RT Journal Article SR Electronic T1 Haplotype-resolved powdery mildew resistance loci reveal the impact of heterozygous structural variation on NLR genes in Muscadinia rotundifolia JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.11.23.469029 DO 10.1101/2021.11.23.469029 A1 Mélanie Massonnet A1 Amanda M. Vondras A1 Noé Cochetel A1 Summaira Riaz A1 Dániel Pap A1 Andrea Minio A1 Rosa Figueroa-Balderas A1 M. Andrew Walker A1 Dario Cantu YR 2022 UL http://biorxiv.org/content/early/2022/01/13/2021.11.23.469029.abstract AB Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew. It carries two powdery mildew resistance-associated genetic loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. In this study, we identified, phased, and reconstructed the two haplotypes of each resistance-associated locus. Haplotype phasing allowed the identification of several structural variation events between haplotypes of both loci. Combined with manual refinement of the gene models, we found that the heterozygous structural variants affected the gene content, with some resulting in duplicated or hemizygous nucleotide-binding leucine-rich repeat (NLR) genes. Structural variations also impacted the domain composition of some NLRs. These findings emphasize the need of generating haplotype-resolved sequences instead of using consensus sequences for identifying haplotype-specific candidate genes. Comparison of the NLRs in the Run1.2 and Run2.2 loci indicated that the two loci are composed of a different number and classes of NLR genes. We provide a list of candidate NLR genes from the Run1.2b and Run2.2 loci, whose expression suggests a role in powdery mildew resistance in Trayshed. These first complete and haplotype-resolved resistance-associated loci, and their candidate NLR genes, represent new resources to develop powdery mildew-resistant grape cultivars.Competing Interest StatementThe authors have declared no competing interest.