splicing factor, a negative regulator of sugar signaling, modulates SNF1-related protein kinase 1 stability. Plant Cell. 28(8):1910–1925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang CY, Lin WD, Tu SL (2014) Genome-wide analysis of heat-sensitive alternative splicing in physcomitrella patens. Plant Physiol 165(2):826–840

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cui P, Zhang S, Ding F, Ali S, Xiong L (2014) Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis. Genome Biol 15(1):R1

  • Ding X, Li X, Xiong L (2011) Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123(5):815–826

    Article  PubMed  Google Scholar 

  • Dixit S, Singh A, Sta Cruz MT, Maturan PT, Amante M, Kumar A (2014) Multiple major QTL lead to stable yield performance of rice cultivars across varying drought intensities. BMC Genet 15:16

    Article  PubMed  PubMed Central  Google Scholar 

  • Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG (1993) hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 62:289–321

    Article  CAS  PubMed  Google Scholar 

  • Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids 38:W64–W70

    Article  CAS  Google Scholar 

  • Du JL, Zhang SW, Huang HW, Cai T, Li L, Chen S et al (2015) The splicing factor PRP31 is involved in transcriptional gene silencing and stress response in Arabidopsis. Mol Plant 8(7):1053–1068

    Article  CAS  PubMed  Google Scholar 

  • Elliott DJ, Venables JP, Newton CS, Lawson D, Boyle S, Eperon IC et al (2000) An evolutionarily conserved germ cell-specific hnRNP is encoded by a retrotransposed gene. Hum Mol Genet 9(14):2117–2124

    Article  CAS  PubMed  Google Scholar 

  • Feng J, Li J, Gao Z, Lu Y, Yu J, Zheng Q et al (2015) SKIP confers osmotic tolerance during salt stress by controlling alternative gene splicing in arabidopsis. Mol Plant 8(7):1038–1052

    Article  CAS  PubMed  Google Scholar 

  • Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE et al (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20(1):45–58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Foissac S, Sammeth M (2007) ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res 35(Web Server issue):W297–W299

  • Fu BY, Xiong JH, Zhu LH, Zhao XQ, Xu HX, Gao YM et al (2007) Identification of functional candidate genes for drought tolerance in rice. Mol Genet Genomics 278(6):599–609

    Article  CAS  PubMed  Google Scholar 

  • Gu J, Yin X, Struik PC, Stomph TJ, Wang H (2012) Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions. J Exp Bot 63(1):455–469

    Article  CAS  PubMed  Google Scholar 

  • Gu J, Xia Z, Luo Y, Jiang X, Qian B, Xie H et al (2018) Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana. Nucleic Acids Res 46(4):1777–1792

    Article  PubMed  Google Scholar 

  • Guan Q, Wu J, Zhang Y, Jiang C, Liu R, Chai C et al (2013) A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell 25(1):342–356

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E (2015) Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms. Front Plant Sci 6(57)

  • Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G et al (2017) Multilevel Regulation of Abiotic Stress Responses in Plants. Front Plant Sci. 8:1564

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang L, Zhang F, Wang W, Zhou Y, Fu B, Li Z (2014) Comparative transcriptome sequencing of tolerant rice introgression line and its parents in response to drought stress. BMC Genomics 15:1026

    Article  PubMed  PubMed Central  Google Scholar 

  • Iida K, Go M (2006) Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants. Mol Biol Evol 23(5):1085–1094

    Article  CAS  PubMed  Google Scholar 

  • Isshiki M, Tsumoto A, Shimamoto K (2006) The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. Plant Cell 18(1):146–158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jang YH, Park HY, Lee KC, Thu MP, Kim SK, Suh MC et al (2014) A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana. Plant J 78(4):591–603

    Article  CAS  PubMed  Google Scholar 

  • Ji K, Wang Y, Sun W, Lou Q, Mei H, Shen S et al (2012) Drought-responsive mechanisms in rice genotypes with contrasting drought tolerance during reproductive stage. J Plant Physiol 169(4):336–344

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30(1):42–46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khurana N, Chauhan H, Khurana P (2012) Expression analysis of a heat-inducible, Myo-inositol-1-phosphate synthase (MIPS) gene from wheat and the alternatively spliced variants of rice and Arabidopsis. Plant Cell Rep 31(1):237–251

