Transcriptome sequencing of Prunus sp. rootstocks roots to identify candidate genes involved in the response to root hypoxia

Tree Genetics and Genomes

Volumn 11, Issue 1, 2015, Pages

  Arismendi, María José ^a,b   Almada, Rubén ^b,c   Pimentel, Paula ^b,c   Bastias, Adriana ^b,c   Salvatierra, Ariel ^b,c   Rojas, Pamela ^b,c   Hinrichsen, Patricio ^b,c   Pinto, Manuel ^b,c   Di Genova, Alex ^d   Travisany, Dante ^d   Maass, Alejandro ^d   Sagredo, Boris ^b,c  

^a UNIVERSIDAD DE LA FRONTERA   (Chile)

^b Centro de Estudios Avanzados en Fruticultura (CEAF)   (Chile)

^c INSTITUTO DE INVESTIGACIONES AGROPECUARIAS   (Chile)

^d UNIVERSITY OF CHILE   (Chile)

Author keywords

Hypoxia; Prunus; qRT PCR; RNA Seq; Rootstock; Transcriptome sequencing

Indexed keywords

PRUNUS; PRUNUS AVIUM; PRUNUS PERSICA;

EID: 84940862266     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-015-0838-1     Document Type: Article

References (55)

1. Almada R, Arismendi M, Pimentel P, Rojas P, Hinrichsen P, Pinto M, Sagredo B (2013) Class 1 non-symbiotic and class 3 truncated hemoglobin-like genes are differentially expressed in stone fruit rootstocks (Prunus L.) with different degrees of tolerance to root hypoxia. Tree Genet Genome 9:1051–1063
2. Amador ML, Sancho S, Rubio-Cabetas MJ (2009) Biochemical and molecular aspects involved in waterlogging tolerance in Prunus rootstocks. Acta Hortic 814:715–720
3. Arismendi MJ (2012) Identificación de genes candidatos asociados a la tolerancia a estrés por hipoxia/anoxia radicular en portainjertos de Prunus. Universidad de la Frontera, Temuco
4. Bailey-Serres J, Voesenek LA (2008) Flooding stress: acclimations and genetic diversity. Annu Rev Plant Biol 59:313–339. doi:10.1146/annurev.arplant.59.032607.092752
5. Blokhina O, Virolainen E, Fagerstedt KV (2003) Antioxidants, oxidative damage and oxygen deprivation stress: a review. Ann Bot 91:179–194
6. Chang S, Pur Year J, Carney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Rep 11:113–116
7. Christianson J, Llewellyn D, Dennis E, Wilson I (2010a) Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species. Plant Signal Behav 5(8):1006–1009
8. Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW (2010b) Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.). Plant Cell Physiol 51(1):21–37
9. Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w (1118); iso-2; iso-3. Fly Austin 6(2):80–92
10. Domingo R, Pérez-pastor A, Ruiz-Sánchez MC (2002) Physiological responses of apricot plants grafted on two different rootstocks to flooding conditions. J Plant Physiol 159:725–732
11. Du Z, Zhou X, Ling Y, Zhang Z, Su Z (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38(suppl 2):W64–W70. doi:10.1093/nar/gkq310
12. Granot D, Kelly G, Stein O, David-Schwartz R (2014) Substantial roles of hexokinase and fructokinase in the effects of sugars on plant physiology and development. J Exp Bot 65:809–819
13. Horchani F, Gallusci P, Baldet P, Cabasson C, Maucourt M, Rolinb D, Aschi-Smitia S, Raymondb P (2008) Prolonged root hypoxia induces ammonium accumulation and decreases the nutritional quality of tomato fruits. J Plant Physiol 165:1352–1359
14. Isaakadis A, Sotiropoulos T, Almaliotis D, Therios I, Stylianidis D (2004) Response to severe water stress of the almond (Prunus amygdalus) ‘Ferragnès’ grafted on eight rootstocks. J Crop Hortic Sci 32:355–362
15. Kennedy RA, Rumpho ME, Fox TC (1992) Anaerobic metabolism in plants. Plant Physiol 84:1204–1209
16. Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES (2002) Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. Plant Cell 14:2481–2494
17. Kozlowski T (1997) Response and adaptation by plants to flooding stress. Ann Bot 96:501–505
18. Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J (2009) Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 149(1):461–473
19. Lang GA (2000) Precocious, dwarfing, and productive—how will new cherry rootstocks impact the sweet cherry industry? Hortic Technol 10:719–725
20. Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S, Licausi F, Novi G, Beretta O, Vitulli F, Alpi A, Perata P (2007) Transcript profiling of the anoxic rice coleoptile. Plant Physiol 144:218–231
21. Lee K-W, Chen P-W, Lu C-A, Chen S, Ho T-HD, Yu S-M (2009) Coordinated responses to oxygen and sugar deficiency allow rice seedlings to tolerate flooding. Sci Signal 2(91):ra61
22. Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11(5):473–483
23. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079
