Genome-Wide Identification, Expression and Functional Analysis Reveal the Involvement of FCS-Like Zinc Finger Gene Family in Submergence Response in Rice

Yamei Ma,Jingfang Dong,David Edwards,Junliang Zhao,Tifeng Yang,Wu Yang,Lian Zhou,Shaohong Zhang,Hua Fu,Jian Wang,Bin Liu,Luo Chen

doi:10.1186/s12284-021-00519-3

Yamei Ma, Jingfang Dong + Show 10 more

Open Access

https://doi.org/10.1186/s12284-021-00519-3

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Abstract

BackgroundDirect seeding is an efficient rice cultivation practice. However, its application is often limited due to O2 deficiency following submergence, leading to poor seed germination, seedling establishment, and consequently yield loss. Identification of genes associated with tolerance to submergence and understanding their regulatory mechanisms is the fundamental way to address this problem. Unfortunately, the molecular mechanism of rice response to submergence stress is still not well understood.ResultsHere, we have performed a genome-wide identification of FCS-like zinc finger (FLZ) proteins and assessed their involvement in submergence response in rice. We identified 29 FLZ genes in rice, and the expression analysis revealed that several genes actively responded to submergence stress. Eight OsFLZ proteins interact with SnRK1A. As a case study, we demonstrated that OsFLZ18 interacted with SnRK1A and inhibited the transcriptional activation activity of SnRK1A in modulating the expression of its target gene αAmy3, a positive regulator in rice flooding tolerance. In line with this, OsFLZ18-overexpression lines displayed retarded early seedling growth and shorter coleoptile following submergence.ConclusionsThese data provide the most comprehensive information of OsFLZ genes in rice, and highlight their roles in rice submergence response.

Highlights

Direct seeding is an efficient rice cultivation practice
Ma et al Rice (2021) 14:76 low oxygen stress caused by submergence is one of the major factors limiting the application of rice direct seeding, which is a newly emerging agricultural practice and increasingly accepted by the farmers due to reduced need for water and labor, and efficient utilization of resources compared with the traditional transplanting practice (Kumar and Ladha 2011; Liu et al 2015)
The results showed that the expression of SUCROSE NONFERMENTING 1-RELATED PROTEIN KINASE 1A (SnRK1A) had no obvious alteration among Nipponbare and OE lines, but the expression level of Alpha-amylase gene 3 (αAmy3) was significantly decreased in OE lines (Fig. 7c)

Summary

Introduction

Direct seeding is an efficient rice cultivation practice. its application is often limited due to O2 deficiency following submergence, leading to poor seed germination, seedling establishment, and yield loss. Studies showed that Sub1A enabled mature plants to tolerate up to 14 days of complete submergence by stimulating the expression of a gene encoding alcohol dehydrogenase (Adh), an enzyme necessary for fermentative metabolism; and repressing GA-mediated induction of genes encoding α-amylase and expansin, which are respectively involved in starch degradation and cell elongation in leaves, thereby preserving energy until floodwaters recede (Fukao et al 2006; Fukao and Bailey-Serres 2008). These results well explain the molecular and physiological mechanisms of the mature rice plant to cope with submergence stress. The seed germination and coleoptile elongation of some rice varieties without Sub1A proceed satisfactorily under hypoxic or anoxic conditions (Magneschi and Perata 2009), indicating that these rice cultivars might use a Sub1A-independent mechanism to cope with low-O2 stress during germination and seedling establishment

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