Re-sequencing and genetic variation identification of a rice line with ideal plant architecture

Rice

Volumn 5, Issue 1, 2012, Pages

  Li, Shuangcheng ^a   Xie, Kailong ^a   Li, Wenbo ^a   Zou, Ting ^a   Ren, Yun ^a   Wang, Shiquan ^a   Deng, Qiming ^a   Zheng, Aiping ^a   Zhu, Jun ^a   Liu, Huainian ^a   Wang, Lingxia ^a   Ai, Peng ^a   Gao, Fengyan ^a   Huang, Bin ^a   Cao, Xuemei ^a   Li, Ping ^a  

^a SICHUAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

InDel; IPA; Re sequencing; Rice; SNP; SV

Indexed keywords

EID: 84865111476     PISSN: 19398425     EISSN: 19398433     Source Type: Journal    
DOI: 10.1186/1939-8433-5-18     Document Type: Article

References (25)

1. Ahmadikhah A, Karlov GI (2006) Molecular mapping of the fertility-restoration gene Rf4 for WA-cytoplasmic male sterility in rice. Plant Breeding 125:363-367.
2. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309:741-745.
3. Bryan G, Wu K, Farrall L, Jia Y, Hershey H, McAdams S, Faulk K, Donaldson G, Tarchini R, Valent B (2000) A Single Amino Acid Difference Distinguishes Resistant and Susceptible Alleles of the Rice Blast Resistance Gene Pi-ta. Plant Cell 12:2033-2046.
4. Duan S, Mao J, Zhu Y (2002) Genetic Variation of Main Restorer Lines of Hybrid Rice in China Was Revealed by Microsatellite Markers. Acta Genetica Sinica 29:250-254.
5. Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164-1171.
6. Fujita N, Yoshida M, Kondo T, Saito K, Utsumi Y, Tokunaga T, Nishi A, Satoh H, Park J, Jane J, Miyao A, Hirochika H, Nakamura Y (2007) Characterization of SSIIIa-Deficient Mutants of Rice: The Function of SSIIIa and Pleiotropic Effects by SSIIIa Deficiency in the Rice Endosperm. Plant Physiol 144:2009-2023.
7. Heather A, Patrick E, Chern M, Pamela C (2005) Alteration of TGA factor activity in rice results in enhanced tolerance to Xanthomonas oryzae pv. Oryzae The Plant Journal 43:335-347.
8. Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494-497.
9. Huang X, Wei X, Sang T, Zhao Q, Feng Q, et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961-967.
10. Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541-544.
11. Kang H, Park S, Matsuoka M, An G (2005) White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C4-type pyruvate orthophosphate dikinase gene (OsPPDKB). Plant J 42:901-911.
12. Lai J, Li R, Xu X, Jin W, Xu M et al (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027-1030.
13. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713-714.
14. Li R, Li Y, Fang X, Yang H, Wang J et al (2009) SNP detection for massively parallel wholegenome resequencing. Genome Res 19:1124-1132.
15. Li S, Wang S, Deng Q, Zheng A, Zhu J et al (2012) Identification of Genome-Wide Variations among Three Elite Restorer Lines for Hybrid-Rice. PLoS One 7(2):e30952. doi:10.1371/journal.pone.0030952.
16. Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci 107:19579-19584.
17. Qu S, Liu G, Zhou B, Bellizzi M, Zeng L et al (2006) The Broad-Spectrum Blast Resistance Gene Pi9 Encodes an NBS-LRR Protein and is a Member of a Multigene Family in Rice. Genetics 105:044891, genetics.105.044891.
18. Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023-1028.
19. Song W, Wang G, Chen L, Kim H, Pi L et al (1995) A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21. Science 270:1804-1806.
20. Sun X, Cao Y, Yang Z, Xu C, Li X et al (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37:517-527.
21. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24:1596-1599.
22. Wang ZX, Yano M, Yamanouchi U, Iwamoto M, Monna L et al (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19:55-64.
23. Wang Z, Zou Y, Li X, Zhang Q, Chen L et al (2006) Cytoplasmic Male Sterility of Rice with Boro II Cytoplasm Is Caused by a Cytotoxic Peptide and Is Restored by Two Related PPR Motif Genes via Distinct Modes of mRNA Silencing. The Plant Cell Online 18:676-687.
24. Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang Z-X et al (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci 95:1663-1668.
25. Zhu Y, Nomura T, Xu Y, Zhang Y, Peng Y et al (2006) ELONGATED UPPERMOST INTERNODE Encodes a Cytochrome P450 Monooxygenase That Epoxidizes Gibberellins in a Novel Deactivation Reaction in Rice. Plant Cell 18:442-45.