SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice

Liao, Zihao; Yu, Hong; Duan, Jingbo; Yuan, Kun; Yu, Chaoji; Meng, Xiangbing; Kou, Liquan; Chen, Mingjiang; Jing, Yanhui; Liu, Guifu; Smith, Steven M.; Li, Jiayang

doi:10.1038/s41467-019-10667-2

Cited by 114 publications

(69 citation statements)

References 50 publications

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“…In this study, we found that the expression of DXS, which is involved in terpenoid anabolism, was up-regulated in the OsSPL14 OE lines, and the GA 3 content increased significantly compared with in WT. The latest research indicated that GA signaling reduces the number of tillers (Liao et al 2019), which corroborates our results. Moreover, the other main function of GA is promoting flowering.…”

Section: Discussionsupporting

confidence: 92%

Overexpression of OsSPL14 results in transcriptome and physiology changes in indica rice ‘MH86’

Lian

Zhang

et al. 2020

Plant Growth Regul

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Oryza sativa SPL14 (OsSPL14), identified as the IDEAL PLANT ARCHITECTURE1 or WEALTHY FARMER'S PANICLE gene, plays a critical role in regulating rice plant architecture. Here, OsSPL14-overexpression transgenic rice plants had shorter growth periods, short narrow flag leaves, and thick green leaves compared with wild type 'MH86' plants (WT). Additionally, transgenic lines had higher chlorophyll a (Chl a), chlorophyll b (Chl b), and carotenoid (Car x) contents at both seedling and mature stages. Expression of OsSPL14 increased at transcriptional level, and OsSPL14 protein level was substantially increased in transgenic lines relative to WT. A transcriptome analysis identified 473 up-regulated and 103 downregulated genes in the transgenic plants. The expression of differentially expressed genes (DEGs) involved in carotenoid biosynthesis, abscisic acid (ABA) metabolism, and lignin biosynthesis increased significantly. Most of DEGs participated in "plant hormone signal transduction" and "starch and sucrose metabolism" were also up-regulated in the transgenic plants. In addition, there were higher ABA and gibberellin acid 3 (GA 3 ) levels in OsSPL14-overexpression rice plants at seedling and tillering stages compared with WT. In contrast with that of WT, lignin and cellulose contents of culm increased distinctly. Also, silicon and potassium contents increased dramatically in transgenic lines. Meanwhile, the chalkiness ratios and chalkiness degrees decreased, and the gel consistency levels improved in transgenic lines. Thus, overexpression of OsSPL14 influenced growth period, leaf development, hormonal levels, culm composition, and grain quality characters of rice, which provides more insight into the function of OsSPL14.

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Section: Discussionsupporting

confidence: 92%

Overexpression of OsSPL14 results in transcriptome and physiology changes in indica rice ‘MH86’

Lian

Zhang

et al. 2020

Plant Growth Regul

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“…6C and 6D,Supplemental Fig. S10,Supplemental Dataset S6) (Liao et al, 2019;. At the CG context, the MH63-biased ASEGs showed higher gene body methylation in the MH63 alleles than the ZS97 alleles, indicating that gene body CG ASM positively correlated with ASE, corroborating the positive effect of gene body CG methylation for gene expression (Bewick and Schmitz, 2017).…”

Section: Allelic-specific Chg Methylation Is Associated With Allelic mentioning

confidence: 59%

Parental CG and CHG methylation variation is associated with allelic-specific expression in elite hybrid rice

Feng

Jia

et al. 2020

Preprint

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Heterosis refers to the superior performance of the hybrid over the inbred parental lines. Besides genetic variation, epigenetic difference between the parental lines has been suggested to be involved in heterosis. However, precise nature and extent of parental epigenome difference and reprograming in hybrids governing heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, of which the high-quality reference genomic sequences are available. We show that the parental varieties display important variation in genic methylation at CG and CHG (H=A, C, or T) sequences. Compared with the parents the hybrids display dynamic methylation variation during development. However, many parental differentially methylated regions (DMR) at CG and CHG sites are maintained in the hybrid. Only a small fraction of the DMRs display non-additive DNA methylation variation which, however, shows no overall correlation with gene expression variation. By contrast, most of the allelic-specific expression (ASE) genes in the hybrid are associated with DNA methylation and the ASE negatively correlates with allelic-specific methylation (ASM) at CHG but positively at CG sites. The results reveal a specific DNA methylation reprogramming pattern in the hybrid rice and point to a role of parental CG and CHG methylation divergence in allelic specific expression that has been associated with phenotype variation and hybrid vigor in several plant species.

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“…5), it is very likely that in 40 DAG the effect of gene expression variation caused by SNP3 masks the effect of protein activity difference caused by Indel-I. So far there have been quite a few genes known to control the tiller formation in rice, such as MOC1 [30][31][32] , SPL genes 33,34 , miR156 35 , LB4D 36 , DWARF10 37 , D14 16 , D53 38 , RCN8/9 39 , and OsTb1 40 . Some of these genes have strong effects on rice tillering.…”

Section: Discussionmentioning

confidence: 99%

Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice

et al. 2020

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The rice orthologue of maize domestication gene Teosinte branched 1 (Tb1) affects tillering. But, unlike maize Tb1 gene, it was not selected during domestication. Here, we report that an OsTb1 duplicate gene (OsTb2) has been artificially selected during upland rice adaptation and that natural variation in OsTb2 is associated with tiller number. Interestingly, transgenic rice overexpressing this gene shows increased rather than decreased tillering, suggesting that OsTb2 gains a regulatory effect opposite to that of OsTb1 following duplication. Functional analyses suggest that the OsTb2 protein positively regulates tillering by interacting with the homologous OsTb1 protein and counteracts the inhibitory effect of OsTb1 on tillering. We further characterize two functional variations within OsTb2 that regulate protein function and gene expression, respectively. These results not only present an example of neofunctionalization that generates an opposite function following duplication but also suggest that the Tb1 homologue has been selected in upland rice.

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SLR1 inhibits MOC1 degradation to coordinate tiller number and plant height in rice

Cited by 114 publications

References 50 publications

Overexpression of OsSPL14 results in transcriptome and physiology changes in indica rice ‘MH86’

Overexpression of OsSPL14 results in transcriptome and physiology changes in indica rice ‘MH86’

Parental CG and CHG methylation variation is associated with allelic-specific expression in elite hybrid rice

Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice

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