Genome-wide identification of putative disease resistance genes (R genes) in carrot (Daucus carota subsp. sativus) by homology-based gene prediction

The cultivated carrot (Daucus carota ssp. sativus) is one of the most important root vegetable crops grown worldwide. Carrots are highly susceptible to several pests and diseases, and disease resistance is currently among the main breeding aims. The inheritance of resistance has been reported for a few carrot foliar diseases and root-knot nematodes, but no functionally characterized resistance gene (R gene) has yet been linked as a candidate gene to any resistance locus in carrot. Knowledge about the inventory of NLR genes (nucleotide-binding leucine-rich repeat receptors) and other R genes encoding transmembrane proteins such as receptor-like proteins (RLPs) and kinases (KIN) would be necessary to associate major QTLs (quantitative trait loci) identified by bi-parental QTL analyses or GWAS (genome-wide association analysis) with functional candidate R genes. In this study, we describe a combination of a genome-wide inventory of putative full-length carrot R genes based on a homology-based gene prediction approach called GeMoMa and subsequent classification by usage of the recent version of PRGdb 4.0 database (Calle-Garcia et al. 2022). A total of 320 putative carrot R genes were identified and bioinformatically characterized, including 72 newly identified gene models, that have not yet been annotated in the currently available carrot whole genome sequence. Based on the DRAGO 3 pipeline, totally 137 putative NLR genes were found, whereas 162 putative functional RLP and KIN genes were identified in the carrot genome. About one third of the R genes was found to be organized in clusters consisting only of NLR, RLP or KIN genes. To determine the evolutionary relationships of carrot R gene predictions, we generated a phylogenetic tree based on the alignment of all 320 R proteins. Three large clades (NLR, RLP and KIN) and a small clade (RLK) were identified, which reflect well the classification obtained after DRAGO 3 analysis. The presented carrot R gene inventory might be useful for resistance gene isolation, the development of (functional) molecular markers and resistance breeding in carrot.