    Article  CAS  PubMed  Google Scholar 

  • Laloum T, Martin G, Duque P (2018) Alternative splicing control of abiotic stress responses. Trends Plant Sci 23(2):140–150

    Article  CAS  PubMed  Google Scholar 

  • Le Roux C, Del Prete S, Boutet-Mercey S, Perreau F, Balague C, Roby D, et al. (2014) The hnRNP-Q protein LIF2 participates in the plant immune response. PloS ONE 9(6):e99343

  • Liu Y, Pang S, Kudla M, Dreumont N, Kister L, Sun Y-H et al (2009) The germ cell nuclear proteins hnRNP G-T and RBMY activate a testis-specific exon. PLoS Genet 5(11):6

    Google Scholar 

  • Loraine AE, McCormick S, Estrada A, Patel K, Qin P (2013) RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol 162(2):1092–1109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lorkovic ZJ, Wieczorek Kirk DA, Lambermon MH, Filipowicz W (2000) Pre-mRNA splicing in higher plants. Trends Plant Sci 5(4):160–167

    Article  CAS  PubMed  Google Scholar 

  • Luhrmann R, Kastner B, Bach M (1990) Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. Biochem Biophys Acta 1087(3):265–292

    CAS  PubMed  Google Scholar 

  • Ly V, Hatherell A, Kim E, Chan A, Belmonte MF, Schroeder DF (2013) Interactions between Arabidopsis DNA repair genes UVH6, DDB1A, and DDB2 during abiotic stress tolerance and floral development. Plant Sci 213:88–97

    Article  CAS  PubMed  Google Scholar 

  • Maniatis T, Tasic B (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418(6894):236–243

    Article  CAS  PubMed  Google Scholar 

  • Marcolino-Gomes J, Rodrigues FA, Fuganti-Pagliarini R, Bendix C, Nakayama TJ, Celaya B, et al. (2014) Diurnal oscillations of soybean circadian clock and drought responsive genes. PloS ONE. 9(1):e86402

  • Mastrangelo AM, Marone D, Laido G, De Leonardis AM, De Vita P (2012) Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity. Plant Sci 185–186:40–49

    Article  PubMed  Google Scholar 

  • Mazeyrat S, Saut N, Mattei MG, Mitchell MJ (1999) RBMY evolved on the Y chromosome from a ubiquitously transcribed X-Y identical gene. Nat Genet 22(3):224–226

    Article  CAS  PubMed  Google Scholar 

  • Ner-Gaon H, Leviatan N, Rubin E, Fluhr R (2007) Comparative cross-species alternative splicing in plants. Plant Physiol 144(3):1632–1641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rabello AR, Guimaraes CM, Rangel PH, da Silva FR, Seixas D, de Souza E et al (2008) Identification of drought-responsive genes in roots of upland rice (Oryza sativa L). BMC Genomics 9:485

    Article  PubMed  PubMed Central  Google Scholar 

  • Raikwar S, Srivastava VK, Gill SS, Tuteja R, Tuteja N (2015) Emerging importance of helicases in plant stress tolerance: characterization of Oryza sativa repair helicase XPB2 promoter and its functional validation in tobacco under multiple stresses. Front Plant Sci. 6:1094

    Article  PubMed  PubMed Central  Google Scholar 

  • Remy E, Cabrito TR, Baster P et al (2013) A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell 25(3):901–926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts A, Pimentel H, Trapnell C, Pachter L (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27(17):2325–2329

    Article  CAS  PubMed  Google Scholar 

  • Rogers MF, Thomas J, Reddy AS, Ben-Hur A (2012) SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol 13(1):R4

  • Roldan-Arjona T, Ariza RR (2009) Repair and tolerance of oxidative DNA damage in plants. Mutat Res 681(2–3):169–179

    Article  CAS  PubMed  Google Scholar 

  • Sandhu N, Singh A, Dixit S, Sta Cruz MT, Maturan PC, Jain RK et al (2014) Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress. BMC Genet 15:63

    Article  PubMed  PubMed Central  Google Scholar 

  • Streitner C, Koster T, Simpson CG, Shaw P, Danisman S, Brown JW et al (2012) An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana. Nucleic Acids Res 40(22):11240–11255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suji KK, Biji KR, Poornima R, Prince KS, Amudha K, Kavitha S et al (2012) Mapping QTLs for plant phenology and production traits using indica rice (Oryza sativa L.) lines adapted to rainfed environment. Mol Biotechnol 52(2):151–160

