Mutant Resources for Functional Analysis of the Rice Genome

Droc, Gaëtan; An, Gynheung; Wu, Changyin; Hsing, Yue‐Ie C.; Hirochika, Hirohiko; Pereira, Andy; Sundaresan, Venkatesan; Han, Chang‐deok; Upadhyaya, Narayana M.; Ramachandran, Srinivasan; Comai, Luca; Leung, Hei; Guiderdoni, Emmanuel

doi:10.1007/978-1-4614-7903-1_7

Cited by 9 publications

(16 citation statements)

References 155 publications

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“…Activation‐tagged mutant populations have so far been developed only in japonica varieties (Kolesnik et al ; Qu et al ; Droc et al ; Yang et al ; Lo et al ). Similar efforts could not be made in any of the indica cultivars because of their recalcitrance to genetic manipulation.…”

Section: Introductionmentioning

confidence: 99%

Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water‐use efficiency and abiotic stress tolerance in plants

Moin

Bakshi

Saha

et al. 2016

Plant Cell & Environment

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We have generated 3900 enhancer-based activation-tagged plants, in addition to 1030 stable Dissociator-enhancer plants in a widely cultivated indica rice variety, BPT-5204. Of them, 3000 were screened for water-use efficiency (WUE) by analysing photosynthetic quantum efficiency and yield-related attributes under water-limiting conditions that identified 200 activation-tagged mutants, which were analysed for flanking sequences at the site of enhancer integration in the genome. We have further selected five plants with low Δ C, high quantum efficiency and increased plant yield compared with wild type for a detailed investigation. Expression studies of 18 genes in these mutants revealed that in four plants one of the three to four tagged genes became activated, while two genes were concurrently up-regulated in the fifth plant. Two genes coding for proteins involved in 60S ribosomal assembly, RPL6 and RPL23A, were among those that became activated by enhancers. Quantitative expression analysis of these two genes also corroborated the results on activating-tagging. The high up-regulation of RPL6 and RPL23A in various stress treatments and the presence of significant cis-regulatory elements in their promoter regions along with the high up-regulation of several of RPL genes in various stress treatments indicate that they are potential targets for manipulating WUE/abiotic stress tolerance.

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Section: Introductionmentioning

confidence: 99%

Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water‐use efficiency and abiotic stress tolerance in plants

Moin

Bakshi

Saha

et al. 2016

Plant Cell & Environment

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“…A functional AC tag insertion leads to up-regulation of the candidate gene in tissues where it is normally expressed, ectopic expression in tissues where the gene normally is not expressed, or both. This approach has been successfully used to generate numerous T-DNA-tagged rice mutant populations (Jeong et al 2002;Guiderdoni et al 2007;Hsing et al 2007;Krishnan et al 2009;Wan et al 2009;Droc et al 2013;Wei et al 2013;Yang et al 2013).…”

Section: Establishment Of T-dna Activation-and Knockout-tagged Rice Mmentioning

confidence: 99%

“…Recently, various genetic resources for functional analysis of the rice genome have been rapidly established, including highquality bacterial artificial chromosome (BAC) libraries, T-DNA-and transposon-tagged rice mutant populations, large-scale expressed sequence tags (ESTs) and full length cDNA collections (Jeong et al 2002;Guiderdoni et al 2007;Hsing et al 2007;Krishnan et al 2009;Wan et al 2009;Droc et al 2013;Wei et al 2013;Yang et al 2013). Many rice bioinformatics websites integrating these genomic resources have also been made accessible worldwide.…”

Section: Introductionmentioning

confidence: 99%

Genetic resources offer efficient tools for rice functional genomics research

Fan

Hsing

et al. 2015

Plant Cell & Environment

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Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T-DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene-rich regions, resulting in direct gene knockout or activation of genes within 20-30 kb up- and downstream of the T-DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T-DNA-tagged rice mutant population. We also discuss important features of T-DNA activation- and knockout-tagging and promoter-trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high-throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.

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“…As in Arabidopsis mediates flagellin perception [65] Os01g52050 (MSU v7.0 in OryGenesDB) with ∼125,000 located in the ∼35,000 genic regions (i.e., an average of 3.6 FSTs/locus) [12,[22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

“…In functional genomics, the challenge is now to system- atically assign a biological function to all genes in the genomes. To help in this task, the rice community worldwide has started to share efforts in the late 90's to produce insertion mutant collections required for gene functional analyses [11,12]. These mutant collections are available in several laboratories around the world: CSIRO in Australia [13], NIAS in Japan [14], OSTID in Europe [15], OTL in France [16], POSTECH [17] and PMBBRC [18] in Korea, RMD in China [19], TRIM in Taiwan [20], and UCD in USA [21].…”

Section: Introductionmentioning

confidence: 99%

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

et al. 2016

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Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.

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Mutant Resources for Functional Analysis of the Rice Genome

Cited by 9 publications

References 155 publications

Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water‐use efficiency and abiotic stress tolerance in plants

Activation tagging in indica rice identifies ribosomal proteins as potential targets for manipulation of water‐use efficiency and abiotic stress tolerance in plants

Genetic resources offer efficient tools for rice functional genomics research

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

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