Transcriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress

详细信息    查看全文

• 作者：B. Shaun Bushman ; Keenan L. Amundsen ; Scott E. Warnke ; Joseph G. Robins…
• 关键词：Poa pratensis ; Kentucky bluegrass ; Salinity stress ; Transcriptome ; RNA ; seq ; Salt tolerance
• 刊名：BMC Genomics
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：17
• 期：1
• 全文大小：1,330 KB
• 参考文献：1.Huff DR. Kentucky bluegrass. In: Casler MD, Duncan RR, editors. Turfgrass biology, genetics, and breeding. Hoboken: John Wiley and Sons Inc; 2003. p. 27–38.
  2.Comstock JP, Ehleringer JR. Plant adaptation in the Great-Basin and Colorado plateau. Great Basin Naturalist. 1992;52(3):195–215.
  3.Marcum KB. Use of saline and non-potable water in the turfgrass industry: constraints and developments. Agric Water Manage. 2006;80(1–3):132–46.CrossRef
  4.Lockett AM, Devittz DA, Morris RL. Impact of reuse water on golf course soil and turfgrass parameters monitored over a 4.5-year period. Hortscience. 2008;43(7):2210–8.
  5.Alshammary SF, Qian YL, Wallner SJ. Growth response of four turfgrass species to salinity. Agric Water Manage. 2004;66(2):97–111.CrossRef
  6.Horst GL, Taylor RM. Germination and initial growth of Kentucky bluegrass in soluble salts. Agron J. 1983;75(4):679–81.CrossRef
  7.Robins JG, Bushman BS, Waldron BL, Johnson PG. Variation within Poa Germplasm for salinity tolerance. Hortscience. 2009;44(6):1517–21.
  8.Poss JA, Russell WB, Bonos SA, Grieve CM. Salt tolerance and canopy reflectance of Kentucky bluegrass cultivars. Hortscience. 2010;45(6):952–60.
  9.Qian YL, Wilhelm SJ, Marcum KB. Comparative responses of two Kentucky bluegrass cultivars to salinity stress. Crop Sci. 2001;41(6):1895–900.CrossRef
  10.Marcum KB. Physiological adaptations of turfgrasses to salinity stress. In: Pessarakli M, editor. Turfgrass management and physiology. Raton: CRC Press; 2008.
  11.Koch MJ, Bonos SA. An overhead irrigation screening technique for salinity tolerance in cool-season turfgrasses. Crop Sci. 2010;50(6):2613–9.CrossRef
  12.Torello WA, Rice LA. Effects of NACL stress on proline and cation accumulation in salt sensitive and tolerant turfgrasses. Plant and Soil. 1986;93(2):241–7.CrossRef
  13.Carrow RN, Duncan RR. Salt-affected turfgrass sites: assessment and management. Hoboken: John Wiley and Sons Inc.; 1998.
  14.Koch MJ, Huang BR, Bonos SA. Salinity tolerance of Kentucky bluegrass cultivars and selections using an overhead irrigated screening technique. Crop Sci. 2011;51(6):2846–57.CrossRef
  15.Arghavani M, Kafi M, Babalar M, Naderi R, Hoque MA, Murata Y. Improvement of salt tolerance in Kentucky bluegrass by trinexapac-ethyl. Hortscience. 2012;47(8):1163–70.
  16.Yang ZM, Yu JJ, Merewitz E, Huang BR. Differential effects of abscisic acid and glycine betaine on physiological responses to drought and salinity stress for two perennial grass species. J Am Soc Hort Sci. 2012;137(2):96–106.
  17.Bushman BS, Warnke SE, Amundsen KL, Combs KM, Johnson PG. Molecular markers highlight variation within and among Kentucky bluegrass varieties and accessions. Crop Sci. 2013;53(5):2245–54.
  18.Jamil A, Riaz S, Ashraf M, Foolad MR. Gene expression profiling of plants under salt stress. Crit Rev Plant Sci. 2011;30(5):435–58.CrossRef
  19.Munns R. Genes and salt tolerance: bringing them together. New Phytologist. 2005;167(3):645–63.PubMed CrossRef
  20.Zeng Q, Ling Q, Fan L, Li Y, Hu F, Chen J, et al. Transcriptome profiling of sugarcane roots in response to low potassium stress. PLoS One. 2015;10(5):e0126306.PubMed PubMedCentral CrossRef
  21.Xiong L, Zhu JK. Abiotic stress signal transduction in plants: Molecular and genetic perspectives. Physiol Plant. 2001;112(2):152–66.PubMed CrossRef
  22.Maathuis FJM. Sodium in plants: perception, signalling, and regulation of sodium fluxes. J Exp Bot. 2014;65(3):849–58.PubMed CrossRef
  23.Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ. Plant cellular and molecular responses to high salinity. Annu Rev Plant Physiol Plant Mol Biol. 2000;51:463–99.PubMed CrossRef
  24.Li JG, Li XJ, Guo L, Lu F, Feng XJ, He K, et al. A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J Exp Bot. 2006;57(6):1263–73.PubMed CrossRef
  25.Mu RL, Cao YR, Liu YF, Lei G, Zou HF, Liao Y, et al. An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in Arabidopsis. Cell Res. 2009;19(11):1291–304.PubMed CrossRef
  26.Reiser L, Sanchez-Baracaldo P, Hake S. Knots in the family tree: evolutionary relationships and functions of knox homeobox genes. Plant Mol Biol. 2000;42(1):151–66.PubMed CrossRef
  27.Giri J, Vij S, Dansana PK, Tyagi AK. Rice A20/AN1 zinc-finger containing stress-associated proteins (SAP1/11) and a receptor-like cytoplasmic kinase (OsRLCK253) interact via A20 zinc-finger and confer abiotic stress tolerance in transgenic Arabidopsis plants. New Phytologist. 2011;191(3):721–32.PubMed CrossRef
