Abstract
Gray leaf spot (GLS) disease in maize, caused by the fungus Cercospora zeina, is a threat to maize production globally. Understanding the molecular basis for quantitative resistance to GLS is therefore important for food security. We developed a de novo assembly pipeline to identify candidate maize resistance genes. Near-isogenic maize lines with and without a QTL for GLS resistance on chromosome 10 from inbred CML444 were produced in the inbred B73 background. The B73-QTL line showed a 20% reduction in GLS disease symptoms compared to B73 in the field (p = 0.01). B73-QTL leaf samples from this field experiment conducted under GLS disease pressure were RNA sequenced. The reads that did not map to the B73 or C. zeina genomes were expected to contain novel defense genes and were de novo assembled. A total of 141 protein-coding sequences with B73-like or plant annotations were identified from the B73-QTL plants exposed to C. zeina. To determine whether candidate gene expression was induced by C. zeina, the RNAseq reads from C. zeina-challenged and control leaves were mapped to a master assembly of all of the B73-QTL reads, and differential gene expression analysis was conducted. Combining results from both bioinformatics approaches led to the identification of a likely candidate gene, which was a novel allele of a lectin receptor-like kinase named L-RLK-CML that (i) was induced by C. zeina, (ii) was positioned in the QTL region, and (iii) had functional domains for pathogen perception and defense signal transduction. The 817AA L-RLK-CML protein had 53 amino acid differences from its 818AA counterpart in B73. A second “B73-like” allele of L-RLK was expressed at a low level in B73-QTL. Gene copy-specific RT-qPCR confirmed that the l-rlk-cml transcript was the major product induced four-fold by C. zeina. Several other expressed defense-related candidates were identified, including a wall-associated kinase, two glutathione s-transferases, a chitinase, a glucan beta-glucosidase, a plasmodesmata callose-binding protein, several other receptor-like kinases, and components of calcium signaling, vesicular trafficking, and ethylene biosynthesis. This work presents a bioinformatics protocol for gene discovery from de novo assembled transcriptomes and identifies candidate quantitative resistance genes.
Highlights
Maize is one of the three main cereal crops that are globally used as a food source and is especially important in regions such as Africa, where it is a staple food (Ranum et al, 2014)
A recent global survey highlighted several fungal foliar diseases that reduce maize yields significantly in Africa, Asia, and the Americas (Savary et al, 2019). One of these foliar diseases is gray leaf spot (GLS), which is present throughout sub-Saharan Africa, where GLS is caused by Cercospora zeina (Meisel et al, 2009; Nsibo et al, 2019)
Our approach led to the identification of an allele of a lectin receptorlike kinase from CML444 positioned in the QTL region and induced by the pathogen as the most likely candidate gene, as well as a range of other defense-related transcripts that could contribute to the Quantitative disease resistance (QDR) to GLS disease
Summary
Maize is one of the three main cereal crops that are globally used as a food source and is especially important in regions such as Africa, where it is a staple food (Ranum et al, 2014). These studies identified 157, 1321, and 2355 novel transcripts from 6, 21, and 368 diverse inbred maize lines, respectively (Lai et al, 2010; Hansey et al, 2012; Jin et al, 2016) These findings imply that comparison to the few sequenced genomes of maize may not facilitate the identification of novel genes or alleles responsible for some cases of QDR. This provides the rationale for this study in which a transcriptomics approach is used to contrast gene expression between near-isogenic lines in the B73 background that differ only in the QTL locus from a diverse maize source. Our approach led to the identification of an allele of a lectin receptorlike kinase from CML444 positioned in the QTL region and induced by the pathogen as the most likely candidate gene, as well as a range of other defense-related transcripts that could contribute to the QDR to GLS disease
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
