Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice

Pan, Yinghua; Chen, Lei; Zhao, Yan; Guo, Haifeng; Li, Jingcheng; Rashid, Muhammad Abdul Rehman; Lu, Chunju; Zhou, Weiyong; Yang, X. F.; Liang, Yuntao; Wu, Hao; Qing, Dongjing; Gao, Lijun; Dai, Gaoxing; Li, Danting; Deng, Gaofeng

doi:10.3389/fpls.2021.784037

Cited by 14 publications

(14 citation statements)

References 57 publications

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“…Furthermore, we found yield-related genes and rice quality-related metabolites ( Table 3 ; Figure 5 ; Figure S6 ). The grain length of hybrid indica rice is closely related to rice quality, and the slender grains allow for fuller grain filling and better appearance and eating quality [ 27 ]. This study found the same phenomenon in TF varieties with slender grains ( Figure 6 H), and the rice quality was rated as national standard high-quality rice grade one.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)

Zhou

Sun

et al. 2022

IJMS

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Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.

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Section: Discussionmentioning

confidence: 99%

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)

Zhou

Sun

et al. 2022

IJMS

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“…Based on the extensive germplasm resources of Guangxi, a typical common wild rice accession DP15 with several important economic traits was identified and selected to develop a set of CSSLs ( Figure S1 ). Our investigation revealed the significant phenotypic difference in various morphological traits observed between DP15 and the indica rice variety 93-11, including PH, awn length, leaf width, LMC, tiller number, tiller angle, spreading panicle, seed color, seed shattering, seed dormancy, GN, GL, GW, TGW, GLWR, and so on [ 72 ]. Through the WGRS, the genomic differences were highlighted by the bioinformatic analysis in this study, and 12,565 pairs of polymorphic InDel markers were designed to establish DP15-CSSLs and mining for novel genome QTLs.…”

Section: Discussionmentioning

confidence: 99%

Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1

et al. 2022

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Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient’s genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.

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“…OsMKK3 [17], and OsGASR7 [18]. However, many unknown genes and proteins have yet to be discovered, and the identification of these genes and proteins is essential for achieving a complete understanding of the molecular network underlying the regulation of grain size.…”

Section: Introductionmentioning

confidence: 99%

Editing of rice (Oryza sativa L.) OsMKK3 gene using CRISPR/Cas9 decreases grain length by modulating the expression of photosystem components

et al. 2023

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Grain size is one of the most important agronomic traits for grain yield determination in rice. To better understand the proteins that are regulated by the grain size regulatory gene OsMKK3, this gene was knocked out using the CRISPR/Cas9 system, and tandem mass tag (TMT) labeling combined with liquid chromatograph‐tandem mass spectrometry analysis was performed to study the regulation of proteins in the panicle. Quantitative proteomic screening revealed a total of 106 differentially expressed proteins (DEPs) via comparison of the OsMKK3 mutant line to the wild‐type YexiangB, including 15 and 91 up‐regulated and down‐regulated DEPs, respectively. Pathway analysis revealed that DEPs were enriched in metabolic pathways, biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and photosynthesis. Strong interactions were detected among seven down‐regulated proteins related to photosystem components in the protein‐protein interaction network, and photosynthetic rate was decreased in mutant plants. The results of the liquid chromatography‐parallel reaction monitoring/mass spectromery analysis and western blot analysis were consistent with the results of the proteomic analysis, and the results of the quantitative reverse transcription polymerase chain reaction analysis revealed that the expression levels of most candidate genes were consistent with protein levels. Overall, OsMKK3 controls grain size by regulating the protein content in cells. Our findings provide new candidate genes that will aid the study of grain size regulatory mechanisms associated with the mitogen‐activated protein kinase (MAPK) signaling pathway.

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Natural Variation in OsMKK3 Contributes to Grain Size and Chalkiness in Rice

Cited by 14 publications

References 57 publications

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)

Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice (Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1

Editing of rice (Oryza sativa L.) OsMKK3 gene using CRISPR/Cas9 decreases grain length by modulating the expression of photosystem components

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