24. Licausi F, van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P (2010) HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant J 62(2):302–315
25. Lillo C (2008) Signalling cascades integrating light-enhanced nitrate metabolism. Biochem J 415:11–19
26. Liu F, Vantoai T, Moy LP, Bock G, Linford LD, Quackenbush J (2005) Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. Plant Physiol 137(3):1115–1129
27. Loreti E, Poggi A, Novi G, Alpi A, Perata P (2005) A genome-wide analysis of the effects of sucrose on gene expression in Arabidopsis seedlings under anoxia. Plant Physiol 137:1130–113
28. Martínez-Gómez P, Crisosto C, Bonghi C, Rubio M (2011) New approaches to Prunus transcriptome analysis. Genetica 139:755–769
29. Mizutani F, Yamada M, Tomana T (1982) Differential water tolerance and ethanol accumulation in Prunus species under flooded conditions. J Japan Soc Hortic Sci 51:29–34
30. Morgan PW, Gausman HW (1966) Effects of ethylene on auxin transport. Plant Physiol 41:45–52
31. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628
32. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis an rice. Plant Physiol 144:411–432
33. Narsai R, Rocha M, Geigenberger P, Whelan J, van Dongen JT (2011) Comparative analysis between plant species of transcriptional and metabolic responses to hypoxia. New Phytol 190(2):472–487
34. Nicolás E, Torrecillas A, Dell’Amico J, Alarcón J (2005) The effect of short-term flooding on the sap flow, gas exchange and hydraulic conductivity of young apricot trees. Trees 19:51–57
35. Pimentel P, Almada RD, Salvatierra A, Toro G, Arismendi MJ, Pino MT, Sagredo B, Pinto M (2014) Physiological and morphological responses of Prunus species with different degree of tolerance to long-term root hypoxia. Sci Hortic 180:14–23
36. Pinochet J (2010) Replantac (Rootpac R), a plum-almond hybrid rootstock for replant situations. Hortic Sci 45:299–301
37. Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA, Campbell CS (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266(1):5–43
38. Qi X, Xu X, Lin X, Zhang W, Chen X (2012) Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile. Genomics 99(3):160–168
39. Ranney TG (1994) Differential tolerance of eleven Prunus taxa to root zone flooding. J Environ Hortic 12(3):138–14
40. Ranney TG, Bassuk NL, Whitlow TM (1991) Osmotic adjustment and solute constituents in leaves and roots of water-stressed cherry (Prunus) trees. J Am Soc Hortic Sci 116:684–688
41. Roberts A, Trapnell C, Donaghey J, Rinn J, Pachter L (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12(3):R22
42. Rubio-Cabetas MJ, Amador ML, Gómez-Aparisi J, Jaime J, Sancho S (2011) Physiological and biochemical parameters involved in waterlogging stress in Prunus. Acta Hortic 903:1215–1223
43. Sekse L (1995) Cuticular fracturing in fruits of sweet cherry (Prunus avium L.) resulting from changing soil water contents. J Hortic Sci 70(4):631–635
44. Sekse L (1998) Cuticular fractures in fruits of sweet cherry (Prunus avium L.) affect fruit quality negatively and their development is influenced by cultivar and rootstock. Acta Hortic 468(2):671–675
45. Shiono K, Takahashi H, Colmer T, Nakazono M (2008) Role of ethylene in acclimations to promote oxygen transport in roots of plants in waterlogged soils. Plant Sci 175:52–58
46. Tong Z, Gao Z, Wang F, Zhou J, Zhang Z (2009) Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol 10:71
47. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111
48. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515
49. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L (2013) Differential analysis of gene regulation at transcript resolution with RNA-Seq. Nat Biotechnol 31(1):46–53
50. van Dongen JT, Fröhlich A, Ramírez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P (2009) Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of Arabidopsis plants. Ann Bot 103:269–280
51. Vidoz ML, Loreti E, Mensuali A, Alpi A, Perata P (2010) Hormonal interplay during adventitious root formation in flooded tomato plants. Plant J 63:551–562
52. Webster AD (2001) Rootstocks for temperate fruit crops: current uses, future potential and alternative strategies. Acta Hortic 557:25–34
53. Wyatt E, Wu R, Rabeh W, Park H-W, Ghanefar M, Ardehali H (2010) Regulation and cytoprotective role of hexokinase III. PLoS One 5:e13823
54. Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705–708
55. Yi X, Du Z, Su Z (2013) PlantGSEA: a gene set enrichment analysis toolkit for plant community. Nucleic Acids Res. doi:10.1093/nar/gkt281