Identification of Transcriptome SNPs for Assessing Allele-Specific Gene Expression in a Super-Hybrid Rice Xieyou9308

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Zhai, Rongrong ^a   Feng, Yue ^a   Zhan, Xiaodeng ^a   Shen, Xihong ^a   Wu, Weiming ^a   Yu, Ping ^a   Zhang, Yingxin ^a   Chen, Daibo ^a   Wang, Huimin ^b   Lin, Zechuan ^a   Cao, Liyong ^a   Cheng, Shihua ^a  

^a CHINA NATIONAL RICE RESEARCH INSTITUTE   (China)

^b SHENYANG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOTIC PROTEASE ACTIVATING FACTOR 1; COMPLEMENTARY DNA;

ARTICLE; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC DIFFERENCE; HETEROSIS; HYBRID; HYBRIDIZATION; NONHUMAN; NUCLEOTIDE BINDING SITE; PLANT BREEDING; PLANT GENETICS; PROTEIN DOMAIN; RICE; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; CROSSES, GENETIC; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HYBRID VIGOR; HYBRIDIZATION, GENETIC; MOLECULAR SEQUENCE ANNOTATION; ORYZA SATIVA; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, MESSENGER; TRANSCRIPTOME;

EID: 84876255919     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060668     Document Type: Article

References (32)

1. Rieseberg LH, (1997) Hybrid origins of plant species. Annu Rev Ecol Evol Syst 28: 359-389.
2. Arnold ML, (2004) Natural hybridization and the evolution of domesticated, pest and disease organisms. Mol Ecol 13: 997-1007.
3. Rieseberg LH, Raymond O, Rosenthal DM, Lai Z, Livingstone K, et al. (2003) Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301: 1211-1216.
4. Hegarty MJ, Hiscock SJ, (2004) Hybrid speciation in plants: new insights from molecular studies. New Phytol 165: 411-423.
5. Zhuang Y, Adams KL, (2007) Extensive allelic variation in gene expression in populus F1 hybrids. Genetics 177: 1987-1996.
6. Birchler JA, Auger DL, Riddle NC, (2003) In search of the molecular basis of heterosis. Plant Cell 15: 2236-2239.
7. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, et al. (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc Natl Acad Sci U S A 103: 6805-6810.
8. Springer NM, Stupar RM, (2007) Allelic variation and heterosis in maize: How do two halves make more than a whole? Genome Res 17: 264-275.
9. Wittkopp PJ, Haerum BK, Clark AG, (2004) Evolutionary changes in cis and trans gene regulation. Nature 430: 85-88.
10. Singh N, Murata Y, Oda S, Mitani H, (2012) Allelic expression changes in Medaka (Oryzias latipes) hybrids between inbred strains derived from genetically distant populations. PLoS One 7: 36875.
11. Cowles CR, Hirschhorn JN, Altshuler D, Lander ES, (2002) Detection of regulatory variation in mouse genes. Nat Genet 32: 432-437.
12. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW, (2002) Allelic variation in human gene expression. Science 297: 1143-1143.
13. Zhang X, Borevitz JO, (2009) Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 182: 943-954.
14. Guo M, Rupe MA, Zinselmeier C, Habben J, Bowen BA, et al. (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16: 1707-1716.
15. He G, Zhu X, Elling AA, Chen L, Wang X, et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
16. Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, et al. (2012) Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A 109: 12040-12045.
17. Cheng SH, Cao LY, Zhuang JY, Chen SG, Zhan XD, et al. (2007) Super hybrid rice breeding in China: achievements and prospects. J Integr Plant Biol 49: 805-810.
18. Li B, Dewey CN, (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323.
19. Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
20. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
21. Shen Y, Catchen J, Garcia T, Amores A, Beldorth I, et al. (2012) Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids. Comp Biochem Physiol C Toxicol Pharmacol 155: 102-108.
22. Pant PK, Tao H, Beilharz EL, Ballinger DG, Cox DR, et al. (2006) Analysis of allelic differential expression in human white blood cells. Genome Res 16: 331-339.
23. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34: 293-297.
24. Pastinen T, (2010) Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 11: 533-538.
25. Stupar RM, Springer NM, (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to addtive expression patterns in the F1 hybrid. Genetics 173: 2199-2210.
26. Tirosh I, Reikhav S, Levy AA, Barkai N, (2009) A yeast hybrid provides insight into the evolution of gene expression. Science 324: 659-662.
27. Yebra MJ, Bhagwat AS, (1995) A cytosine methyltransferase converts 5-methylcytosine in DNA to thymine. Biochemistry 34: 14752-14757.
28. Bransteitter R, Pham P, Scharff MD, Goodman MF, (2003) Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc Natl Acad Sci U S A 100: 4102-4107.
29. Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK, (2004) Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J Biol Chem 279: 52353-52360.
30. Bird A, (2007) Perceptions of epigenetics. Nature 447: 396-398.
31. Suzuki MM, Bird A, (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
32. Springer NM, Stupar RM, (2007) Allelic-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 19: 2391-2402.