Transcriptome atlas of the Arabidopsis funiculus - A study of maternal seed subregions

Plant Journal

Volumn 82, Issue 1, 2015, Pages 41-53

  Khan, Deirdre ^a   Millar, Jenna L ^a   Girard, Ian J ^a   Chan, Ainsley ^a   Kirkbride, Ryan C ^b   Pelletier, Julie M ^b   Kost, Sara ^a   Becker, Michael G ^a   Yeung, Edward C ^c   Stasolla, Claudio ^a   Goldberg, Robert B ^d   Harada, John J ^b   Belmonte, Mark F ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALGARY   (Canada)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Arabidopsis thaliana; chalazal seed coat; funiculus; laser microdissection; seed; seed coat; transcriptome

Indexed keywords

BIOCHEMISTRY; BIOINFORMATICS; GENES; GENETIC PROGRAMMING; METABOLISM; MICRODISSECTION;

ARABIDOPSIS THALIANA; FUNICULUS; LASER MICRO DISSECTIONS; SEED COATS; TRANSCRIPTOMES;

SEED;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; GLUCOSINOLATE; INDOLEACETIC ACID DERIVATIVE; PHYTOHORMONE; TRANSCRIPTOME;

ARABIDOPSIS; CLUSTER ANALYSIS; DNA MICROARRAY; FLOWER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GROWTH, DEVELOPMENT AND AGING; LASER CAPTURE MICRODISSECTION; METABOLISM; PLANT SEED;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CLUSTER ANALYSIS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GLUCOSINOLATES; INDOLEACETIC ACIDS; LASER CAPTURE MICRODISSECTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT GROWTH REGULATORS; SEEDS; TRANSCRIPTOME;

EID: 84925678331     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12790     Document Type: Article

References (46)