    Article  CAS  PubMed  Google Scholar 

  • Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (New York, NY) 321(5891):956–960

    Article  CAS  Google Scholar 

  • Swamy BP, Ahmed HU, Henry A, Mauleon R, Dixit S, Vikram P, et al. (2013) Genetic, physiological, and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought. PloS ONE 8(5):e62795

  • Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW (2012) Alternative splicing in plants–coming of age. Trends Plant Sci 17(10):616–623

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thatcher SR, Zhou W, Leonard A, Wang BB, Beatty M, Zastrow-Hayes G et al. (2014) Genome-wide analysis of alternative splicing in zea mays: landscape and genetic regulation. Plant Cell

  • Thatcher SR, Danilevskaya ON, Meng X, Beatty M, Zastrow-Hayes G, Harris C et al (2016) Genome-wide analysis of alternative splicing during development and drought stress in Maize. Plant Physiol 170(1):586–599

    Article  CAS  PubMed  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trijatmiko KR, Supriyanta Prasetiyono J, Thomson MJ, Vera Cruz CM, Moeljopawiro S et al (2014) Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population. Mol Breed 34:283–295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vassileva V, Simova-Stoilova L, Demirevska K, Feller U (2009) Variety-specific response of wheat (Triticum aestivum L.) leaf mitochondria to drought stress. J Plant Res 122(4):445–454

    Article  CAS  PubMed  Google Scholar 

  • Vikram P, Swamy BP, Dixit S, Ahmed HU, Teresa Sta Cruz M, Singh AK, et al. (2011) qDTY(1).(1), a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC genetics. 12:89

  • Vikram P, Swamy BP, Dixit S, Trinidad J, Sta Cruz MT, Maturan PC et al (2016) Linkages and interactions analysis of major effect drought grain yield QTLs in rice. PLoS ONE 11(3):e0151532

    Article  PubMed  PubMed Central  Google Scholar 

  • Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D’Angelo M et al (2014) A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype. BMC Plant Biol 14:99

    Article  PubMed  PubMed Central  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78

    Article  CAS  PubMed  Google Scholar 

  • Walters B, Lum G, Sablok G, Min XJ (2013) Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res 20(2):163–171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang XS, Zhu J, Mansueto L, Bruskiewich R (2005) Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map. J Zhejiang Univ Sci B. 6(5):382–388

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang X, Li G, Yang Y, Wang W, Zhang W, Pan H et al (2012) An RNA architectural locus control region involved in Dscam mutually exclusive splicing. Nat Commun 3:1255

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang M, Yuan F, Hao H et al (2013) BolOST1, an ortholog of Open Stomata 1 with alternative splicing products in Brassica oleracea, positively modulates drought responses in plants. Biochem Biophys Res Commun 442(3–4):214–220

    Article  CAS  PubMed  Google Scholar 

  • Wu HP, Su YS, Chen HC, Chen YR, Wu CC, Lin WD, et al. (2014) Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome Biol 15(1):R10

  • Xing D, Wang Y, Hamilton M, Ben-Hur A, Reddy AS (2015) Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININE-RICH45 uncovers the unexpected roles of this RNA binding protein in RNA processing. Plant Cell 27(12):3294–3308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yeap WC, Ooi T, Namasivayam P, Kulaveerasingam H, Ho CL (2012) EgRBP42 encoding an hnRNP-like RNA-binding protein from Elaeis guineensis Jacq. is responsive to abiotic stresses. Plant Cell Rep 31(10):1829–1843

    Article  CAS  PubMed  Google Scholar 

  • Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K et al (2006) Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics 172(2):1213–1228

    Article  PubMed  PubMed Central  Google Scholar 

  • Zeng L, Zhang Q, Sun R, Kong H, Zhang N, Ma H (2014) Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun 5:4956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang T, Huang XH, Dong L, Hu D, Ge C, Zhan YQ et al (2010a) PCBP-1 regulates alternative splicing of the CD44 gene and inhibits invasion in human hepatoma cell line HepG2 cells. Mol Cancer 9:72

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R et al (2010b) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20(5):646–654

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Zhang S, Zhang Y, Wang X, Li D, Li Q et al (2011) Arabidopsis floral initiator SKB1 confers high salt tolerance by regulating transcription and pre-mRNA splicing through altering histone H4R3 and small nuclear ribonucleoprotein LSM4 methylation. Plant Cell. 23(1):396–411

