Genome-wide identification and prediction of disease resistance genes in Hirschfeldia incana

Abstract

Brassica species, globally cultivated as economically important vegetable and oilseed crops, face challenges from pathogens impacting their growth and productivity. Among these, blackleg, caused by the fungal pathogen Leptosphaeria maculans, stands out as a significant concern. Genetic resistance, primarily mediated by resistance gene analogues (RGAs), is key to sustainable blackleg control. Utilising wild relatives of Brassica species presents a promising avenue for enhancing resistance to blackleg in cultivated crops. In this study, we employed the newly published Hirschfeldia incana reference genome to identify the genome-wide RGAs in H. incana. A total of 914 candidate RGAs were identified; the receptor-like protein kinases (RLK) family contained the highest number with 608 (66.53%), followed by the Transmembrane coiled-coil (TM-CC) family with 167 (18.27%), nucleotide-binding site-leucine-rich repeats (NLR) family with 98 (10.72%) and receptor-like proteins (RLPs) with 41 (4.48%). We conducted duplication analysis on the 914 candidate RGAs, which revealed gene duplication occurs frequently to expand the RGAs in H. incana and significantly contributes to plant defence responsiveness. The phylogenetic analysis provided insights into the diversification and functional implications of the identified groups. We used the sequences of the 49 cloned R genes to identify homologs across H. incana. A total of 75 cloned disease-resistance gene homologs (CDRHs) were found. Cis-acting elements (CREs) were analysed in promoter sequences of 914 RGAs in H. incana, which confirmed their potential function in disease defence. Overall, the results suggest that the wild species H. incana could be a potential R gene source for various disease resistances, including blackleg.