1. Augustine, R., Mukhopadhyay, A., and, Bisht, N.C., (2013) Targeted silencing of BjMYB28 transcription factor gene directs development of low glucosinolate lines in oilseed Brassica juncea. Plant Biotechnol. J. 11, 855-866.
2. Balasubramanian, S., and, Schneitz, K., (2000) NOZZLE regulates proximal-distal pattern formation, cell proliferation and early sporogenesis during ovule development in Arabidopsis thaliana. Development, 127, 4227-4238.
3. Baud, S., and, Lepiniec, L., (2009) Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiol. Biochem. 47, 448-455.
4. Baud, S., Mendoza, M.S., To, A., Harscoët, E., Lepiniec, L., and, Dubreucq, B., (2007) WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis. Plant J. 50, 825-838.
5. Belmonte, M.F., Kirkbride, R.C., Stone, S.L., et al. (2013) Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc. Natl Acad. Sci. USA, 110, E435-E444.
6. Bencivenga, S., Simonini, S., Benková, E., and, Colombo, L., (2012) The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis. Plant Cell, 24, 2886-2897.
7. Benjamini, Y., and, Hochberg, Y., (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289-300.
8. Brady, S.M., Orlando, D.A., Lee, J.-Y., Wang, J.Y., Koch, J., Dinneny, J.R., Mace, D., Ohler, U., and, Benfey, P.N., (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science, 318, 801-806.
9. Cairns, N.G., Pasternak, M., Wachter, A., Cobbett, C.S., and, Meyer, A.J., (2006) Maturation of Arabidopsis seeds is dependent on glutathione biosynthesis within the embryo. Plant Physiol. 141, 446-455.
10. Chan, A., and, Belmonte, M., (2013) Histological and ultrastructural changes in canola (Brassica napus) funicular anatomy during the seed lifecycle. Botany, 91, 671-679.
11. Cheng, Y., Dai, X., and, Zhao, Y., (2006) Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. Genes Dev. 20, 1790-1799.
12. Dai, M., Wang, P., Boyd, A.D., et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 33, e175.
13. Dinkova-Kostova, A.T., and, Kostov, R.V., (2012) Glucosinolates and isothiocyanates in health and disease. Trends Mol. Med. 18, 337-347.
14. Endo, Y., (2012) Anatomical diversity of funicles in Leguminosae. J. Plant. Res. 125, 41-53.
15. Fang, W., Wang, Z., Cui, R., Li, J., and, Li, Y., (2012) Maternal control of seed size by EOD3/CYP78A6 in Arabidopsis thaliana. Plant J. 70, 929-939.
16. Focks, N., and, Benning, C., (1998) wrinkled1: a novel, low-seed-oil mutant of Arabidopsis with a deficiency in the seed-specific regulation of carbohydrate metabolism. Plant Physiol. 118, 91-101.
17. Gigolashvili, T., Yatusevich, R., Berger, B., Müller, C., and, Flügge, U.-I., (2007) The R2R3-MYB transcription factor HAG1/MYB28 is a regulator of methionine-derived glucosinolate biosynthesis in Arabidopsis thaliana. Plant J. 51, 247-261.
18. Gill, S.S., and, Tuteja, N., (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol. Biochem. 48, 909-930.
19. Grubb, C.D., and, Abel, S., (2006) Glucosinolate metabolism and its control. Trends Plant Sci. 11, 89-100.
20. Guo, R., Qian, H., Shen, W., Liu, L., Zhang, M., Cai, C., Zhao, Y., Qiao, J., and, Wang, Q., (2013a) BZR1 and BES1 participate in regulation of glucosinolate biosynthesis by brassinosteroids in Arabidopsis. J. Exp. Bot. 64, 2401-2412.
21. Guo, R., Shen, W., Qian, H., Zhang, M., Liu, L., and, Wang, Q., (2013b) Jasmonic acid and glucose synergistically modulate the accumulation of glucosinolates in Arabidopsis thaliana. J. Exp. Bot. 64, 5707-5719.
22. Hasan, M., Friedt, W., Pons-Kühnemann, J., Freitag, N.M., Link, K., and, Snowdon, R.J., (2008) Association of gene-linked SSR markers to seed glucosinolate content in oilseed rape (Brassica napus ssp. napus). Theor. Appl. Genet. 116, 1035-1049.
23. Jackson, P., (2010) Food stories: consumption in an age of anxiety. Cultur. Geogr. 17, 147-165.
24. Khan, D., Millar, J.L., Girard, I.J., and, Belmonte, M.F., (2014) Transcriptional circuitry underlying seed coat development in Arabidopsis. Plant Sci. 219-220, 51-60.
25. Klein, M., Reichelt, M., Gershenzon, J., and, Papenbrock, J., (2006) The three desulfoglucosinolate sulfotransferase proteins in Arabidopsis have different substrate specificities and are differentially expressed. FEBS J. 273, 122-136.
26. Le, B.H., Cheng, C., Bui, A.Q., et al. (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc. Natl Acad. Sci. USA, 107, 8063-8070.
