Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon

• Published in: Nature communications Vol. 13; no. 1; pp. 7897 - 14
• Main Authors: Vaughn, Justin N., Branham, Sandra E., Abernathy, Brian, Hulse-Kemp, Amanda M., Rivers, Adam R., Levi, Amnon, Wechter, William P.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.12.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/22; 45/23; 631/114/2785; 631/208/205; 631/208/8; 631/449/1870; Airborne microorganisms; Copy number; Cucumis melo - genetics; Cucumis melo - microbiology; Cucurbitaceae - genetics; Disease resistance; Divergence; DNA Copy Number Variations; Error reduction; Gene mapping; Genetic diversity; Genetic variance; Genetics; Genomes; Genomics; Genotype; Genotypes; Genotyping; Humanities and Social Sciences; multidisciplinary; Plant Breeding; Population genetics; Populations; Powdery mildew; Quantitative Trait Loci - genetics; Recombination; Science; Science (multidisciplinary); Specialty crops; Wilt
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-35621-7

The genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. Here, we examine the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon ( Cucumis melo ). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping two Fusarium wilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations. The power of pangenomic graphs to improve genetic mapping is still unclear. Here, the authors demonstrate its value in identification of genetic variants associated with disease resistance traits in melon using PanPipes, a pangenome construction and low-coverage genotype-by-sequencing pipeline.