Mutations in the microRNA172 binding site of SUPERNUMERARY BRACT (SNB) suppress internode elongation in rice

Hyeonso Ji,Jeongho Baek,Do-Yu Kang,Chang-Deok Han,Kyung-Hwan Kim,Jun Oh,Kyeong-Seong Cheon,Gang-Seob Lee,Inchan Choi,Ki-Hong Jung,Hyoja Oh,Song Lim Kim

doi:10.1186/s12284-019-0324-8

Abstract

BackgroundInternode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui4 (shortened uppermost internode 4) mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is particularly severely affected. The present study was performed to identify the molecular nature and function of the SUI4 gene during internode elongation.ResultsOur previous study showed that the SUI4 gene was mapped to a 1.1-Mb interval on chromosome 7 (Ji et al. 2014). In order to isolate the gene responsible for the sui4 phenotype, genomic DNA resequencing of sui4 mutants and wild-type plants and reciprocal transformation of wild-type and mutant alleles of the putative SUI4 gene was performed. The data revealed that the causative mutation of sui4 was a T to A nucleotide substitution at the microRNA172 binding site of Os07g0235800, and that SUI4 is a new allele of the previously reported gene SUPERNUMERARY BRACT (SNB), which affects flower structure. In order to understand the effect of this mutation on expression of the SUI4/SNB gene, SUI4/SNB native promoter-fuzed GUS transgenics were examined, along with qRT-PCR analysis at various developmental stages. In sui4 mutants, the SUI4/SNB gene was upregulated in the leaves, culms, and panicles, especially when internodes were elongated. In culms, SUI4/SNB was expressed in the nodes and the lower parts of elongating internodes. In order to further explore the molecular nature of SUI4/SNB during internode elongation, RNA-seq and qRT-PCR analysis were performed with RNAs from the culms of sui4 mutants and wild-type plants in the booting stage. The data showed that in sui4 mutants, genes deactivating bioactive gibberellins and cytokinin were upregulated while genes related to cell expansion and cell wall synthesis were downregulated.ConclusionIn summary, this paper shows that interaction between SUI4/SNB and microRNA172 could determine internode elongation during the reproductive stage in rice plants. Due to a mutation at the microRNA172 binding site in sui4 mutants, the expression of SUI4/SNB was enhanced, which lowered the activities of cell expansion and cell wall synthesis and consequently resulted in shortened internodes.

Highlights

Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui4 mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is severely affected
Laccase and cinnamoyl CoA reductase are involved in biosynthesis of lignin which is predominantly deposited in the secondary cell walls (Park et al 2017; Swetha et al 2018). These results indicate that SUI4/SUPERNUMERARY BRACT (SNB) activates GA and cytokinin degradation and suppresses genes involved in cell expansion in rice culms
It was reported that the second AP2 domain of Arabidopsis APETALA2 (AP2) which has two AP2 domains like SUI4/SNB binds ‘TTTGTT’ motif and the presence of this motif in the AGAMOUS (AG) second intron is important for the restriction of AG expression in vivo (Dinh et al 2012)

Summary

Introduction

Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. sui (shortened uppermost internode 4) mutants show reduced internode length and a dwarf phenotype due to shortened internodes; the uppermost internode is severely affected. Internode elongation is an important agronomic trait in rice that determines culm length, which is related to lodging, panicle exsertion, and biomass. Internode elongation is an important agronomic trait that determines culm length, which is related to lodging, panicle exsertion, and biomass. At the base of the internode is the IM, where cell division generates new internodal cells. These new cells are displaced into the EZ, where they elongate until they reach their final length, and growth ceases in the DZ, where formation of the secondary wall and xylem takes place (Kende et al 1998). Mutations in genes involved in GA biosynthesis and signaling hamper internode elongation and cause dwarfism, as exemplified in rice sd, d18, d35, d1, gid, and gid mutants. GA signals promote cellulose synthesis by preventing interaction between SLENDER RICE1 (SLR1), a DELLA repressor of GA signaling, and NACs, the top-layer transcription factors for secondary wall formation (Huang et al 2015)

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Conclusion