Comparative transcriptome analysis of ovules reveals stress related genes associated with nucellar polyembryony in citrus

Tree Genetics and Genomes

Volumn 10, Issue 3, 2014, Pages 449-464

  Kumar, Vajinder ^a   Malik, Surendra Kumar ^b   Pal, Digvender ^b   Srinivasan, Ramamurthy ^a   Bhat, Shripad Ramachandra ^a  

^a NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

^b NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

Author keywords

Citrus sinensis; Expressed sequence tags; Microarray; Nucellar polyembryony; Suppression subtractive hybridization

Indexed keywords

EID: 84901458612     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-013-0690-0     Document Type: Article

References (48)

1. Altschul SF, Gish W, Miller W, Myres EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Angenent GC, Colombo L (1996) Molecular control of ovule development. Trends Plant Sci 1: 228-232.
3. Bicknell RA, Koltunow AM (2004) Understanding apomixis: recent advances and remaining conundrums. Plant Cell 16: S228-S245.
4. Boutilier K, Offringa R, Sharma VK, Kieft H, Ouellet T, Zhang LM, Hattori J, Liu CM, van Lammeren AAM, Miki BLA, Custers JBM, Campagne MMV (2002) Ectopic expression of BABY BOOM triggers a conversion from vegetative to embryonic growth. Plant Cell 14: 1737-1749.
5. Brien TPO, Feder N, McCully ME (1964) Polychromatic staining of plant cell walls by toluidine blue O. Protoplasma 59: 367-373.
6. Cao W, Epstein C, Liu H, DeLoughery C, Ge N, Lin J, Diao R, Cao H, Long F, Zhang X, Chen Y, Wright PS, Busch S, Wenck M, Wong K, Saltzman AG, Tang Z, Liu L, Zilberstein A (2004) Comparing gene discovery from Affymetrix Gene Chip microarrays and Clontech PCR-select cDNA subtraction: a case study. BMC Genomics 5: 26.
7. Church M, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81: 1991-1995.
8. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
9. Dean G, Cao YG, Xiang DQ, Provart NJ, Ramsay L, Ahad A, White R, Selvaraj G, Datla R, Haughn G (2011) Analysis of gene expression patterns during seed coat development in Arabidopsis. Mol Plant 4: 1074-1091.
10. deHoon MJ, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20: 1453-1454.
11. Despres B, Delseny M, Devic M (2001) Partial complementation of embryo defective mutations, a general strategy to elucidate gene function. Plant J 27: 149-159.
12. Esen A, Soost RK (1977) Adventive embryogenesis in citrus and its relation to pollination and fertilization. Am J Bot 64: 607-614.
13. Garcia R, Asins MJ, Forner J, Carbonell EA (1999) Genetic analysis of apomixis in Citrus and Poncirus by molecular markers. Theor Appl Genet 99: 511-518.
14. Garcia-Lor A, Garcia-Martinez JL, Perez-Amador MA (2012) Identification of ovule and seed genes from Citrus clementina. Tree Genet Genomes 8: 227-235.
15. Garcion C, Guilleminot J, Kroj T, Parcy F, Giraudat J, Devic M (2006) AKRP and EMB506 are two ankyrin repeat proteins essential for plastid differentiation and plant development in Arabidopsis. Plant J 48: 895-906.
16. Ge XX, Chai LJ, Liu Z, Wu XM, Deng XX, Guo WW (2012) Transcriptional profiling of genes involved in embryogenic, non-embryogenic calluses and somatic embryogenesis of Valencia sweet orange by SSH-based microarray. Planta 236: 1107-1124.
17. Hong QB, Xiang SQ, Chen KL, Chen LG (2001) Two complementary dominant genes controlling apomixis in genus Citrus and Poncirus. Acta Genet Sin 28: 1062-1067.
18. Jensen WA (1962) Botanical histochemistry-principles and practice. WH Freeman, San Francisco.
19. Johnston AJ, Meier P, Gheyselinck J, Wuest SEJ, Federer M, Schlagenhauf E, Becker JD, Grossniklaus U (2007) Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte. Genome Biol 8: R204.
20. Kepiro JL, Roose ML (2010) AFLP markers closely linked to a major gene essential for nucellar embryony (apomixis) in Citrus maxima × Poncirus trifoliata. Tree Genet Genomes 6: 1-11.
21. Kirik V, Kolle K, Misera S, Baumlein H (1998) Two novel MYB homologues with changed expression in late embryogenesis-defective Arabidopsis mutants. Plant Mol Biol 37: 819-827.
22. Kobayashi S, Ieda I, Nakantani M (1979) Studies on the nucellar embryogenesis in Citrus. Formation of the primordium cell of the nucellar embryo in the ovule of the flower bud, and its meristematic activity. J Jpn Soc Hort Sci 48: 179-185.
