A Reference-Quality NLRome for the Hexaploid Sweetpotato and Diploid Wild Relatives

Abstract

Breeding for sweetpotato (Ipomea batatas) resistance requires accelerating our understanding of genomic sources of resistance. Nucleotide-binding domain leucine-rich repeat receptor (NLR) proteins represent a key component of the plant immune system that mediate plant immune responses. We cataloged the NLR diversity in 32 hexaploid sweetpotato genotypes and three diploid wild relatives using resistance gene enrichment sequencing (RenSeq) to capture and sequence full NLRs. A custom-designed NLR bait library enriched NLR genes with an average 97% target capture rate. We employed a curated database of cloned and functionally characterized NLRs to assign sequenced sweetpotato NLRs to canonical phylogenetic clades. We identified between 800 and 1,200 complete NLRs, highlighting the expanded diversity of coiled-coil NLRs (CNLs) across all genotypes. NLRs among sweetpotato genotypes exhibited large conservation across genotypes. The phylogenetic distance between 6× (hexaploid) and 2× (diploid) genotypes revealed that a small repertoire of I. batatas CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid (Ipomoea trifida) genomes and recorded clustering of NLRs on chromosomes arms. Our study provides a catalog of NLR genes that can be used to accelerate breeding and increase our understanding of the evolutionary dynamics of sweetpotato NLRs. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Keywords: Ipomoea batatas (sweetpotato); NLRs; RenSeq; hexaploid; wild relatives.