RNA-seq Analysis Reveals Ethylene-Mediated Reproductive Organ Development and Abscission in Soybean (Glycine max L. Merr.)

Plant Molecular Biology Reporter

Volumn 31, Issue 3, 2013, Pages 607-619

  Cheng, Yun Qing ^a   Liu, Jian Feng ^a   Yang, Xiangdong ^b   Ma, Rui ^b   Liu, Chunming ^a   Liu, Qiang ^a  

^a JILIN NORMAL UNIVERSITY   (China)

^b JILIN ACADEMY OF AGRICULTURAL SCIENCES   (China)

Author keywords

Abscission; Development; Reproductive organ; RNA Seq analysis; Soybean

Indexed keywords

GLYCINE MAX;

EID: 84877814362     PISSN: 07359640     EISSN: 15729818     Source Type: Journal    
DOI: 10.1007/s11105-012-0533-4     Document Type: Article

References (48)

1. Adams DO, Yang SF (1979) Ethylene biosynthesis: identification of 1-aminocyclopropane-l -carboxylic acid as an intermediate in the conversion of methionine to ethylene. Proc Natl Acad Sci USA 76: 170-174.
2. Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7: 524-536.
3. Amit I, Garber M, Chevrier N, Leite AP, Donner Y et al (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326: 257-263.
4. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995.
5. Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29: 1165-1188.
6. Chen MK, Hsu WH, Lee PF, Thiruvengadam M, Chen HI et al (2011) The MADS box gene, FOREVER YOUNG FLOWER, acts as a repressor controlling floral organ senescence and abscission in Arabidopsis. Plant J 68: 168-185.
7. Cheng YQ, Yang J, An LJ, Liu JF, Chen ZW (2008) Effects of ethylene on yield and floral organ development in soybean (Glycine max). J Zhejiang Univ (Agric Life Sci) 34: 540-545.
8. Cheng YQ, Zhao GL, Liu JF, Chen ZW, Zhang WW (2010) Effects of ethylene inhibitor and promoter on photosynthetic characteristics of soybean (Glycine max) seedling leaves. J Zhejiang Univ (Agric Life Sci) 36: 419-426.
9. Chervin C, Deluc L (2010) Ethylene signaling receptors and transcription factors over the grape berry development: gene expression profiling. Vitis 49: 129-136.
10. Cloonan N, Grimmond SM (2008) Transcriptome content and dynamics at single-nucleotide resolution. Genome Biol 9: 234.
11. Djanaguiraman M, Prasad PVV, Al-Khatib K (2011) Ethylene perception inhibitor 1-MCP decreases oxidative damage of leaves through enhanced antioxidant defense mechanisms in soybean plants grown under high temperature stress. Environ Exp Bot 71: 215-223.
12. Dong CH, Jang M, Scharein B, Malach A, Rivarola M et al (2010) Molecular association of the Arabidopsis ETR1 Ethylene receptor and a regulator of ethylene signaling, RTE1. J Biol Chem 285: 40706-40713.
13. Eveland A, Satoh-Nagasawa N, Goldshmidt A, Meyer S, Beatty M et al (2010) Digital gene expression signatures for maize development. Plant Physiol 154: 1024-1039.
14. Fehr WR, Caviness CF, Burmood DT, Pennington JS (1971) Stage of development descriptions for soybeans, glycine max. (L). Merrill. Fehr & Caviness et al. Crop Sci 11: 929-931.
15. Gniazdowska A, Krasuska U, Czajkowska K, Bogatek R (2010) Nitric oxide, hydrogen cyanide and ethylene are required in the control of germination and undisturbed development of young apple seedlings. Plant Growth Regul 61: 75-84.
16. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW et al (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
17. Hamilton AJ, Bouzayen M, Grierson D (1991) Identification of a tomato gene for the ethylene-forming enzyme by expression in yeast. Proc Natl Acad Sci USA 88: 7434-7437.
18. Heindl JC, Brun WA (1984) Patterns of reproductive abscission, seed yield, and yield components in soybean. Crop Sci 24: 542-545.
19. Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J 61: 1041-1052.
20. Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH et al (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and interlab portability over five microarray platforms. Nucleic Acids Res 36: e141.
21. Iqbal N, Nazar R, Syeed S, Masood A, Khan NA (2011) Exogenously-sourced ethylene increases stomatal conductance, photosynthesis, and growth under optimal and deficient nitrogen fertilization in mustard. J Exp Bot 62: 4955-4963.
22. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: 480-484.
23. Kubis S, Patel R, Combe J, Bedard J, Kovacheva S et al (2004) Functional specialization amongst the Arabidopsis Toc159 family of chloroplast protein import receptors. Plant Cell 16: 2059-2077.
24. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
25. Li RQ, Yu C, Li YR, Lam TW, Yiu SM et al (2009) SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
26. Lin ZF, Zhong SL, Grierson D (2009) Recent advances in ethylene research. J Exp Bot 60: 3311-3336.
27. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC et al (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
28. Lorbiecke R, Sauter M (1999) Adventitious root growth and cell cycle induction in deepwater rice (Oryza sativa L.). Plant Physiol 119: 21-29.
29. Ma Y, Szostkiewicz I, Korte A, Moes D, Yang Y et al (2009) Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 324: 1064-1068.
30. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
31. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
32. Nambeesan S, AbuQamar S, Laluk K, Mattoo AK, Mickelbart MV et al (2012) Polyamines attenuate ethylene-mediated defense responses to abrogate resistance to Botrytis cinerea in tomato. Plant Physiol 158: 1034-1045.
33. Neumann PM (1995) The role of cell wall adjustment in plant resistance to water deficits (review and interpretation). Crop Sci 35: 1258-1266.
34. Nieuwland J, Feron R, Huisman BAH, Fasolino A, Hilbers CW et al (2005) Lipid transfer proteins enhance cell wall extension in tobacco. Plant Cell 17: 2009-2019.
35. Pasek S, Risler JL, Brezellec P (2006) The role of domain redundancy in genetic robustness against null mutations. J Mol Biol 362: 184-191.
36. Rylott PD, Smith ML (1990) Effects of applied plant growth substances on pod set in broad beans (Vicia faba var. Major). J Agric Sci Camb 114: 41-47.
37. Sato T, Theologis A (1989) Cloning the mRNA encoding 1-aminocyclopropane-1- carboxylate synthase, the key enzyme for ethylene biosynthesis in plants. Proc Natl Acad Sci USA 86: 6621-6625.
38. Schaller GE (2012) Ethylene and the regulation of plant development. BMC Biol 10: 9. doi: 10. 1186/1741-7007-10-9.
39. Singh AP, Tripathi SK, Nath P, Sane AP (2011) Petal abscission in rose is associated with the differential expression of two ethylene-responsive xyloglucan endotransglucosylase/hydrolase genes, RbXTH1 and RbXTH2. J Exp Bot 62: 5091-5103.
40. Stangeland B, Nestestog R, Grini PE, Skrbo N, Berg A et al (2005) Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5′ end of genes. J Exp Bot 56: 2495-2505.
41. Trivellini A, Ferrante A, Vernieri P, Serra G (2011) Effects of promoters and inhibitors of ethylene and ABA on flower senescence of Hibiscus rosa-sinensis L. J Plant Growth Regul 30: 175-184.
42. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
43. Wiebold W, Ashley D, Boerma HR (1981) Reproductive abscission levels and patterns for eleven determinate soybean cultivars. Agron J 73: 43-46.
44. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V et al (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453: 1239-1243.
45. Xue JQ, Li YH, Tan H, Yang F, Ma N et al (2008) Expression of ethylene biosynthetic and receptor genes in rose floral tissues during ethylene-enhanced flower opening. J Exp Bot 59: 2161-2169.
46. Xue J, Bao YY, Li BL, Cheng YB, Peng ZY et al (2010) Transcriptome analysis of the brown planthopper Nilaparvata lugens. PLoS One 5: e14233.
47. Zhang W, Wen CK (2010) Preparation of ethylene gas and comparison of ethylene responses induced by ethylene, ACC and ethephon. Plant Physiol Biochem 48: 45-53.
48. Zhu H, Dardick CD, Beers EP, Callanhan AM, Xia R et al (2011) Transcriptomics of shading-induced and NAA induced abscission in apple (Malus domestica) reveals a shared pathway involving reduced photosynthesis, alterations in carbohydrate transport and signaling and hormone crosstalk. BMC Plant Biology 11: 138.