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang ZF, Li YY, Xiao BZ (2016) Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice. Sci Rep 6:19349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Z, Ma H, Lin K, Zhao Y, Chen Y, Xiong Z et al (2015) RNA-seq reveals complicated transcriptomic responses to drought stress in a nonmodel tropic plant, Bombax ceiba L. Evol Bioinform Online 11(Suppl 1):27–37

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank Dr. Shweta Kalve Kulkarni for her critical reading and comments on the manuscript and Professor Hongyu Zhang (College of informatics in Huazhong Agricultural University) for providing computing support. This work was supported financially by the National Natural Science Foundation of China (Grant Nos. 31000116 and 30800680), the Fundamental Research Fund for the Central Universities (Grant No. 2012ZYTS045), the self-determined research fund of Central China Normal University from the colleges’ basic research and operation of MOE (Grant No. CCNU2015A05033) and the National Special Key Project of China on Transgenic Research (Grant No. 2016ZX 08001-003).

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  1. Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China

    Zhengfeng Zhang

  2. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Benze Xiao

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  1. Zhengfeng Zhang
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ZZ conceived the study, performed data analysis, and wrote the manuscript. BX designed the project and wrote the manuscript. All authors read and approved the final manuscript.

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Correspondence to Benze Xiao.

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Supplemental Figure 1 The overall alternative splicing events in each replicate

. A represents the AS events in each replicate for lowland rice ZhenShan97. A represents the AS events in each replicate for upland rice IRAT109. Supplementary material 1 (EMF 4540 kb)

Supplemental Figure 2 The distribution of log2FPKM for isoforms with various number of reads between Zhenshan97 and for IRAT109.

A shows isoforms with higher amount of reads support in upland IRAT109 than lowland Zhenshan97; B shows isoforms with higher amount of reads support in Zhenshan97 than in IRAT109. X axis represents the log2 (FPKM) of isoforms in Zhenshan97 and Y axis represents the log2 (FPKM) of isoforms in IRAT109. Supplementary material 2 (WMF 8741 kb)

Supplemental Figure 3 Sequencing for AS PCR products of gene LOC_Os05g32600 in Panel D shown in Figure 2

. A shows the sequence amplified in Zhenshan97 leaf under drought stress. B shows the shorter sequence amplified in IRAT109 leaf under drought stress. The part of exon 3,4 and part of exon 2, 5 were amplified and sequenced using primers designed in exon 2, 5 and with the cDNA sequences as template. The black arrows show the primers and exon 2-5 was shown as light yellow, blue, pink and green, respectively. The sequences underlined with red line in A shows the sequence in the 5’ of exon 3 whereas it was spliced out in B, therefore present as an AA event. Supplementary material 3 (EMF 8135 kb)

Supplemental Figure 4 The GO terms in biological process for genes with changing AS patterns between the present rice genotypes.

The darker the box color, the significant level is higher. Supplementary material 4 (EMF 1956 kb)

Supplemental Figure 5 The GO terms in cell compartment for genes with changing AS patterns between the present rice genotypes.

The darker the box color, the significant level is higher. Supplementary material 5 (EMF 3693 kb)

Supplemental Figure 6 The GO terms in molecular function for genes with changing AS patterns between the present rice genotypes.

The darker the box color, the significant level is higher. Supplementary material 6 (EMF 1956 kb)

Supplemental Table 1.

The primers used for AS validation. Supplementary material 7 (DOCX 13 kb)

Supplemental Table 2.

The annotation for genes with changing AS patterns between Zhenshan97 and IRAT109 and involved in the spliceosome pathways including KO terms in KEGG and encoded proteins. Supplementary material 8 (DOCX 14 kb)

Supplemental Table 3.

The annotation for genes with changing AS patterns between Zhenshan97 and IRAT109 and involved in other pathways including KO terms in KEGG and encoded proteins. Supplementary material 9 (DOCX 18 kb)

Supplemental Table 4.

The drought related QTLs collected from references of 2006 to 2016. Supplementary material 10 (XLSX 18 kb)

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Zhang, Z., Xiao, B. Comparative alternative splicing analysis of two contrasting rice cultivars under drought stress and association of differential splicing genes with drought response QTLs. Euphytica 214, 73 (2018). https://doi.org/10.1007/s10681-018-2152-0

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