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

Abstract

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.

Pseudomonas syringaepv.tomatoDC3000 induces defense responses in diverse maize inbred lines

“…Such knowledge will be valuable in determining the molecular and cellular mechanisms underlying nucleotide-binding leucine-rich repeat immune receptors (NLR)-dependent recognition of P. syringae pv. tomato DC3000 effectors (Prigozhin et al, 2022; Thatcher et al, 2023).…”

Applications, Benefits, and Challenges of Genome Edited Crops

“…In yet another application, Corteva Agriscience is advancing a novel approach to breeding for disease resistance in corn for Northern corn leaf blight (Exserohilum turcicum), Southern rust (Puccinia polysora), gray leaf spot (Cercospora zeae-maydis), and Anthracnose stalk rot (Colletotrichum graminicola). The concept would relocate numerous disease resistance alleles (i.e., matching genes) to a common location in the genome, which has the benefit of conferring more durable disease resistance in addition to maintaining linked traits during subsequent breeding cycles (Thatcher et al 2023;Corteva 2023). For all plant species, this strategy of multiplexing and co-locating favorable disease-resistant genes leaves the remainder of the genome available for achieving genetic gains in other yield or quality traits by testing and leveraging genetic variation (Box 2).…”