Identification and Analysis of Differentially Expressed Genes During Seed Development Using Suppression Subtractive Hybridization (SSH) in Phaseolus vulgaris
Baudoin, Jean-Pierre ; Université de Liège - ULiège > Sciences agronomiques > Phytotechnie tropicale et horticulture
Language :
English
Title :
Identification and Analysis of Differentially Expressed Genes During Seed Development Using Suppression Subtractive Hybridization (SSH) in Phaseolus vulgaris
Abid G, Muhovski Y, Jacquemin JM, Silue S, Toussaint A, Baudoin JP (2009) Abortive seed development in common bean (Phaseolus vulgaris L.). Bean Improvement Cooperative 52: 8-9.
Albani D, Hammond-Kosack MCU, Smith C, Conlan S, Colot V, Holdsworth M, Bevan MW (1997) The wheat transcriptional activator SPA: a seed-specific bZIP protein that recognizes the GCN4-like motif in the bifactorial endosperm box of prolamin genes. The Plant Cell 9: 171-184.
Basyuni M, Kinjo Y, Baba S, Shinzato N, Iwasaki H, Siregar EBM, Oku H (2011) Isolation of salt stress tolerance gene from roots of mangrove plant, Rhizophora stylosa Griff., using PCR-based suppression subtractive hybridization. Plant Mol Biol Rep 29: 533-543.
Baud S, Guyon V, Kronenberger J, Wuilleme S, Miquel M, Caboche M, Lepiniec L, Rochat C (2003) Multifunctional acethyl-CoA carboxylase 1 is essential for very long chain fatty acid elongation and embryo development in Arabidopsis. Plant J 33: 75-86.
Baud S, Bellec Y, Miquel M, Bellini C, Caboche M, Lepiniec L, Faure JD, Rochat C (2004) gurke and pasticcino3 mutants affected in embryo development are impaired in acetyl-CoA carboxylase. EMBO reports 5: 515-520.
Baudoin JP, Silué S, Geerts P, Mergeai G, Jacquemin JM, Toussaint A (2004) Interspecific hybridization with Phaseolus vulgaris L.: embryo development and its genetics. In: Pandalai SG (ed) Recent research development in genetics and breeding. Research Signpost, India, pp 349-364.
Bayer M, Nawy T, Giglione C, Galli M, Meinnel T, Lukowitz W (2009) Paternal control of embryonic patterning in Arabidopsis thaliana. Science 323: 1485-1488.
Ben C, Hewezi T, Jardinaud MF, Bena F, Ladouce N, Moretti S, Tamborindeguy C, Liboz T, Petitprez M, Gentzbittel L (2005) Comparative analysis of early embryonic sunflower cDNA libraries. Plant Mol Biol 57: 255-270.
Bentollia S, Alfonso AA, Hanson MR (2002) A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. PNAS 16: 10887-10892.
Bishop-Hurley SL, Gardner RC, Walter C (2003) Isolation and molecular characterization of genes expressed during somatic embryo development in Pinus radiata. Plant Cell Tissue Organ Cult 74: 267-281.
Boston RS, Fontes EBP, Shank BB, Wrobel RL (1991) Increased expression of the maize immunoglobulin binding protein homolog b-70 in three zein regulatory mutants. Plant Cell 3: 497-505.
Busogoro JP, Jijakli MH, Lepoivre P (1999) Identification of a novel source of resistance to angular leaf spot disease of common bean within the secondary gene pool. Plant Breed 118: 417-423.
Caixeta ZT, Borém A, Azevedo Fagundes S, Niestche S, Barros EG, Moreira MA (2003) Inheritance of angular leaf spot resistance in common bean line BAT 332 and identification of RAPD marker linked to the resistance gene. Euphytica 134: 297-303.
Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116.
Chapman A, Blebacq AS, Vasseur J, Hilbert JL (2000) Arabinogalactan-proteins in Cichorium somatic embryogenesis: effet of beta-glucosyl Yariv reagent and epitope localization during embryo development. Planta 211: 305-314.
