Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection

Zhenhui Zhong,Yahong Lin,Xiaofeng Chen,Lili Lin,Huakun Zheng,Lianyu Lin,Meilian Chen,Justice Norvienyeku,Zonghua Wang,Xi Chen

doi:10.1186/s12284-019-0270-5

Zhenhui Zhong, Yahong Lin + Show 8 more

Open Access

https://doi.org/10.1186/s12284-019-0270-5

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Abstract

BackgroundRice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited.ResultsHere, we explored gene expression divergence between a japonica rice cultivar Nipponbare and an indica rice cultivar 93–11 in response to invasion by the filamentous ascomycete fungus Magnaporthe oryzae (Pyricularia oryzae), a plant pathogen that causes significant loss to rice production worldwide. We investigated differentially expressed genes in the two cultivars and observed that evolutionarily conserved orthologous genes showed highly variable expression patterns under rice blast infection. Analysis of promoter region of these differentially expressed orthologous genes revealed the existence of cis-regulatory elements associated with the differentiated expression pattern of these genes in the two rice cultivars. Further comparison of these regions in global rice population indicated their fixation and close relationship with rice population divergence.ConclusionWe proposed that variation in the expression patterns of these orthologous genes mediated by cis-regulatory elements in the two rice cultivars, may constitute an alternative evolutionary mechanism that distinguishes these two genetically and ecologically divergent rice cultivars in response to M. oryzae infection.

Highlights

Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide
Our analysis showed that the distinct expression patterns exhibited by orthologous genes identified in the two rice cultivars corresponded with the high sequence diversity prevailing in the promoter region
This study provides an insight into how variation in the promoter region of orthologous genes contribute to the differential response of two rice cultivars, NPB and 93–11 each from japonica and indica subspecies during M. oryzae infection

Summary

Introduction

Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Rice has evolved into several subspecies as a result of purposeful breeding and intensive domestication These different rice subspecies are often endowed with distinct agronomic traits, such as larger grain size, superior grain quality as well as biotic and abiotic stress tolerance (Wang et al 1998). Recent rice population genetic studies demonstrated that the two most widely distributed rice subspecies japonica Group and indica Group evolved from a common ancestor, Oryza rufipogon several thousand years ago (Huang et al 2012, Wang et al 2018b, Xie et al 2015). Many of the domestication related genes have been identified as key regulators of important agronomic traits, such as seed shattering, pericarp color, amylose content, as well as grain number or size in rice, and these genes have shown significant variation between rice subspecies. The origin and genomic foundations related with SNPs or InDels mediated variation on gene expression still need to be uncovered

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