Proteomics Analysis to Identify Proteins and Pathways Associated with the Novel Lesion Mimic Mutant E40 in Rice Using iTRAQ-Based Strategy

A novel rice lesion mimic mutant (LMM) was isolated from the mutant population of Japonica rice cultivar Hitomebore generated by ethyl methane sulfonate (EMS) treatment. Compared with the wild-type (WT), the mutant, tentatively designated E40, developed necrotic lesions over the whole growth period along with detectable changes in several important agronomic traits including lower height, fewer tillers, lower yield, and premature death. To understand the molecular mechanism of mutation-induced phenotypic differences in E40, a proteomics-based approach was used to identify differentially accumulated proteins between E40 and WT. Proteomic data from isobaric tags for relative and absolute quantitation (iTRAQ) showed that 233 proteins were significantly up- or down-regulated in E40 compared with WT. These proteins are involved in diverse biological processes, but phenylpropanoid biosynthesis was the only up-regulated pathway. Differential expression of the genes encoding some candidate proteins with significant up- or down-regulation in E40 were further verified by qPCR. Consistent with the proteomic results, substance and energy flow in E40 shifted from basic metabolism to secondary metabolism, mainly phenylpropanoid biosynthesis, which is likely involved in the formation of leaf spots.

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Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Rice ◽

10.1186/s12284-020-00447-8 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Kiyosumi Hori ◽

Keitaro Suzuki ◽

Haruka Ishikawa ◽

Yasunori Nonoue ◽

Kazufumi Nagata ◽

...

Keyword(s):

Agronomic Traits ◽

Heading Date ◽

Rice Cultivar ◽

Eating Quality ◽

Japonica Rice ◽

Rice Cultivars ◽

Substitution Lines ◽

Chromosome Segment Substitution Lines ◽

Chromosome Segments

Abstract Background In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both desirable eating quality and resilience to high temperatures. Eating quality and agronomic traits were evaluated in a reciprocal set of chromosome segment substitution lines derived from crosses between a japonica rice cultivar ‘Koshihikari’ and an indica rice cultivar ‘Takanari’. Results We detected 112 QTLs for amylose and protein contents, whiteness, stickiness, hardness and eating quality of cooked rice grains. Almost of ‘Koshihikari’ chromosome segments consistently improved eating quality. Among detected QTLs, six QTLs on chromosomes 1–5 and 11 were detected that increased whiteness and stickiness of cooked grains or decreased their hardness for 3 years. The QTLs on chromosomes 2–4 were not associated with differences in amylose or protein contents. QTLs on chromosomes 1–5 did not coincide with QTLs for agronomic traits such as heading date, culm length, panicle length, spikelet fertility and grain yield. Genetic effects of the detected QTLs were confirmed in substitution lines carrying chromosome segments from five other indica cultivars in the ‘Koshihikari’ genetic background. Conclusion The detected QTLs were associated with differences in eating quality between indica and japonica rice cultivars. These QTLs appear to be widely distributed among indica cultivars and to be novel genetic factors for eating quality traits because their chromosome regions differed from those of the GBSSI (Wx) and SSIIa (Alk) genes. The detected QTLs would be very useful for improvement of eating quality of indica rice cultivars in breeding programs.

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Uncoupled Expression of Nuclear and Plastid Photosynthesis-Associated Genes Contributes to Cell Death in a Lesion Mimic Mutant

The Plant Cell ◽

10.1105/tpc.18.00813 ◽

2019 ◽

Vol 31 (1) ◽

pp. 210-230 ◽

Cited By ~ 19

Author(s):

Ruiqing Lv ◽

Zihao Li ◽

Mengping Li ◽

Vivek Dogra ◽

Shanshan Lv ◽

...

Keyword(s):

Cell Death ◽

Lesion Mimic ◽

Lesion Mimic Mutant

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Identification of quantitative trait loci for leaf traits in rice

Genetika ◽

10.2298/gensr1602643j ◽

2016 ◽

Vol 48 (2) ◽

pp. 643-652 ◽

Cited By ~ 2

Author(s):

Baoyan Jia ◽

Xinhua Zhao ◽

Yang Qin ◽

Muhammad Irfan ◽

Tae-Heon Kim ◽

...

