Identification of rice blast resistance candidate genes based on integrating Meta-QTL and RNA-seq analysis

Abstract

<p id="C3"><italic>Magnaporthe oryzae</italic> seriously devastates rice production, and resistant cultivars can lose resistance within a few years due to the pathogenic variability of <italic>M. oryzae.</italic> Therefore, it is essential to explore continuously novel blast-resistance genes for breeding broad-spectrum resistance cultivars. In this study, firstly, 50 Meta-QTLs (including at least 2 original QTLs) were identified on 12 chromosomes by meta-analysis of blast-resistance 783 QTLs from 43 literatures. The average interval distance was 0.87 Mb in these Meta-QTLs, which contained a total of 4718 interval genes. Subsequently, based on integrated analysis of blast-resistance Meta-QTLs and RNA-seq, the result identified 2193 common genes which were not only located on blast-resistance Meta-QTLs, but also significantly differentially expressed in response to the <italic>M. oryzae</italic>. Among them, 22 cloned genes had been reported to be involved in defense responses to <italic>M. oryzae</italic> and other stresses. Furthermore, 99 resistance gene analogues (RGA) and 112 transcription factors (TF) were screened out from the above common genes, which were utilized to construct gene co-expression networks (GCEN). Based on the Top 20 of the connection degrees, hub genes were identified in the GCEN. Among them, <italic>OsJAMyb</italic>, <italic>bsr-d1</italic>, and <italic>OsWRKY76</italic> had been reported to be against rice blast, and <italic>OsSPL9</italic> was related to resistance to rice stripe virus. The left hub genes were considered as important potential resistance genes which need further functional verification to prepare for breeding broad-spectrum resistance rice cultivars.