Cushing DA, Forsthoefel NR, Gestaut DR, Vernon DM (2005) Arabidopsis emb175 and other ppr knockout mutant reveal essential roles for pentatricopeptides repeat (PPR) proteins in plant embryogenesis. Planta 221: 424-436.
Diatchenko L, Chris Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93: 6025-6030.
Ding YH, Liu NY, Tang ZS, Liu J, Yang WC (2006) Arabidopsis GLUTAMINE-RICH PROTEIN23 is essential for early embryogenesis and encodes a novel nuclear PPR motif protein that interacts with RNA polymerase II subunit III. Plant Cell 18: 815-830.
Geerts P, Toussaint A, Mergeai G, Baudoin JP (2002) Study of the early abortion in reciprocal crosses between Phaseolus vulgaris L. and Phaseolus polyanthus Greenm. Biotechnol Agron Soc Environ 6: 109-119.
Geng YJ, Gao ST, Huang DN, Zhao YR, Liu JP, Li XH, Zhang RL (2009) Differentially expressed genes between female and male adult Anopheles anthropophagus. Parasitol Res 105: 843-851.
Gutierrez-Marcos JF, Dal Pra M, Giulini A, Costa LM, Gavazzi G, Cordelier S, Sellam O, Tatout C, Paul W, Perez P, Dickinson H, Consonni G (2007) empty pericarp4 encodes a mitochondrial-targeted pentatricopeptide repeat protein necessary for seed development and plant growth in maize. Plant Cell 19: 196-210.
José-Estanyol M, Ruiz-Avila M, Puidomènech P (1992) A maize embryo-specific gene encodes a proline-riche and hydrophobic protein. Plant Cell 4: 413-423.
Kaplan DR, Cooke TJ (1997) Fundamental concepts in the embryogenesis of dicotyledons: a morphological interpretation of embryo mutant. Plant Cell 9: 1903-1919.
Konishi T, Sassaki Y (1994) Compartmentalization of two forms of acetyl-CoA carboxylase in plants and the origin of their tolerance toward herbicides. Proc Natl Acad Sci USA 91: 3598-3601.
Lara P, Onate-Sanchez L, Abraham Z, Ferrandiz C, Diaz I, Carbonero P, Vicente-Carbajosa J (2003) Synergetic activation of seed storage protein gene expression in Arabidopsis by ABI3 and two bZIPs related to OPAQUE2. J Biol Chem 23: 21003-21011.
Legrand S, Hendriks T, Hilbert J, Quillet M (2007) Characterization of expressed sequence tags obtained by SSH during somatic embryogenesis in Chichorium intybus L. BMC Plant Biol 7: 27.
Linkiewicz A, Filipecki M, Tomczak A, Grabowska A, Malepszy S (2004) The cloning of sequences differentially transcribed during the induction of somatic embryogenesis in cucumber (Cucumis sativus L.). Cell Mol Biol Lett 9: 795-804.
Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Ret ML, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat (PPR) proteins reveals their essential role in organelle biogenesis. Plant Cell 16: 2089-2103.
Mahuku GS, Jara CE, Cajiao C, Beebe S (2002) Sources of resistance to Colletotrichum lindemuthianum in the secondary gene pool of Phaseolus vulgaris and in crosses of primary and secondary gene pools. Plant Dis 86: 1383-1387.
Marenda MS, Vilei EM, Poumarat F, Frey J, Berthelot X (2004) Validation of the suppressive subtractive hybridization method in Mycoplasma agalactiae species by the comparison of a field strain with the type strain PG2. Vert Res 35: 199-212.
Miller NA, Gong Q, Bryan R, Ruvolvo M, Turner LA, LaBrie ST (2002) Cross-hybridization of closely related genes on high-density macroarrays. Biotechniques 32: 620-625.
Müller M, Knudsen S (1993) The nitrogen response of a barely C-hordein promoter is controlled by positive and negative regulation of the GCN4 and endosperm box. Plant J 4: 343-355.
Namasivayam P, Hanke D (2006) Identification of differentially expressed sequences in pre-embryonic tissue of oilseed rape by suppression subtractive hybridization (SSH). Plant Cell Tiss Organ Cult 86: 417-421.
