Muts HOMOLOG1-derived epigenetic breeding potential in tomato

Plant Physiology

Volumn 168, Issue 1, 2015, Pages 222-232

  Yang, Xiaodong ^a,b   Kundariya, Hardik ^b   Xu, Ying Zhi ^b   Sandhu, Ajay ^b   Yu, Jiantao ^b   Hutton, Samuel F ^c   Zhang, Mingfang ^a   Mackenzie, Sally A ^b  

^a ZHEJIANG UNIVERSITY   (China)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^c UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBRYOPHYTA; LYCOPERSICON ESCULENTUM;

PLANT PROTEIN;

ADAPTATION; ARABIDOPSIS; BREEDING; CROSS BREEDING; DNA METHYLATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REPRESSION; GENETIC EPIGENESIS; GENETICS; GROWTH, DEVELOPMENT AND AGING; INHERITANCE; METABOLISM; PHENOTYPE; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCTION; RNA INTERFERENCE; SEEDLING; SEQUENCE ANALYSIS; TOMATO; TRANSGENE; TRANSGENIC PLANT;

ADAPTATION, PHYSIOLOGICAL; ARABIDOPSIS; BREEDING; CROSSES, GENETIC; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; INHERITANCE PATTERNS; LYCOPERSICON ESCULENTUM; PHENOTYPE; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCTION; RNA INTERFERENCE; SEEDLINGS; SEQUENCE ANALYSIS, RNA; SUPPRESSION, GENETIC; TRANSGENES;

EID: 84929470533     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.15.00075     Document Type: Article

References (32)

1. Abdelnoor RV, Yule R, Elo A, Christensen AC, Meyer-Gauen G, Mackenzie SA (2003) Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc Natl Acad Sci USA 100: 5968–5973
2. Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, Weigel D (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480: 245–249
3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289–300
4. Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M, Labadie K, Caillieux E, Hospital F, Aury JM, Wincker P, et al (2014) Mapping the epigenetic basis of complex traits. Science 343: 1145–1148
5. Cubas P, Vincent C, Coen E (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157–161
6. Davila JI, Arrieta-Montiel MP, Wamboldt Y, Cao J, Hagmann J, Shedge V, Xu YZ, Weigel D, Mackenzie SA (2011) Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis. BMC Biol 9: 64
7. de la Rosa Santamaria R, Shao MR, Wang G, Nino-Liu DO, Kundariya H, Wamboldt Y, Dweikat I, Mackenzie SA (2014) MSH1-induced nongenetic variation provides a source of phenotypic diversity in Sorghum bicolor. PLoS ONE 9: e108407
8. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA 109: E2183–E2191
9. Greaves IK, Groszmann M, Wang A, Peacock WJ, Dennis ES (2014) Inheritance of trans-chromosomal methylation patterns from Arabidopsis F1 hybrids. Proc Natl Acad Sci USA 111: 2017–2022
10. Grimanelli D, Roudier F (2013) Epigenetics and development in plants: green light to convergent innovations. Curr Top Dev Biol 104: 189–222
11. Hauben M, Haesendonckx B, Standaert E, Van Der Kelen K, Azmi A, Akpo H, Van Breusegem F, Guisez Y, Bots M, Lambert B, et al (2009) Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield. Proc Natl Acad Sci USA 106: 20109–20114
12. Herberich E, Sikorski J, Hothorn T (2010) A robust procedure for comparing multiple means under heteroscedasticity in unbalanced designs. PLoS ONE 5: e9788
13. Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44–57
14. Hutton SF, Scott JW, Vallad GE (2014) Association of the Fusarium wilt race 3 resistance gene, I-3, on chromosome 7 with increased susceptibility to bacterial spot race T4 in tomato. J Am Soc Hortic Sci 139: 282–289
15. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36
16. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
17. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550
18. Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ, Seymour GB (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38: 948–952
19. Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14: 267–274
20. Reinders J, Wulff BB, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, Bucher E, Theiler G, Paszkowski J (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 23: 939–950
21. Rivard CL, Louws FJ (2006) Grafting for Disease Resistance in Heirloom Tomatoes. College of Agriculture and Life Sciences, North Carolina Cooperative Extension Service http://www4.ncsu.edu/~clrivard/TubeGraftingTechnique. pdf (April 22, 2015)
22. Roux F, Colomé-Tatché M, Edelist C, Wardenaar R, Guerche P, Hospital F, Colot V, Jansen RC, Johannes F (2011) Genome-wide epigenetic perturbation jump-starts patterns of heritable variation found in nature. Genetics 188: 1015–1017
23. Sahu PP, Pandey G, Sharma N, Puranik S, Muthamilarasan M, Prasad M (2013) Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Rep 32: 1151–1159
24. Sandhu AP, Abdelnoor RV, Mackenzie SA (2007) Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants. Proc Natl Acad Sci USA 104: 1766–1770
25. Schermerhorn LG (1934) Scientific breeding gives New Jersey the ‘Rutgers’ tomato. NJ State Hortic Soc News 15: no. 6
26. Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science 334: 369–373
27. Shedge V, Davila J, Arrieta-Montiel MP, Mohammed S, Mackenzie SA (2010) Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance. Plant Physiol 152: 1960–1970
28. Shivaprasad PV, Dunn RM, Santos BA, Bassett A, Baulcombe DC (2012) Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. EMBO J 31: 257–266
29. Vergeer P, Wagemaker NC, Ouborg NJ (2012) Evidence for an epigenetic role in inbreeding depression. Biol Lett 8: 798–801
30. Virdi KS, Laurie JD, Xu YZ, Yu J, Shao MR, Sanchez R, Kundariya H, Wang D, Riethoven JJ, Wamboldt Y, et al (2015) Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth. Nat Commun 6: 6386
31. Xu YZ, Arrieta-Montiel MP, Virdi KS, de Paula WB, Widhalm JR, Basset GJ, Davila JI, Elthon TE, Elowsky CG, Sato SJ, et al (2011) MutS HOMOLOG1 is a nucleoid protein that alters mitochondrial and plastid properties and plant response to high light. Plant Cell 23: 3428–3441
32. Xu YZ, Santamaria RdeL, Virdi KS, Arrieta-Montiel MP, Razvi F, Li S, Ren G, Yu B, Alexander D, Guo L, et al (2012) The chloroplast triggers developmental reprogramming when mutS HOMOLOG1 is suppressed in plants. Plant Physiol 159: 710–720