Overexpression of a methyl-CpG-binding protein gene OsMBD707 leads to larger tiller angles and reduced photoperiod sensitivity in rice

Qu, Mengyu; Zhang, Zhujian; Liang, Tingmin; Niu, Peipei; Wu, Mingji; Chi, Wenchao; Chen, Ziqiang; Chen, Zaijie; Zhang, Shubiao; Chen, Songbiao

doi:10.1186/s12870-021-02880-3

Cited by 12 publications

(8 citation statements)

References 60 publications

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“…By contrast, extremely compact rice varieties are less e cient in capturing light and are more susceptible to infection by pathogen attack. Thus, a suitable tiller angle is very important for rice yield (Jiang et al 2012;Huang et al 2016;Qu et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study

Bai

Hong

et al. 2022

Plant Cell Rep

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Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association study (GWAS) on tiller angle in rice using a population of 164 japonica varieties derived from the 3K Rice Genomes Project (3K RGP). We detected a total of 18 QTLs using 1,135,519 single-nucleotide polymorphisms (SNP) based on three GWAS models (GLM, FastLMM and FarmCPU).Among them, two identi ed QTLs, qTA8.3 and qTA8.4, overlapped with PAY1 and TIG1, respectively, and additional 16 QTLs were identi ed for the rst time. Combined with haplotype and expression analyses, we further revealed that PAY1 harbors one non-synonymous variation at its coding region, likely leading to variable tiller angle in the population, and that nature variations in the promoter of TIG1 signi cantly affect its expression, closely correlating with tiller angle phenotypes observed. Similarly, using qRT-PCR and haplotype analysis, we identi ed 1 and 7 candidate genes in qTA6.1 and qTA8.1 that were commonly detected by two GWAS models, respectively. In addition, we identi ed 3 more candidate genes in the remaining 14 novel QTLs after ltering by transcriptome analysis and qRT-PCR. In summary, this study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding. Key MessageNovel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identi ed by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis.

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Section: Introductionmentioning

confidence: 99%

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study

Bai

Hong

et al. 2022

Plant Cell Rep

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“…MBD9 strongly interacts with Imitation SWItch (ISWI) chromatin remodeling complexes and has been shown to be involved in DNA demethylation [ 15 – 17 ]. In Arabidopsis mutants with MBD gene knockdown, nucleolar dominance was disturbed, and their growth and development were abnormal [ 18 ]. In mammals, MBD proteins are involved in tumorigenesis, schizophrenia, pulmonary fibrosis and many other diseases [ 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Xiao

Wang

2022

BMC Plant Biol

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Background Polyploidization promotes species formation and is widespread in angiosperms. Genome changes dramatically bring opportunities and challenges to plants after polyploidy. Methyl-CpG-Binding Domain (MBD) proteins can recognize and bind to methylation sites and they play an important role in the physiological process related to methylation in animals and plants. However, research on the influence of the allopolyploidization process on the MBD gene family is still lacking, so it is necessary to conduct a comprehensive analysis. Results In this study, twenty-two, ten and eleven MBD genes were identified in the genome of allotetraploid B. napus and its diploid ancestors, B. rapa and B. oleracea, respectively. Based on the clades of the MBD gene in Arabidopsis, rice and maize, we divided the new phylogenetic tree into 8 clades. Among them, the true MBD genes in Brassica existed in only 5 clades. Clade IV and Clade VI were unique in term of MBD genes in dicotyledons. Ka/Ks calculations showed that MBD genes underwent purifying selection in Brassica and may retain genes through sequence or functional differentiation early in evolution. In the process of allopolyploidization, the number of MBD gene introns increased, and the protein motifs changed. The MBD proteins had their own special motifs in each clade, and the MBD domains were only conserved in their clades. At the same time, the MBD genes were expressed in flower, leaf, silique, and stem tissues, and the expression levels of the different genes were significantly different, while the tissue specificity was not obvious. The allopolyploidization process may increase the number of cis-acting elements and activate the transposable elements. During allopolyploidization, the expression pattern of the MBD gene changes, which may be regulated by cis-acting elements and transposable elements. The number imbalance of cis-acting elements and transposable elements in An and Cn subgenomes may also lead to biased An subgenome expression of the MBD gene in B. napus. Conclusions In this study, by evaluating the number, structure, phylogeny and expression of the MBD gene in B. napus and its diploid ancestors, we increased the understanding of MBD genes in allopolyploids and provided a reference for future analysis of allopolyploidization.

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“…Flowering. Flowering and photoperiodic insensitivity results from overexpression of OsMeCP (Os12g0620400 (Qu et al, 2021) or by knocking out several genes. For example, Se5, Hd2 and Hd1 (Andrés et al, 2009;Gao et al, 2014;Shen et al, 2017;Tanaka et al, 2020).…”

Section: Grain Number Quality Weight and Plant Structurementioning

confidence: 99%

Rice breeding in the new era: comparison of useful agronomic traits

Hernández-Soto

Echeverría-Beirute

Abdelnour-Esquivel

et al. 2021

Preprint

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Understanding agronomic traits at a genetic level enables the leveraging of this knowledge to produce crops that are more productive and resilient, have better quality and are adjusted for consumer preferences. In the last decade, rice has become a model to validate the function of specific genes, resulting in valuable but scattered information. Here, we aimed to identify particular genes in rice related to traits that can be targeted by different mutation techniques in the breeding of crops. We selected gain of function, misfunction, and specific mutations associated with phenotypes of agronomic interest. The review includes specific trait-related genes involved in domestication, stress, herbicide tolerance, pathogen resistance, grain number/quality/weight, plant structure, nitrogen use, and others. The information presented can be used for rice, other cereals, and orphan crops to achieve a superior and sustainable production in challenging farming conditions.

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Overexpression of a methyl-CpG-binding protein gene OsMBD707 leads to larger tiller angles and reduced photoperiod sensitivity in rice

Cited by 12 publications

References 60 publications

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

Rice breeding in the new era: comparison of useful agronomic traits

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