  28.Wang R, Jing W, Xiao L, Jin Y, Shen L, Zhang W. The rice high-affinity potassium Transporter1;1 is involved in salt tolerance and regulated by an MYB-type transcription factor. Plant Physiol. 2015;168(3):1076–90.PubMed CrossRef
  29.Jacoby RP, Taylor NL, Millar AH. The role of mitochondrial respiration in salinity tolerance. Trends Plant Sci. 2011;16(11):614–23.PubMed CrossRef
  30.Biswas MS, Mano J. Lipid peroxide-derived short-chain carbonyls mediate hydrogen peroxide-induced and salt-induced programmed cell death in plants. Plant Physiol. 2015;168(3):885–98.PubMed CrossRef
  31.Qi YC, Liu WQ, Qiu LY, Zhang SM, Ma L, Zhang H. Overexpression of glutathione S-transferase gene increases salt tolerance of arabidopsis. Russ J Plant Physiol. 2010;57(2):233–40.CrossRef
  32.Guo L, Devaiah SP, Narasimhan R, Pan X, Zhang Y, Zhang W, et al. Cytosolic glyceraldehyde-3-phosphate dehydrogenases interact with phospholipase Dδ to transduce hydrogen peroxide signals in the Arabidopsis response to stress. Plant Cell. 2012;24(5):2200–12.PubMed PubMedCentral CrossRef
  33.Zhang X-H, Rao X-L, Shi H-T, Li R-J, Lu Y-T. Overexpression of a cytosolic glyceraldehyde-3-phosphate dehydrogenase gene OsGAPC3 confers salt tolerance in rice. Plant Cell Tiss Organ Cult. 2011;107(1):1–11.CrossRef
  34.Ouellet F, Overvoorde PJ, Theologis A. IAA17/AXR3: Biochemical insight into an auxin mutant phenotype. Plant Cell. 2001;13(4):829–42.PubMed PubMedCentral CrossRef
  35.Nakano T, Suzuki K, Fujimura T, Shinshi H. Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice. Plant Physiol. 2006;140(2):411–32.PubMed PubMedCentral CrossRef
  36.Cheng XF, Wang ZY. Overexpression of COL9, a CONSTANS-LIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. Plant J. 2005;43(5):758–68.PubMed CrossRef
  37.Dietz KJ, Tavakoli N, Kluge C, Mimura T, Sharma SS, Harris GC, et al. Significance of the V-type ATPase for the adaptation to stressful growth conditions and its regulation on the molecular and biochemical level. J Exp Bot. 2001;52(363):1969–80.PubMed CrossRef
  38.Sarda X, Tousch D, Ferrare K, Legrand E, Dupuis JM, Casse-Delbart F, et al. Two TIP-like genes encoding aquaporins are expressed in sunflower guard cells. Plant J. 1997;12(5):1103–11.PubMed CrossRef
  39.Jiang X, Leidi EO, Pardo JM. How do vacuolar NHX exchangers function in plant salt tolerance? Plant Signal Behav. 2010;5(7):792–5.PubMed PubMedCentral CrossRef
  40.Alscher RG, Erturk N, Heath LS. Role of superoxide dismutases (SODs) in controlling oxidative stress in plants. J Exp Bot. 2002;53(372):1331–41.PubMed CrossRef
  41.Fatehi F, Hosseinzadeh A, Alizadeh H, Brimavandi T, Struik PC. The proteome response of salt-resistant and salt-sensitive barley genotypes to long-term salinity stress. Mol Biol Rep. 2012;39(5):6387–97.PubMed CrossRef
  42.Boursiac Y, Chen S, Luu D-T, Sorieul M, van den Dries N, Maurel C. Early effects of salinity on water transport in Arabidopsis roots. Molecular and cellular features of aquaporin expression. Plant Physiol. 2005;139(2):790–805.PubMed PubMedCentral CrossRef
  43.Peel MD, Waldron BL, Jensen KB, Chatterton NJ, Horton H, Dudley LM. Screening for salinity tolerance in alfalfa: a repeatable method. Crop Sci. 2004;44(6):2049–53.CrossRef
  44.Ritchie ME, Phipson B, Wu D, Hu YF, Law CW, Shi W, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.PubMed PubMedCentral CrossRef
  45.Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512.PubMed CrossRef
  46.Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.PubMed PubMedCentral CrossRef
  47.Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BMG, et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013;29(8):1035–43.PubMed PubMedCentral CrossRef
  48.Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.PubMed PubMedCentral CrossRef
  49.Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(D1):D222–30.PubMed PubMedCentral CrossRef
  50.Team RC. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2015.
  
• 作者单位：B. Shaun Bushman (1)
  Keenan L. Amundsen (2)
  Scott E. Warnke (3)
  Joseph G. Robins (1)
  Paul G. Johnson (4)
  
  1. USDA-ARS Forage and Range Research Laboratory, 700 North 1100 East, Logan, UT, 84322-6300, USA
  2. Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
  3. USDA-ARS Floral and Nursery Plants Research Unit, Beltsville, MD, USA
  4. Department of Plants, Soils, and Climate, Utah State University, Logan, UT, USA
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Kentucky bluegrass (Poa pratensis L.) is a prominent turfgrass in the cool-season regions, but it is sensitive to salt stress. Previously, a relatively salt tolerant Kentucky bluegrass accession was identified that maintained green colour under consistent salt applications. In this study, a transcriptome study between the tolerant (PI 372742) accession and a salt susceptible (PI 368233) accession was conducted, under control and salt treatments, and in shoot and root tissues.