Nonsense-mediated decay of sucrose synthase 1 mRNA with induced premature chain termination codon during cold acclimation in winter wheat

Cold acclimation induces the expression of cold-regulated genes needed to protect plants against freezing damage. Fourteen candidate genes were identified as being differentially expressed (presence/absence) between cold acclimated and nonacclimated crown and leaf tissues of 2 winter wheat lines using the cDNA-AFLP method. Two TILLING populations originating from the 2 winter wheat lines were further developed in order to create mutant forms of the candidate genes to verify their role in freezing-tolerance formation. Exon 8 of the identified differentially expressed sucrose synthase 1 (Ss1) gene was chosen for mutation detection by high-resolution melting analysis. A total of 75.68 kb of DNA was screened and 2 novel alleles of the Ss1 gene were identified, of which 1 was silent and 1 was a nonsense (premature stop codon) mutation. qRT-PCR analysis showed that premature stop codon mutation has a strong negative effect on Ss1 gene expression in nonacclimated leaves as well as in crowns and leaves collected at 2, 4, and 6 weeks of cold acclimation compared with the wild-type winter wheat line. Further work will reveal the effect of the mutation on cold tolerance of winter wheat and will enable the assessment of the role of Ss1 in the cold acclimation process.

Anahtar Kelimeler:

High-resolution melting analysis, premature stop codon, Triticum aestivum L., TILLING

Nonsense-mediated decay of sucrose synthase 1 mRNA with induced premature chain termination codon during cold acclimation in winter wheat

Keywords:

High-resolution melting analysis, premature stop codon, Triticum aestivum L., TILLING,

