Mutations in <i><scp>MIR</scp>396e</i> and <i><scp>MIR</scp>396f</i> increase grain size and modulate shoot architecture in rice

Miao, Chunbo; Wang, Dong; He, Reqing; Liu, shenkui; Zhu, Jian‐Kang

doi:10.1111/pbi.13214

Cited by 82 publications

(21 citation statements)

References 37 publications

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“…In the flanking region of SZ3, we identified a microRNA, miRNA396, and gene Rc03G006134. MiRNA396 is implicated in the regulation of seed size and yield in rice [ 50 , 51 ] and Rc03G006134 encodes an orthologue of the transposase-like DAYSLEEPER gene in Arabidopsis and is essential for normal plant growth, especially cotyledon development [ 52 ]. The gene Rc05G010958 near the flanking region of the GWAS signal for SA and SSW (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Yang

et al. 2021

Genome Biol

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Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. Results Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. Conclusions This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

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Section: Resultsmentioning

confidence: 99%

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Yang

et al. 2021

Genome Biol

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“…Notably, some DEMs such as miR156, miR160, miR166, miR167, miR168, miR395, miR396, miR397, miR398, miR399, and miR408 were also found to be differentially expressed during seed development in many seed plants [ 4 , 18 , 19 , 21 – 30 ]. In rice, miR156, miR160, miR167, miR396, miR397, miR389, and miR408 have been functionally verified to regulate the rice seed development [ 31 – 38 , 40 ]. These suggested that these known miRNAs were the key and conserved miRNAs in different plant seed development regulation and could also be used as candidate miRNAs for Tartary buckwheat seed development.…”

Section: Discussionmentioning

confidence: 99%

Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

Meng

Sun

et al. 2021

BMC Plant Biol

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Background Tartary buckwheat seed development is an extremely complex process involving many gene regulatory pathways. MicroRNAs (miRNAs) have been identified as the important negative regulators of gene expression and performed crucial regulatory roles in various plant biological processes. However, whether miRNAs participate in Tartary buckwheat seed development remains unexplored. Results In this study, we first identified 26 miRNA biosynthesis genes in the Tartary buckwheat genome and described their phylogeny and expression profiling. Then we performed small RNA (sRNA) sequencing for Tartary buckwheat seeds at three developmental stages to identify the miRNAs associated with seed development. In total, 230 miRNAs, including 101 conserved and 129 novel miRNAs, were first identified in Tartary buckwheat, and 3268 target genes were successfully predicted. Among these miRNAs, 76 exhibited differential expression during seed development, and 1534 target genes which correspond to 74 differentially expressed miRNAs (DEMs) were identified. Based on integrated analysis of DEMs and their targets expression, 65 miRNA-mRNA interaction pairs (25 DEMs corresponding to 65 target genes) were identified that exhibited significantly opposite expression during Tartary buckwheat seed development, and 6 of the miRNA-mRNA pairs were further verified by quantitative real-time polymerase chain reaction (qRT-PCR) and ligase-mediated rapid amplification of 5′ cDNA ends (5′-RLM-RACE). Functional annotation of the 65 target mRNAs showed that 56 miRNA-mRNA interaction pairs major involved in cell differentiation and proliferation, cell elongation, hormones response, organogenesis, embryo and endosperm development, seed size, mineral elements transport, and flavonoid biosynthesis, which indicated that they are the key miRNA-mRNA pairs for Tartary buckwheat seed development. Conclusions Our findings provided insights for the first time into miRNA-mediated regulatory pathways in Tartary buckwheat seed development and suggested that miRNAs play important role in Tartary buckwheat seed development. These findings will be help to study the roles and regulatory mechanism of miRNAs in Tartary buckwheat seed development.

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“…The expression of miR396a was suppressed to approximately 50% in the tomato plants that overexpressed lncRNA44664 (OE-lnc44664), and the target genes of Solyc10g083510.1 were significant increased ( Figure 6B). miR396 was found to be associated with GRFs (growth-regulating factors) [24]. The expression of miR156d was suppressed to approximately 50% in the tomato plants that overexpressed lncRNA48734 (OE-lnc48734), and the target genes of Solyc05g012040.2 were significantly increased ( Figure 6C).…”

Section: Function Verification Of Lncrnasmentioning

confidence: 99%

Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita

Yang

Zhao

Fan

et al. 2020

IJMS

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Root-knot nematodes (RKNs) severely affect plants growth and productivity, and several commercial biocontrol bacteria can improve plants resistance to RKNs. Pseudomonas putida Sneb821 isolate was found to induce tomatoes resistance against Meloidogyne incognita. However, the molecular functions behind induced resistance remains unclear. Long non-coding RNA (lncRNA) is considered to be a new component that regulates the molecular functions of plant immunity. We found lncRNA was involved in Sneb821-induced tomato resistance to M. incognita. Compared with tomato inoculated with M. incognita, high-throughput sequencing showed that 43 lncRNAs were upregulated, while 35 lncRNAs were downregulated in tomatoes previously inoculated with Sneb821. A regulation network of lncRNAs was constructed, and the results indicated that 12 lncRNAs were found to act as sponges of their corresponding miRNAs. By using qRT-PCR and the overexpression vector pBI121, we found the expression of lncRNA44664 correlated with miR396/GRFs (growth-regulating factors) and lncRNA48734 was correlated with miR156/SPL (squamosal promoter-binding protein-like) transcription factors. These observations provided a novel molecular model in biocontrol bacteria-induced tomato resistance to M. incognita.

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Mutations in MIR396e and MIR396f increase grain size and modulate shoot architecture in rice

Cited by 82 publications

References 37 publications

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita

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