MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Fekih, Rym ^a   Takagi, Hiroki ^a,b   Tamiru, Muluneh ^a   Abe, Akira ^a   Natsume, Satoshi ^a,b   Yaegashi, Hiroki ^a   Sharma, Shailendra ^a   Sharma, Shiveta ^a   Kanzaki, Hiroyuki ^a   Matsumura, Hideo ^a   Saitoh, Hiromasa ^a   Mitsuoka, Chikako ^a   Utsushi, Hiroe ^a   Uemura, Aiko ^a   Kanzaki, Eiko ^a   Kosugi, Shunichi ^a   Yoshida, Kentaro ^a   Cano, Liliana ^c   Kamoun, Sophien ^c   Terauchi, Ryohei ^a  

^a IWATE BIOTECHNOLOGY RESEARCH CENTER   (Japan)

^b IWATE UNIVERSITY   (Japan)

^c SAINSBURY LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CROP; CROSS BREEDING; GENE FREQUENCY; GENE ISOLATION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENETIC IDENTIFICATION; HETEROZYGOSITY; NONHUMAN; PHENOTYPIC VARIATION; PROGENY; RICE; SINGLE NUCLEOTIDE POLYMORPHISM; WILD TYPE;

AMINO ACID SEQUENCE; BREEDING; CHROMOSOME MAPPING; CROSSES, GENETIC; DNA MUTATIONAL ANALYSIS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE DATA; MUTATION; ORYZA SATIVA; PHENOTYPE; PLANTS, GENETICALLY MODIFIED; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84879999401     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068529     Document Type: Article

References (23)

1. Zerbino DR, Birney E, (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
2. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, et al. (2011) High-quality draft assemblies of mammalin genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108: 1513-1518.
3. Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, et al. (2009) SHOREmap: simulrineous mapping and mutation identification by deep sequencing. Nat Methods 6: 550-551.
4. Birkeland SR, Jin N, Ozdemir AC, Lyons Jr RH, Weisman LS, et al. (2010) Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole-genome sequencing. Genetics 186: 1127-2237.
5. Arnold CN, Xia Y, Lin P, Ross C, Schwander M, et al. (2011) Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. Geneticsi 187: 633-641.
6. Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, et al. (2011) Next-generation mapping of Arabidopsis genes. Plant J 67: 715-725.
7. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, et al. (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30: 174-178.
8. Gonzaga-Jauregui C, Lupski JR, Gibbs RA, (2012) Human genome sequencing in health and disease. Annu Rev Med 63: 35-61.
9. Rakshit S, Kanzaki H, Matsumura H, Rakshit A, Fujibe T, et al. (2010) Use of TILLING for reverse and forward genetics of rice. In: Meksem K, Kahl G, editors. The Handbook of Plant Mutation Screening: Mining of Natural and Induced Alleles. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA. 187-197.
10. Fisher RA, (1935) The logic of inductive inference. J Roy Stat Soc 98: 39-54.
11. Hjorth E, Hadfi K, Zauner S, Maier U, (2005) Unique genetic compartmentalization of the SUF system in crptophytes and chracterization of a SufD mutant in Arabidopsis thaliana. FEBS Lett 579: 1129-1135.
12. Miki D, Shimamoto K, (2004) RNA Simple RNAi Vectors for Stable and Transient Suppression of Gene Function in Rice. Plant Cell Physiol 45: 490-495.
13. Xu XM, Moller G, (2004) AtNAP7 is a plastidic SufC-like ATP-binding cassette/ATPase essential for Arabidopsis embryogenesis. Proc Natl Acad Sci USA 101: 9143-9148.
14. Fontecave M, Ollagnier de Choudens S, Py B, Barras F, (2005) Mechanisms of iron-sulfur cluster assembly: the SUF machinery. J Biol Inorg Chem 10: 713-721.
15. Wollers S, Layer G, Garcia-Serres R, Signor L, Clemancey M, et al. (2010) Iron-Sulfur (Fe-S) cluster assembly: the SufBCD complex is a new type of Fe-S scaffold with a flavin redox cofactor. J Biol Chem 285: 23331-23341.
16. Chatterjee M, Sparvoli S, Edmunds C, Garosi P, Findlay K, et al. (1996) DAG, a gene required for chloroplast differentiation and palisade development in Antirrhinum majus. EMBO J 15: 4194-4207.
17. Chatterjee M, Martin C, (1997) Tam3 produces a suppressible allele of the DAG locus of Antirrhinum majus similar to Mu-suppressible alleles of maize. Plant J 11: 759-771.
18. Yu F, Fu A, Aluru M, Park S, Xu Y, et al. (2007) Variegation mutants and mechanisms of chloroplast biogenesis. Plant Cell Environ 30: 350-365.
19. Lindner H, Raissig MT, Sailer C, Shimosato-Asano H, Bruggmann R, et al. (2012) SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next generation sequencing. Genetics 191: 1381-1386.
20. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, et al. (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J. 74: 174-183.
21. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and samtools. Bioinformatics 25: 2078-2079.
23. Toki S, Hara N, Ono K, Onodera H, Tagiri A, et al. (2006) Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J 46: 969-976.