Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea

BMC Plant Biology

Volumn 15, Issue 1, 2015, Pages

  Bhardwaj, Ankur R ^a   Joshi, Gopal ^a   Kukreja, Bharti ^a   Malik, Vidhi ^a   Arora, Priyanka ^a   Pandey, Ritu ^a   Shukla, Rohit N ^b   Bankar, Kiran G ^b   Katiyar Agarwal, Surekha ^a   Goel, Shailendra ^a   Jagannath, Arun ^a   Kumar, Amar ^a   Agarwal, Manu ^a  

^a UNIVERSITY OF DELHI   (India)

^b Bionivid Technology Private Limited   (India)

Author keywords

Brassica juncea; Differential gene expression; Drought stress; Gene ontologies and pathways; High temperature stress; Kinases; Transcription factors; Transcriptome

Indexed keywords

MESSENGER RNA; PLANT PROTEIN; TRANSCRIPTOME;

CROP; DROUGHT; DRUG EFFECTS; ECONOMICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; MUSTARD; PHYSIOLOGICAL STRESS; PLANT GENE; QUALITY CONTROL; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TEMPERATURE;

CROPS, AGRICULTURAL; DROUGHTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENES, PLANT; MOLECULAR SEQUENCE ANNOTATION; MUSTARD PLANT; PLANT PROTEINS; QUALITY CONTROL; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL; TEMPERATURE; TRANSCRIPTOME;

EID: 84937708289     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/s12870-014-0405-1     Document Type: Article

References (68)

