Prediction of the tomato Ph-3 late blight disease resistance gene using public marker data and the re-annotated tomato NB-LRR complement

<p>Members of the nucleotide-binding leucine-rich repeat (NB-LRR) class of plant disease resistance (<em>R</em>) genes are key-receptors during the innate immunity response against a wide range of pests and diseases. Many efforts are therefore carried out to identify and annotate this gene family within genome sequencing projects of crop plants to, for example, provide plant breeders with a genomic toolbox.</p> <p>Genome sequencing efforts of members of the genus Solanum, which includes the crops potato and tomato, have not only aided the identification of the full <em>R</em> gene complements, but also further showed that the chromosomal location of gene subfamilies is highly conserved. In a previous publication (Andolfo et al., 2014), we exploited this fact together with publicly available genetic marker data, to predict the potential candidate for the tomato late blight <em>R</em> gene <em>Ph-3</em>. By superimposing four markers from two independent publications (Andolfo et al., 2013 and Zhang et al., 2013) over the <em>R</em> gene-annotated tomato chromosome 9, we pin-pointed to a single candidate Solyc09g092310. The recent publication of the Ph-3 sequence (Zhang et al., 2014) allowed us to compare this sequence, which is derived from <em>S. pimpinellifolium</em> L3708, with our candidate Solyc09g092310 from the tomato reference <em>S. lycopersicum</em> Heinz1706. Initial blastn searches against the Heinz1706 NB-LRR complement returned the four candidates flanked by Indel_3 and P55 (Figure A). However the highest sequence similarity with over 95% (nucleotide) over the full coding sequence was identified for our candidate Solyc09g092310 (Figure B), delimited between markers TG591 and P55.</p> <p>This result shows another important application of the reannotated NB-LRR gene complement in predicting <em>R</em> gene candidates in conjunction with previously derived genetic marker data that describe yet uncharacterised disease resistance loci.</p> <p> </p> <p> </p> <p>Andolfo G, Jupe F, Witek K, Etherington GE, Ercolano MR, Jones JDG. (2014). Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq. BMC Plant Biology 14(120). doi:10.1186/1471-2229-14-120</p> <p>Zhang C, Liu L, Wang X, Vossen J, Li G, Li T, Zheng Z, Gao J, Guo W, Visser RGF, Li J, Bai Y, Du Y (2014). The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theoretical and Applied Genetics. doi:10.1007/s00122-014-2303-1</p> <p>Andolfo G, Sanseverino W, Aversano R, Frusciante L, Ercolano MR (2013) Genome-wide identification and analysis of candidate genes for disease resistance in tomato. Mol breeding, 9928:7. doi:10.1007/s11032-013-9928-7</p> <p>Zhang C, Liu L, Zheng Z, Sun Y, Zhou L, Yang Y, Cheng F, Zhang Z, Wang X, Huang S, Xie B, Du Y, Bai Y, Li J (2013) Fine mapping of the Ph‐3 gene conferring resistance to late blight (Phytophthora infestans) in tomato. Theor Appl Genet, 126:2643–2653. doi: 10.1007/s00122-013-2162-1