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Armonienė R, Jonavičienė K, Ruzgas V, Brazauskas G (2013a). Isolation of differentially expressed genes in wheat caryopses with contrasting starch granule size. Cent Eur J Biol 8: 297–305.
Armonienė R, Liatukas Ž, Brazauskas G (2013b). Evaluation of freezing tolerance of winter wheat under controlled conditions and in the field. Zemdirbyste 100: 417–424.
Bolouri-Moghaddam MR, Le Roy K, Xiang L, Rolland F, Van den Ende W (2010). Sugar signalling and antioxidant network connections in plant cells. FEBS J 277: 2022–2037.
Botticella E, Sestili F, Hernandez-Lopez A, Phillips A, Lafiandra D (2011). High Resolution Melting analysis for the detection of EMS induced mutations in wheat Sbella genes. BMC Plant Biol 11: 156.
Chen A, Dubcovsky J (2012). Wheat TILLING mutants show that the vernalization gene VRN1 down-regulates the flowering repressor VRN2 in leaves but is not essential for flowering. PLoS Genet 8: e1003134.
Chen Y, Wilde HD (2011). Mutation scanning of peach floral genes. BMC Plant Biol 11: 96.
Chawade A, Sikora P, Brautigamet M, Larsson M, Vivekanand V, All Nakash M, Chen T, Olsson O (2010). Development and characterization of an oat TILLING-population and identification of mutations in lignin and beta-glucan biosynthesis genes. BMC Plant Biol 10: 86.
Crespi MD, Zabaleta EJ, Pontis HG, Salerno GL (1991). Sucrose synthase expression during cold acclimation in wheat. Plant Physiol 96: 887–891.
Dong C, Vincent K, Sharp P (2009). Simultaneous mutation detection of three homoeologous genes in wheat by High Resolution Melting analysis and Mutation Surveyor®. BMC Plant Biol 9: 143.
Gady ALF, Hermans FWK, Van de Wal MHBJ, Van Loo EN, Visser RGF, Bachem CWB (2009). Implementation of two high through-put techniques in a novel application, detecting point mutations in large EMS mutated plant populations. Plant Methods 5: 13.
Gilchrist EJ, Sidebottom CH D, Koh CS, MacInnes T, Sharpe AG, Haughn GWA (2013). A mutant Brassica napus (Canola) population for the identification of new genetic diversity via TILLING and next generation sequencing. PLoS ONE 8: e84303.
Gilmour SJ, Sebolt AM, Salazar MP, Everard JD, Thomashow MF (2000). Overexpression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol 124: 1854–1865.
Gottwald S, Bauer P, Komatsuda T, Lundqvist U, Stein N (2009). TILLING in the two-rowed barley cultivar ‘Barke’ reveals preferred sites of functional diversity in the gene HvHox1. BMC Res Notes 2: 2581.
Horst I, Welham T, Kelly S, Kaneko T, Sato S, Tabata S, Parniske M, Wang TL (2007). TILLING mutants of Lotus japonicus reveal that nitrogen assimilation and fixation can occur in the absence of nodule-enhanced sucrose synthase. Plant Physiol 144: 806–820.
Janská, Aprile A, Zámečník J, Cattivelli L, Ovesná J (2011). Transcriptional responses of winter barley to cold indicate nucleosome remodelling as a specific feature of crown tissues. Funct Integr Genomic 11: 307–325.
Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J et al. (2012). Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 40: 1–16.
Kaplan F, Sung DY Guy CL (2006). Roles of β-amylase and starch breakdown during temperatures stress. Physiol Plantarum 126: 120–128.
Kosová K, Prásil IT, Prásilová P, Vítámvás P, Chrpová J (2010). The development of frost tolerance and DHN5 protein accumulation in barley (Hordeum vulgare) doubled haploid lines from Atlas 68 × Igri cross during cold acclimation. J Plant Physiol 167: 343– 350.
Kurowska M, Daszkowska-Golec A, Gruszka D, Marzec M, Szurman M, Szarejko I, Maluszynski M (2011). TILLING - a shortcut in functional genomics. J Appl Genet 52: 371–390.
Lassner MW, Peterson P, Yoder JI (1989). Simultaneous amplification of multiple DNA fragments by polymerase chain reaction in the analysis of transgenic plants and their progeny. Plant Mol Biol Rep 7: 116–128.
Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C (2004). Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clin Chem 50: 1156–1164.
Livak KJ, Schmittgen TD (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method. Methods 25: 402–408.
Livingston DP, Premakumar R, Tallury SP (2006). Carbohydrate partitioning between upper and lower regions of the crown in oat and rye during cold acclimation and freezing. Cryobiology 52: 200–208.
Lochlainn SÓ, Amoah S, Graham S, Alamer K, Rios JJ, Kurup S, Stoute A, Hammond JP, Østergaard L, King GJ et al. (2011). High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. Plant Methods 7: 43.
Maraña C, Garcla-Olmedo F, Carbonero P (1988). Linked sucrose synthase genes in group-7 chromosomes in hexaploid wheat (Triticum aestivum L.). Gene 63: 253–260.
Martín B, Ramiro M, Martínez-Zapater J M, Alonso-Blanco C (2009). A high-density collection of EMS-induced mutations for TILLING in Landsberg erecta genetic background of Arabidopsis. BMC Plant Biol 9: 147.
Martinez de Ilarduya O, Vicente-Carbajosa J, Sanchez de la Hoz P, Carbonero P (1993). Sucrose synthase genes in barley. cDNA cloning of the Ss2 type and tissue-specific expression of Ss1 and Ss2. FEBS Lett 320: 177–181.
Martino A, Mancuso T, Rossi AM (2010). Application of high- resolution melting to large-scale, high-throughput SNP genotyping: a comparison with the TaqMan® method. J Biomol Screen 15: 623–629.
Nägele T, Stutz S, Hörmiller II, Heyer AG (2012). Identification of a metabolic bottleneck for cold acclimation in Arabidopsis thaliana. Plant J 72: 102–114.
Paolacci AR, Tanzarella OA, Porceddu E, Ciaffi M (2009). Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 10: 11.
RahaieM, Xue GP, SchenkPM (2013). The role of transcription factors in wheat under different abiotic stresses. In: Vahdati K, Leslie C, editors. Abiotic stress - plant responses and applications in agriculture. Rijeka, Croatia: InTech, pp. 367–385.
Rakszegi M, Kisgyörgy BN, Tearall K, Shewry PR, Láng L, Phillips A, Bed Z (2010). Diversity of agronomic and morphological traits in a mutant population of bread wheat studied in the Health grain program. Euphytica 174: 409–421.
Reddy TV, Dwivedi S, Sharma NK (2012). Development of TILLING by sequencing platform towards enhanced leaf yield in tobacco. Ind Crop Prod 40: 324–335.
Reinheimer JL, Barr AR, Eglinton JK (2004). QTL mapping of chromosomal regions conferring reproductive frost tolerance in barley (Hordeum vulgare L.). Theor Appl Genet 109: 1267– 1274.
Reulland E, Vaultier M, Zachowski A, Hurry V (2009). Cold signalling and cold acclimation in plants. Adv Bot Res 49: 36–150.
Saito M, Nakamura T (2005). Two point mutations identified in emmer wheat generate null Wx-A1 alleles. Theor Appl Genet 110: 276–282.
Sasaki H, Ichimura K, Imada S, Yamaki S (2001). Sucrose synthase and sucrose phosphate synthase, but not acid invertase, are regulated by cold acclimation and deacclimation in cabbage seedlings. J Plant Physiol 158: 847–852.
Savitch LV, Harney T, Huner NPA (2000). Sucrose metabolism in spring and winter wheat in response to high irradiance, cold stress and cold acclimation. Physiol Plantarum 108: 270–278.
Sikora P, Chawade A, Larsson M, Olsson J, Olsson O (2011). Mutagenesis as a tool in plant genetics, functional genomics, and breeding. Int J Plant Genomics 2011: 314829.
Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005). A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 23: 75–81.
Slade AJ, McGuire C, Loeffler D, Mullenberg J, Skinner W, Fazio G, Holm A, Brandt KM, Steine MN, Goodstal J et al. (2012). Development of high amylose wheat through TILLING. BMC Plant Biol 12: 69.
Steponkus PL (1984). Role of the plasma-membrane in freezing injury and cold-acclimation. Ann Rev Plant Physiol 35: 543– 584.
Thomashow MF (1999). Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Ann Rev Plant Physio 50: 571–599.
Thomashow MF (2010). Molecular basis of plant cold acclimation: Insights gained from studying the CBF cold response pathway. Plant Physiol 154: 571–577.
Uauy C, Paraiso F, Colasuonno P, Tran RK, Tsai H, Berardi S, Comai L, Dubcovsky J (2009). A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol 9: 115.
Wang T, Uauy C, Till B, Liu CM (2010). TILLING and associated technologies. J Integr Plant Biol 52: 1027–1030.
Winfield MO, Lu C, Wilson ID, Coghill JA, Edwards KJ (2010). Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol J 8: 749–771.
Zhang LL, Zhao MG, Tian QY, Zhang WH (2011). Comparative studies on tolerance of Medicago truncatula and Medicago falcata to freezing. Planta 234: 445–457.