1. Ding Y, Tao Y, Zhu C. Emerging roles of microRNAs in the mediation of drought stress response in plants. J Exp Bot. 2013;64(11):3077-86.
2. Sunkar R, Li Y-F, Jagadeeswaran G. Functions of microRNAs in plant stress responses. Trends Plant Sci. 2012;17(4):196-203.
3. Lu X-Y, Huang X-L. Plant miRNAs and abiotic stress responses. Biochem Biophys Res Commun. 2008;368(3):458-62.
4. Ashraf M. Inducing drought tolerance in plants: recent advances. Biotechnol Adv. 2010;28(1):169-83.
5. Varshney RK, Bansal KC, Aggarwal PK, Datta SK, Craufurd PQ. Agricultural biotechnology for crop improvement in a variable climate: hope or hype? Trends Plant Sci. 2011;16(7):363-71.
6. Zhu J-K. Salt and drought stress signal transduction in plants. Annu Rev Plant Biol. 2002;53(1):247-73.
7. Mousavi S, Alisoltani A, Shiran B, Fallahi H, Ebrahimie E, Imani A, et al. De-novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS One. 2014;9(8):e104541.
8. Yates SA, Swain MT, Hegarty MJ, Chernukin I, Lowe M, Allison GG, et al. De-novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics. 2014;15(1):453.
9. Qi B, Yang Y, Yin Y, Xu M, Li H. De-novo sequencing, assembly, and analysis of the Taxodium 'Zhongshansa' roots and shoots transcriptome in response to short-term waterlogging. BMC Plant Biol. 2014;14(1):201.
10. Burton W, Salisbury P, Potts D: The potential of canola quality Brassica juncea as an oilseed crop for Australia. In: Proceeding of the 11th international rapeseed congress: 6-10th July 2003, Pages 5-7. The Royal Veterinary and Agricultural University, Copenhagen, Denmark
11. Liu S, Liu Z, Guan C. Advances in germplasm of oilseed Brassica juncea. J Plant Genetic Resour. 2007;3:351-8.
12. Oram R, Kirk J, Veness P, Hurlstone C, Edlington J, Halsall D. Breeding Indian mustard [Brassica juncea (L.) Czern.] for cold-pressed, edible oil production-a review. Crop Pasture Sci. 2005;56(6):581-96.
13. Pradhan A, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi Y, Pental D. A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers. Theor Appl Genet. 2003;106(4):607-14.
14. Pandey M, Srivastava AK, D'Souza SF, Penna S. Thiourea, a ROS scavenger, regulates source-to-sink relationship to enhance crop yield and oil content in Brassica juncea (L.). PLoS One. 2013;8(9):e73921.
15. Augustine R, Mukhopadhyay A, Bisht NC. Targeted silencing of BjMYB28 transcription factor gene directs development of low glucosinolate lines in oilseed Brassica juncea. Plant Biotechnol J. 2013;11(7):855-66.
16. Y-b L, Z-x T, Darmency H, Stewart Jr CN, Di K, Wei W, et al. The effects of seed size on hybrids formed between oilseed rape (Brassica napus) and wild brown mustard (B. juncea). PLoS One. 2012;7(6):e39705.
17. Østergaard L, Kempin SA, Bies D, Klee HJ, Yanofsky MF. Pod shatter-resistant Brassica fruit produced by ectopic expression of the FRUITFULL gene. Plant Biotechnol J. 2006;4(1):45-51.
18. Ramineni R, Sadumpati V, Khareedu VR, Vudem DR. Transgenic pearl millet male fertility restorer line (ICMP451) and hybrid (ICMH451) expressing Brassica juncea nonexpressor of Pathogenesis Related Genes 1 (BjNPR1) exhibit resistance to downy mildew disease. PLoS One. 2014;9(3):e90839.
19. Kaur P, Jost R, Sivasithamparam K, Barbetti MJ. Proteome analysis of the Albugo candida-Brassica juncea pathosystem reveals that the timing of the expression of defence-related genes is a crucial determinant of pathogenesis. J Exp Bot. 2011;62(3):1285-98.
20. Roussel S, Nicole M, Lopez F, Renard M, Chevre A, Brun H. Cytological investigation of resistance to Leptosphaeria maculans conferred to Brassica napus by introgressions originating from B. juncea or B. nigra B genome. Phytopathology. 1999;89(12):1200-13.
21. Mondal KK, Bhattacharya R, Koundal K, Chatterjee S. Transgenic Indian mustard (Brassica juncea) expressing tomato glucanase leads to arrested growth of Alternaria brassicae. Plant Cell Rep. 2007;26(2):247-52.
22. Zou X, Tan X, Hu C, Zeng L, Lu G, Fu G, et al. The transcriptome of Brassica napus L. roots under waterlogging at the seedling stage. Int J Mol Sci. 2013;14(2):2637-51.
23. Yu S, Zhang F, Yu Y, Zhang D, Zhao X, Wang W. Transcriptome profiling of dehydration stress in the Chinese cabbage (Brassica rapa L. ssp. pekinensis) by tag sequencing. Plant Mol Biol Report. 2012;30(1):17-28.
24. Torabi B, Ardestani FG. Effect of salt and drought stresses on germination components in canola (Brassica napus L.). Intl J Agri Crop Sci. 2013;5(15):1642-7.
25. Omidi H, Khazaei F, Hamzi Alvanagh S, Heidari-Sharifabad H. Improvement of seed germination traits in canola (Brassica napus L.) as affected by saline and drought stresses. Plant Ecophysiol. 2009;1(3):151-8.
26. Anand A, Nagarajan S, Kishore N, Verma A. Impact of high temperature at pod development stage on yield and quality of Brassica juncea cultivars under controlled conditions. Indian J Agric Sci. 2010;80(12):1043-7.
27. Youssefi A, Nshanian A, Aziz M. Evaluation of influences of drought stress in terminal growth duration on yield and yield components of different spring Brassica oilseed species. Am-Euras J Agric Environ Sci. 2011;11(3):406-10.
28. Sun Q, Zhou G, Cai Y, Fan Y, Zhu X, Liu Y, et al. Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing. BMC Plant Biol. 2012;12(1):53.
29. Liu X, Lu Y, Yuan Y, Liu S, Guan C, Chen S, et al. De-novo transcriptome of Brassica juncea seed coat and identification of genes for the biosynthesis of flavonoids. PLoS One. 2013;8(8):e71110.
30. Paritosh K, Gupta V, Yadava SK, Singh P, Pradhan AK, Pental D. RNA-Seq based SNPs for mapping in Brassica juncea (AABB): synteny analysis between the two constituent genomes A (from B. rapa) and B (from B. nigra) shows highly divergent gene block arrangement and unique block fragmentation patterns. BMC Genomics. 2014;15(1):396.
31. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de-novo assembler. Gigascience. 2012;1(1):18.
32. Kumar PP. Regulation of biotic and abiotic stress responses by plant hormones. Plant Cell Rep. 2013;32(7):943.
33. Munne-Bosch S, Muller M. Hormonal cross-talk in plant development and stress responses. Frontiers Plant Sci. 2013;4:529.
34. Peleg Z, Blumwald E. Hormone balance and abiotic stress tolerance in crop plants. Curr Opin Plant Biol. 2011;14(3):290-5.
35. The Arabidopsis Genome Initiative (AGI). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796-815.
36. Surget-Groba Y, Montoya-Burgos JI. Optimization of de-novo transcriptome assembly from next-generation sequencing data. Genome Res. 2010;20(10):1432-40.
37. Rismani-Yazdi H, Haznedaroglu BZ, Reeves D, Peccia J. Optimization of de-novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms. BMC Bioinformatics. 2012;13:170.
38. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, et al. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 2007;50(2):347-63.
39. Langridge P, Paltridge N, Fincher G. Functional genomics of abiotic stress tolerance in cereals. Brief Funct Genomic Proteomic. 2006;4(4):343-54.
40. Liu HT, Gao F, Cui SJ, Han JL, Sun DY, Zhou RG. Primary evidence for involvement of IP3 in heat-shock signal transduction in Arabidopsis. Cell Res. 2006;16(4):394-400.
41. Mittler R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002;7(9):405-10.
42. Nakashima K, Ito Y, Yamaguchi-Shinozaki K. Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol. 2009;149(1):88-95.
43. Rizhsky L, Liang H, Shuman J, Shulaev V, Davletova S, Mittler R. When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol. 2004;134(4):1683-96.
44. Sreenivasulu N, Sopory S, Kavi Kishor P. Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches. Gene. 2007;388(1):1-13.
45. Wang W, Vinocur B, Altman A. Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta. 2003;218(1):1-14.
46. Lata C, Prasad M. Role of DREBs in regulation of abiotic stress responses in plants. J Exp Bot. 2011;62(14):4731-48.
47. Scharf K-D, Berberich T, Ebersberger I, Nover L. The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. 2012;1819(2):104-19.
48. Chen L, Song Y, Li S, Zhang L, Zou C, Yu D. The role of WRKY transcription factors in plant abiotic stresses. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms. 2012;1819(2):120-8.
49. Li C, Ng CK-Y, Fan L-M. MYB transcription factors, active players in abiotic stress signaling. Environ Experiment Botany 2014. doi:10.1016/j.envexpbot.2014.06.014
50. Rao X-L, Zhang X-H, Li R-J, Shi H-T, Lu Y-T. A calcium sensor-interacting protein kinase negatively regulates salt stress tolerance in rice (Oryza sativa). Function Plant Biol. 2011;38(6):441-50.
51. Snedden WA, Fromm H. Calmodulin, calmodulin-related proteins and plant responses to the environment. Trends Plant Sci. 1998;3(8):299-304.
52. Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, et al. Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica. Eukaryot Cell. 2006;5(5):871-5.
53. Kotak S, Larkindale J, Lee U, von Koskull-Döring P, Vierling E, Scharf K-D. Complexity of the heat stress response in plants. Curr Opin Plant Biol. 2007;10(3):310-6.
54. Queitsch C, Hong S-W, Vierling E, Lindquist S. Heat shock protein 101 plays a crucial role in thermotolerance in Arabidopsis. Plant Cell Online. 2000;12(4):479-92.
55. Nieto-Sotelo J, Martínez LM, Ponce G, Cassab GI, Alagón A, Meeley RB, et al. Maize HSP101 plays important roles in both induced and basal thermotolerance and primary root growth. Plant Cell Online. 2002;14(7):1621-33.
56. Y-y C, H-c L, N-y L, W-t C, C-n W, S-h C, et al. A heat-inducible transcription factor, HsfA2, is required for extension of acquired thermotolerance in Arabidopsis. Plant Physiol. 2007;143(1):251-62.
57. Busch W, Wunderlich M, Schöffl F. Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana. Plant J. 2005;41(1):1-14.
58. Tunnacliffe A, Wise MJ. The continuing conundrum of the LEA proteins. Naturwissenschaften. 2007;94(10):791-812.
59. Veeranagamallaiah G, Prasanthi J, Reddy KE, Pandurangaiah M, Babu OS, Sudhakar C. Group 1 and 2 LEA protein expression correlates with a decrease in water stress induced protein aggregation in horsegram during germination and seedling growth. J Plant Physiol. 2011;168(7):671-7.
60. Goyal K, Walton L, Tunnacliffe A. LEA proteins prevent protein aggregation due to water stress. Biochem J. 2005;388:151-7.
61. Garg AK, Kim J-K, Owens TG, Ranwala AP, Do Choi Y, Kochian LV, et al. Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proc Natl Acad Sci. 2002;99(25):15898-903.
62. Kaplan F, Kopka J, Haskell DW, Zhao W, Schiller KC, Gatzke N, et al. Exploring the temperature-stress metabolome of Arabidopsis. Plant Physiol. 2004;136(4):4159-68.
63. Ferrari S, Vairo D, Ausubel FM, Cervone F, De Lorenzo G. Tandemly duplicated Arabidopsis genes that encode polygalacturonase-inhibiting proteins are regulated coordinately by different signal transduction pathways in response to fungal infection. Plant Cell Online. 2003;15(1):93-106.
64. Kumar GM, Mamidala P, Podile AR. Regulation of Polygalacturonase-inhibitory proteins in plants is highly dependent on stress and light responsive elements. Plant Omics. 2009;2(6):238.
65. Zhong R, Ye Z-H. The SAC domain-containing protein gene family in Arabidopsis. Plant Physiol. 2003;132(2):544-55.
66. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987;162(1):156-9.
67. Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619.
68. Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010;26(5):680-2.