Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.)

Qiao, Yongli; Piao, Rihua; Shi, Jinxia; Lee, Song-I; Jiang, Wenzhu; Kim, Baek-Ki; Lee, Joohyun; Han, Longzhi; Ma, Wenbo; Koh, Hee‐Jong

doi:10.1007/s00122-011-1543-6

Cited by 110 publications

(77 citation statements)

References 46 publications

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“…These results suggest that OsMADS34 mainly controls grain size on the spb by regulating cell expansion but not cell number. GN1 , DEP1 , DEP2 , DEP3 , APO1 , and NAL1 are closely associated with panicle architecture in rice (Ashikari et al, 2005; Ikeda et al, 2007; Huang et al, 2009; Li F. et al, 2010; Qiao et al, 2011; Fujita et al, 2013). We investigated the expression levels of these genes in young panicles of the m34-z mutant and the wild-type.…”

Section: Resultsmentioning

confidence: 99%

Regulatory Role of OsMADS34 in the Determination of Glumes Fate, Grain Yield, and Quality in Rice

et al. 2016

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Grasses produce seeds on spikelets, a unique type of inflorescence. Despite the importance of grass crops for food, the genetic mechanisms that control spikelet development remain poorly understood. In this study, we used m34-z, a new mutant allele of the rice (Oryza sativa) E-class gene OsMADS34, to examine OsMADS34 function in determining the identities of glumes (rudimentary glume and sterile lemma) and grain size. In the m34-z mutant, both the rudimentary glume and sterile lemma were homeotically converted to the lemma-like organ and acquired the lemma identity, suggesting that OsMADS34 plays important roles in the development of glumes. In the m34-z mutant, most of the grains from the secondary panicle branches (spb) were decreased in size, compared with grains from wild-type, but no differences were observed in the grains from the primary panicle branches. The amylose content and gel consistency, and a seed-setting rate from the spb were reduced in the m34-z mutant. Interesting, transcriptional activity analysis revealed that OsMADS34 protein was a transcription repressor and it may influence grain yield by suppressing the expressions of BG1, GW8, GW2, and GL7 in the m34-z mutant. These findings revealed that OsMADS34 largely affects grain yield by affecting the size of grains from the secondary branches.

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Section: Resultsmentioning

confidence: 99%

Regulatory Role of OsMADS34 in the Determination of Glumes Fate, Grain Yield, and Quality in Rice

et al. 2016

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“…Rice varieties carrying the dep1 mutation, a dominant allele at the DEP1 locus, exhibit reduced length of inflorescence internodes, increased number of grains per panicle, and enhanced grain yield (Huang et al, 2009). Recently, more genes involved in the regulation of rice architecture have been characterized, such as DEP3, RICE LEAFY HOMOLOG, MADS-BOX TRANSCRIPTION FACTOR57 (MADS57), and SQUAMOSA PRO-MOTER BINDING-LIKE PROTEIN16 (SPL16) (Rao et al, 2008;Qiao et al, 2011;Wang et al, 2012;Guo et al, 2013). However, the molecular mechanisms underlying plant architecture remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture

et al. 2013

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(J.L.).IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.

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“…There are several reports on genetic and molecular mechanisms controlling panicle architecture in rice such as DEP1 (dense and erect panicle 1) (Huang et al 2009), DEP2 (dense and erect panicle 2) (Li et al 2010), DEP3 (dense and erect panicle 3) (Qiao et al 2011), EP (erect pose panicle) (Wang et al 2009), EP2 (erect panicle 2) (Zhu et al 2010) and EP3 (erect panicle 3) (Piao et al 2009). DEP1 locus is a gain-of-function mutation causing truncation of a phosphatidylethanolamine-binding protein-like domain protein.…”

Section: Introductionmentioning

confidence: 99%

Fine Mapping and Candidate Gene Analysis of Small Round Grain Mutant in Rice

Seo

Bordiya

Lee

et al. 2017

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Grain size and panicle architecture are important traits determining yield. Here we report a new allele of DEP2 (dense and erect panicle 2) which has a pleiotropic effect on grain size/shape and panicle architecture. A small round grain and erect panicle mutant was obtained by treating japonica cultivar Hwacheong waxy with MNU (N-methyl-N-nitrosourea). Through fine mapping sequence analysis, we identified the single nucleotide substitution in the mutant, which caused splicing error of the first intron, on previously reported DEP2 locus in rice. Since the dep2-1 and dep2-2 have been reported in previous studies, we named this new allele as dep2-3. The dep2-3 mutant manifested reduced grain size and plant height, dense and erect panicle and erect plant architecture. When we crossed the mutant with wild type, panicle and grain of F1 plant showed intermediate phenotype, indicating that dep2-3 showed incomplete dominance, which was not reported in the previous study. Scanning electron microscopy (SEM) results showed that increase in width of mutant grain was due to the increased width of glume cells. Paraffin section of peduncle revealed that outgrowth in outer layer of peduncle compared to inner layer caused the erectness of the panicle. Our results collectively indicated that the dep2-3 might play a significant role in the regulation of grain size/shape and formation of vascular bundles.

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Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.)

Cited by 110 publications

References 46 publications

Regulatory Role of OsMADS34 in the Determination of Glumes Fate, Grain Yield, and Quality in Rice

Regulatory Role of OsMADS34 in the Determination of Glumes Fate, Grain Yield, and Quality in Rice

Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture

Fine Mapping and Candidate Gene Analysis of Small Round Grain Mutant in Rice

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