Nguema Ndoutoumou P, Toussaint A, Baudoin JP (2007) Embryo abortion and histological features in the interspecific cross between Phaseolus vulgaris L. and Phaseolus coccineus L. Plant Cell Tissue Organ Cult 88: 329-332.
Prabu G, Kawar PG, Pagariya MC, Prasad DT (2011) Identification of water deficit stress upregulated genes in sugarcane. Plant Mol Biol Rep 29: 291-304.
Rainey KM, Griffiths PD (2005) Inheritance of heat tolerance during reproductive development in snap bean (Phaseolus vulgaris L.). J Am Soc Hortic Sci 130: 700-706.
Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365-386.
Saha D, Prasad AM, Srinivasan R (2007) Pentatricopeptide repeat proteins and their emerging roles in plants. Plant Physiol Biochem 45: 521-534.
Schaller A (2004) A cut above the rest: the regulatory function of plant proteases. Planta 220: 183-197.
Schmidt RJ, Ketudat M, Aukerman MJ, Hoschek G (1992) Opaque-2 is a transcriptional activator that recognizes a specific target site in 22-kD zein genes. Plant Cell 4: 689-700.
Schmit V, Baudoin JP (1992) Screening for resistance to Ascochyta blight in populations of P. coccineus L. and P. polyanthus Greenman. Field Crops Res 30: 155-165.
Schmitz-linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13: 663-670.
Schmitz-linneweber C, Williams-Carrier R, Barkan A (2005) RNA immunoprecipitation and microarray analysis show a chloroplast pentatricopeptide repeat protein to be associated with the 5′ region of mRNAs whose translation it activates. Plant Cell 17: 2791-2804.
Showalter AM (2001) Arabinogalactan-proteins: structure, expression and function. Cell Mol Life Sci 58: 1399-1417.
Suda CNK, Giorgini JF (2003) Multiple forms of endo-1, 4-β-1, 3-glucanases in the endosperm of Euphorbia heterophylla L. J Exp Bot 54: 2045-2052.
Sun MM, Li LH, Xie H, Ma RC, He YK (2007) Differentially expressed genes under cold acclimatation in Physcomitrella patens. J Biochem Mol Biol 40: 986-1001.
Toussaint A, Geerts P, Clement F, Mergeai G, Baudoin JP (2004) Early abortion in reciprocal crosses between Phaseolus vulgaris and Phaseolus polyanthus, and in vitro culture of immature embryos from these species. Belgium J Botany 137: 47-54.
Tsuwamoto R, Fukuoka H, Takahata Y (2007) Identification and characterization of gene expressed in early embryogenesis from microspores of Brassica napus. Planta 225: 641-652.
Tzafrir I, Pena-Muralla R, Dickerman A, Berg M, Rogers R, Hutchens S, Sweeney TC, McElver J, Aux G, Patton D, Meinke DW (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135: 1206-1220.
Von Stein OD, Thies WG, Hofmann M (1997) A high throughput screening for rarely transcribed differentially expressed genes. Nucleic Acids Res 25: 2598-2603.
Wang G, Gao Y, Yang L, Shi J (2007) Identification and analysis of differentially expressed genes in differentiating xylem of Chinese fir (Cunninghamia lanceolata) by suppression subtractive hybridization. Genome 50: 1141-1155.
Williamson MP (1994) The structure and function of proline-rich regions in proteins. Biochem J 297: 249-260.
Yang G, Zhou R, Tang T, Chen X, Ouyang J, He L, Li W, Chen S, Guo M, Li X, Zhang C, Shi S (2011a) Gene expression profiles in response to salt stress in Hibiscus tiliacens. Plant Mol Biol Rep 29: 609-617.
Yang Z, Peng Z, Yang H, Yang J, Wei S, Cai P (2011b) Suppression subtractive hybridization identified differentially expressed genes in pistil mutations in wheat. Plant Mol Biol Rep 29: 431-439.
Zhou MB, Yang P, Gao PJ, Tang D (2011) Identification of differentially expressed sequence taqs in rapidly elongating Phyllostachys pubescens internodes by suppressive subtractive hybridization. Plant Mol Biol Rep 29: 224-231.