Keyword(s):

Recombinant Inbred Lines ◽

Leaf Traits ◽

Rice Cultivar ◽

Interval Mapping ◽

Mapping Method ◽

Japonica Rice ◽

Phenotypic Variance ◽

Simple Sequence ◽

Variance Explained ◽

Map Distance

A recombinant inbred lines (RILs) population of 90 lines were developed from a subspecies cross between an indica type cultivar, ?Cheongcheong?, and a japonica rice cultivar, ?Nagdong? was evaluated for leaf traits in 2009. A genetic linkage map consisting of 154 simple sequence repeat (SSR) markers was constructed, covering 1973.6 cM of 12 chromosomes with an average map distance of 13.9 cM between markers. By composite interval mapping method a total of 19 QTLs were identified for the leaf traits on 5 chromosomes (Chr.1, Chr.3, Chr.6, Chr.8 and Chr.11). The percentage of phenotypic variance explained by each QTL varied from 8.1% to 29.4%. Five pleiotropic effects loci were identified on chromosomes 1,6.

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Characterization and mapping of a lesion mimic mutant in rice (Oryza sativa L.)

Science Bulletin ◽

10.1007/bf03325671 ◽

2003 ◽

Vol 48 (9) ◽

pp. 892-896 ◽

Cited By ~ 1

Author(s):

Daofeng Liu ◽

Zhukuan Cheng ◽

Guoqing Liu ◽

Guozhen Liu ◽

Yun Wang ◽

...

Keyword(s):

Oryza Sativa ◽

Oryza Sativa L ◽

Lesion Mimic ◽

Lesion Mimic Mutant

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Registration of Katy Lesion Mimic Mutant 1

Crop Science ◽

10.2135/cropsci2004.0481 ◽

2005 ◽

Vol 45 (4) ◽

pp. 1675-1675 ◽

Cited By ~ 7

Author(s):

Y. Jia

Keyword(s):

Lesion Mimic ◽

Lesion Mimic Mutant

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Variation in the Abundance of OsHAK1 Transcript Underlies the Differential Salinity Tolerance of an indica and a japonica Rice Cultivar

Frontiers in Plant Science ◽

10.3389/fpls.2017.02216 ◽

2018 ◽

Vol 8 ◽

Cited By ~ 9

Author(s):

Guang Chen ◽

Chaolei Liu ◽

Zhenyu Gao ◽

Yu Zhang ◽

Anpeng Zhang ◽

...

Keyword(s):

Salinity Tolerance ◽

Rice Cultivar ◽

Japonica Rice

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Effect of high temperature on starch biosynthetic enzymes and starch structure in japonica rice cultivar ‘Akitakomachi’ (Oryza sativa L.) endosperm and palatability of cooked rice

Journal of Cereal Science ◽

10.1016/j.jcs.2019.04.001 ◽

2019 ◽

Vol 87 ◽

pp. 209-214 ◽

Cited By ~ 4

Author(s):

Kazunao Kato ◽

Yuta Suzuki ◽

Yuko Hosaka ◽

Ryuichi Takahashi ◽

Ikuko Kodama ◽

...

Keyword(s):

Oryza Sativa ◽

High Temperature ◽

Oryza Sativa L ◽

Rice Cultivar ◽

Biosynthetic Enzymes ◽

Japonica Rice ◽

Cooked Rice ◽

Starch Structure

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LMM24 Encodes Receptor-Like Cytoplasmic Kinase 109, Which Regulates Cell Death and Defense Responses in Rice

International Journal of Molecular Sciences ◽

10.3390/ijms20133243 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3243 ◽

Cited By ~ 6

Author(s):

Yue Zhang ◽

Qunen Liu ◽

Yingxin Zhang ◽

Yuyu Chen ◽

Ning Yu ◽

...

Keyword(s):

Cell Death ◽

Molecular Mechanisms ◽

Indica Rice ◽

Defense Responses ◽

Rice Cultivar ◽

Histochemical Staining ◽

Lesion Mimic ◽

Ros Accumulation ◽

Mutant Pool ◽

Defense Response Genes

Lesion mimic mutants are excellent models for research on molecular mechanisms of cell death and defense responses in rice. We identified a new rice lesion mimic mutant lmm24 from a mutant pool of indica rice cultivar “ZhongHui8015”. The LMM24 gene was identified by MutMap, and LMM24 was confirmed as a receptor-like cytoplasmic kinase 109 by amino acid sequence analysis. The lmm24 mutant displayed dark brown lesions in leaves and growth retardation that were not observed in wild-type ZH8015. The results of histochemical staining and TUNEL assays showed enhanced ROS accumulation and cell death in lmm24. Chloroplast degradation was observed in lmm24 leaves, with decreased expression of photosynthesis-related genes and increased expression of the senescence-induced STAYGREEN (SGR) gene and other senescence-associated genes. Furthermore, lmm24 exhibited enhanced resistance to rice blast fungus Magnaporthe oryzae (M. oryzae) and up-regulation of defense response genes. Our data demonstrate that LMM24 regulates cell death and defense responses in rice.

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