The NLRomes of Zea mays NAM founder lines and Zea luxurians display presence-absence variation, integrated domain diversity, and mobility

Plant pathogens cause significant crop loss worldwide, and new resistance genes deployed to combat diseases can be overcome quickly. Understanding the existing resistance gene diversity within the germplasm of major crops, such as maize, is crucial for the development of new disease-resistant varieties. We analysed the nucleotide-binding leucine-rich repeat receptors (NLRs) of 26 recently sequenced diverse founder lines from the maize nested association mapping (NAM) population and compared them to the R gene complement present in a wild relative of maize, Zea luxurians. We found that NLRs in both species contain a large diversity of atypical integrated domains, including many domains that have not previously been found in the NLRs of other species. Additionally, the single Z. luxurians genome was found to have greater integrated atypical domain diversity than all 26 NAM founder lines combined, indicating that this species may represent a rich source of novel resistance genes. NLRs were also found to have very high sequence diversity and presence-absence variation among the NAM founder lines, with a large NLR cluster on Chr10 representing a diversity hotspot. Additionally, NLRs were shown to be mobile within maize genomes, with several putative interchromosomal translocations identified.

Automated summary

Plant pathogens cause crop loss worldwide, and new resistance genes can be quickly overcome. Understanding resistance gene diversity in major crops like maize is crucial for developing disease-resistant varieties. By analyzing the nucleotide-binding leucine-rich repeat receptors (NLRs) in maize and its wild relative Zea luxurians, we found a large diversity of atypical integrated domains in both species, with Z. luxurians potentially being a rich source of novel resistance genes. NLRs also showed high sequence diversity and presence-absence variation among maize populations, with mobile NLRs and putative interchromosomal translocations identified.