23. Koltunow AM (1993) Apomixis: embryo sacs and embryos formed without meiosis or fertilization in ovules. Plant Cell 5: 1425-1437.
24. -ΔΔCT method. Methods 25: 402-408.
25. Lotan T, Ohto M, Yee KM, West MAL, Lo R, Kwong RW, Yamagishi K, Fischer RL, Goldberg RB, Harada JJ (1998) Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93: 1195-1205.
26. Maraschin SF, de Priester W, Spaink HP, Wang M (2005) Androgenic switch: an example of plant embryogenesis from the male gametophyte perspective. J Exp Bot 56: 1711-1726.
27. Marco C, Roberta B (2006) BLAST Parser (the excel style viewer). BITS Conference (Bologna, Italy). Abstract no. 115.
28. Mittler R, Finka A, Goloubinoff P (2012) How do plants feel the heat? Trend Biochem Sci 37: 118-125.
29. Mostafavi S, Ray D, Farley DW, Grouios C, Morris Q (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol 9: S4.
30. Nakano M, Shimizu T, Fuji H, Shimada T, Endo T, Nesumi H, Kuniga T, Omura M (2008a) Marker enrichment and construction of haplotype-specific BAC contigs for the polyembryony region in Citrus. Breed Sci 58: 375-383.
31. Nakano M, Shimizu T, Kuniga T, Nesumi H, Omura M (2008b) Mapping and haplotyping of the flanking region of the polyembryony locus in Citrus unshiu Marcow. J Jpn Soc Hort Sci 77: 109-114.
32. Nakano M, Shimada T, Endo T, Fujii H, Nesumi H, Kita M, Ebina M, Shimizu T, Omura M (2012) Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus. Plant Sci 183: 131-142.
33. Nakano M, Kigoshi K, Shimizu T, Endo T, Shimada T, Fujii H, Omura M (2013) Characterization of genes associated with polyembryony and in vitro somatic embryogenesis in Citrus. Tree Genet Genomes 9: 795-803.
34. Pagnussat GC, Alandete-Saez M, Bowman JL, Sundaresan V (2009) Auxin-dependent patterning and gamete specification in the Arabidopsis female gametophyte. Science 324: 1684-1689.
35. Rose RJ, Nolan KE (2006) Genetic regulation of somatic embryogenesis with particular reference to Arabidopsis thaliana and Medicago truncatula. In Vitro Cell Dev Biol-Plant 42: 473-481.
36. Sánchez-León N, Arteaga-Vázquez M, Alvarez-Mejía C, Mendiola-Soto J, Durán-Figueroa N, Rodríguez-Leal D, Rodríguez-Arévalo I, García-Campayo V, García-Aguilar M, Olmedo-Monfil V, Arteaga-Sánchez M, de la Vega OM, Nobuta K, Vemaraju K, Meyers BC, Vielle-Calzada JP (2012) Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing. J Exp Bot 63: 3829-3842.
37. Schmidt EDL, Guzzo F, Toonen MAJ, de Vries S (1997) A leucine rich repeat containing receptor-like kinase marks somatic plant cells competent to form embryos. Development 124: 2049-2062.
38. Schmidt A, Wuest SE, Vijverberg K, Baroux C, Kleen D, Grossniklaus U (2011) Transcriptome analysis of the Arabidopsis megaspore mother cell uncovers the importance of RNA helicases for plant germline development. PLoS Biol 9: e1001155.
39. Steffen JG, Kang IH, Macfarlane J, Drews GN (2007) Identification of genes expressed in the Arabidopsis female gametophyte. Plant J 51: 281-292.
40. Talon M, Gmitter FG Jr (2008) Citrus genomics. Int J Plant Genomics 528361.
41. Wu KL, Guo ZJ, Wang HH, Li J (2005) The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res 12: 9-26.
42. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45: 59-66.
43. Yang H (2006) EST generation and analyses towards identifying female gametophyte-specific genes in Zea mays L. Planta 224: 1004-1014.
44. Yang X, Zang X (2010) Regulation of somatic embryogenesis in higher plants. Crit Rev Plant Sci 29: 36-57.
45. Yang WC, Shi DQ, Chen YH (2010) Female gametophyte development in flowering plants. Annu Rev Plant Biol 61: 89-108.
46. Yu HJ, Hogan P, Sundaresan V (2005) Analysis of the female gametophyte transcriptome of Arabidopsis by comparative expression profiling. Plant Physiol 139: 1853-1869.
47. Zavattieri MA, Frederico AM, Lima M, Sabino R, Arnholdt-Schmitt B (2010) Induction of somatic embryogenesis as an example of stress-related plant reactions. Electron J Biotechnol 13: 1-9.
48. Zhu M, Zhao S (2007) Candidate gene identification approach: progress and challenges. Int J Biol Sci 3: 420-427.