27. Maeo, K., Tokuda, T., Ayame, A., Mitsui, N., Kawai, T., Tsukagoshi, H., Ishiguro, S., and, Nakamura, K., (2009) An AP2-type transcription factor, WRINKLED1, of Arabidopsis thaliana binds to the AW-box sequence conserved among proximal upstream regions of genes involved in fatty acid synthesis. Plant J. 60, 476-487.
28. Malitsky, S., Blum, E., Less, H., Venger, I., Elbaz, M., Morin, S., Eshed, Y., and, Aharoni, A., (2008) The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators. Plant Physiol. 148, 2021-2049.
29. Marty, L., Siala, W., Schwarzländer, M., Fricker, M.D., Wirtz, M., Sweetlove, L.J., Meyer, Y., Meyer, A.J., Reichheld, J.-P., and, Hell, R., (2009) The NADPH-dependent thioredoxin system constitutes a functional backup for cytosolic glutathione reductase in Arabidopsis. Proc. Natl Acad. Sci. USA, 106, 9109-9114.
30. Mawson, B.T., Steghaus, A.K., and, Yeung, E.C., (1994) Structural development and respiratory activity of the funiculus during bean seed (Phaseolus vulgaris L.) maturation. Ann. Bot. 74, 587-594.
31. Mewis, I., Appel, H.M., Hom, A., Raina, R., and, Schultz, J.C., (2005) Major signaling pathways modulate Arabidopsis glucosinolate accumulation and response to both phloem-feeding and chewing insects 1. Plant Physiol. 138, 1149-1162.
32. Miao, H., Wei, J., Zhao, Y., Yan, H., Sun, B., Huang, J., and, Wang, Q., (2013) Glucose signalling positively regulates aliphatic glucosinolate biosynthesis. J. Exp. Bot. 64, 1097-1109.
33. Mizzotti, C., Mendes, M.A., Caporali, E., Schnittger, A., Kater, M.M., Battaglia, R., and, Colombo, L., (2012) The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development. Plant J. 70, 409-420.
34. Nour-Eldin, H.H., Andersen, T.G., Burow, M., Madsen, S.R., Jørgensen, M.E., Olsen, C.E., Dreyer, I., Hedrich, R., Geiger, D., and, Halkier, B.A., (2012) NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds. Nature, 488, 531-534.
35. Pagnussat, G.C., Alandete-Saez, M., Bowman, J.L., and, Sundaresan, V., (2009) Auxin-dependent patterning and gamete specification in the Arabidopsis female gametophyte. Science, 324, 1684-1689.
36. Pinyopich, A., Ditta, G.S., Savidge, B., Liljegren, S.J., Baumann, E., Wisman, E., and, Yanofsky, M.F., (2003) Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature, 424, 85-88.
37. Rademacher, E.H., Lokerse, A.S., Schlereth, A., et al. (2012) Different auxin response machineries control distinct cell fates in the early plant embryo. Dev. Cell, 22, 211-222.
38. Ray, A., Robinson-Beers, K., Ray, S., Baker, S.C., Lang, J.D., Preuss, D., Milligan, S.B., and, Gasser, C.S., (1994) Arabidopsis floral homeotic gene BELL (BEL1) controls ovule development through negative regulation of AGAMOUS gene (AG). Proc. Natl Acad. Sci. 91, 5761-5765.
39. Roszak, P., and, Köhler, C., (2011) Polycomb group proteins are required to couple seed coat initiation to fertilization. Proc. Natl Acad. Sci. 108, 20826-20831.
40. Saeed, A.I., Bhagabati, N.K., Braisted, J.C., Liang, W., Sharov, V., Howe, E.A., Li, J., Thiagarajan, M., White, J.A., and, Quackenbush, J., (2006) TM4 microarray software suite. Methods Enzymol. 411, 134-193.
41. Schruff, M.C., Spielman, M., Tiwari, S., Adams, S., Fenby, N., and, Scott, R.J., (2006) The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development, 133, 251-261.
42. Schweizer, F., Fernandez-Calvo, P., Zander, M., Diez-Diaz, M., Fonseca, S., Glauser, G., Lewsey, M.G., Ecker, J.R., Solano, R., and, Reymond, P., (2013) Arabidopsis Basic Helix-Loop-Helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell, 25, 3117-3132.
43. Sønderby, I.E., Geu-Flores, F., and, Halkier, B.a., (2010) Biosynthesis of glucosinolates-gene discovery and beyond. Trends Plant Sci. 15, 283-290.
44. Tusher, V.G., Tibshirani, R., and, Chu, G., (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA, 98, 5116-5121.
45. Ursache, R., Miyashima, S., Chen, Q., Vatén, A., Nakajima, K., Carlsbecker, A., Zhao, Y., Helariutta, Y., and, Dettmer, J., (2014) Tryptophan-dependent auxin biosynthesis is required for HD-ZIP III-mediated xylem patterning. Development, 141, 1250-1259.
46. Velasco, P., Soengas, P., Vilar, M., Cartea, M.E., and, del Rio, M., (2008) Comparison of glucosinolate profiles in leaf and seed tissues of different Brassica napus crops. J. Am. Soc. Hortic. Sci. 133, 551-558.