Transposon Insertional Mutants: A Resource for Rice Functional Genomics

Zhu, Qian‐Hao; Eun, Moo Young; Han, Chang‐deok; Kumar, Chellian Santhosh; Pereira, Andy; Ramachandran, Srinivasan; Sundaresan, Venkatesan; Eamens, Andrew L.; Upadhyaya, Narayana M.; Wu, Ray

doi:10.1007/0-387-48914-2_10

Cited by 15 publications

(9 citation statements)

References 134 publications

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“…In rice, the two-component maize transposon Ac-Ds (Chin et al, 1999;Upadhyaya et al, 2002;Greco et al, 2003;Kolesnik et al, 2004) and En/Spm-dSpm (Greco et al, 2004;Kumar et al, 2008) systems have been well characterized, and good genetic selection schemes have been developed to select for transpositional activity useful for large-scale mutagenesis (Hirochika et al, 2004;Zhu et al, 2007). In addition, the endogenous rice Tos17 retrotransposon is active in specific genotypes and conditions and is an effective insertion mutagen in the rice genome .…”

Section: Development Of Rice Mutant Resources Insertion Mutantsmentioning

confidence: 99%

“…To alleviate this problem, genetic segregation analysis and the use of multiple mutants of the gene are useful. Transposon inserts have a much lower frequency of background mutations, leading to many genes identified by forward screens (Zhu et al, 2007), and the use of reversions that restore the wild-type phenotype is a convenient approach to prove genephenotype relationships.…”

Section: Utility Of Mutant Resources For Functional Genomics In Rice mentioning

confidence: 99%

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Mutant Resources in Rice for Functional Genomics of the Grasses

et al. 2009

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Section: Development Of Rice Mutant Resources Insertion Mutantsmentioning

confidence: 99%

Section: Utility Of Mutant Resources For Functional Genomics In Rice mentioning

confidence: 99%

Mutant Resources in Rice for Functional Genomics of the Grasses

et al. 2009

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“…For the same reason, tagging efficiency with T-DNA insertions seems quite low and only a few examples of forward genetics studies using T-DNA insertions have been reported (Jung et al 2003). In the Ac/Ds system, insertional mutagenesis can be separated from tissue culture, resulting in a relatively low background of mutations and some genes have been identified by a forward genetic strategy (Zhu et al 2007).…”

Section: Forward Genetics Studiesmentioning

confidence: 99%

“…T-DNA insertion mutants , Guiderdoni et al 2007) and transposon insertion mutants (Zhu et al 2007) for forward and reverse genetics studies in rice have been recently reviewed. More recently, the current status of rice mutant resources has been summarized by Krishnan et al (2009).…”

Section: Introductionmentioning

confidence: 99%

Insertional mutagenesis with Tos17 for functional analysis of rice genes

Hirochika

2010

Breed. Sci.

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Genomic sequencing of rice followed by curated genome annotation predicted that the rice genome carries 32,000 genes. To reveal functions of all the predicted genes is the next important challenge. One of the most effective ways to discover gene function is to analyze genetic mutations induced by insertion elements. Different insertion elements, such as T-DNA, Ds, dSpm, and the endogenous retrotransposon Tos17, have been utilized in rice and mutant lines carrying more than 1,500,000 insertions produced. In this article, features of Tos17, Tos17-induced mutant lines, related resources such as flanking sequence tags and phenome databases, and functional analysis of genes using these resources are reviewed.

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“…The 135 K rice microarrays were used to identify novel genes that associate consistently with anthocyanin pigmentation in Dissociation (Ds) insertion lines 13. These Ds insertion lines are one of the most important methods used in breeding rice and in understanding the function of the genome 14. Several studies have used microarray successfully to analyze gene expression changes in a number of crop species, including black rice 15,16…”

Section: Introductionmentioning

confidence: 99%

Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm

Kim

Kikuchi

Hahn

et al. 2010

Evol Bioinform Online

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This study identifies 2,617 candidate genes related to anthocyanin biosynthesis in rice using microarray analysis and a newly developed maximum boundary range algorithm. Three seed developmental stages were examined in white cultivar and two black Dissociation insertion mutants. The resultant 235 transcription factor genes found to be associated with anthocyanin were classified into nine groups. It is compared the 235 genes by transcription factor analysis and 593 genes from among clusters of COGs related to anthocyanin functions. Total 32 genes were found to be expressed commonly. Among these, 9 unknown and hypothetical genes were revealed to be expressed at each developmental stage and were verified by RT-PCR. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation, our results underline the potential usefulness of the newly developed algorithm.

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Transposon Insertional Mutants: A Resource for Rice Functional Genomics

Cited by 15 publications

References 134 publications

Mutant Resources in Rice for Functional Genomics of the Grasses

Mutant Resources in Rice for Functional Genomics of the Grasses

Insertional mutagenesis with Tos17 for functional analysis of rice genes

Computational identification of anthocyanin-specific transcription factors using a rice microarray and maximum boundary range algorithm

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