Haplotype phasing of de novo chromosome-level assembly of ‘Antonovka’ facilitated the identification of candidate genes for apple scab resistance

Abstract

Malus genomic resources with improved quality are becoming an integral part of candidate gene identification and functional validation. Recently, we released a reference-based phased chromosome-level genome assembly of ‘Antonovka’ 172670B Malus domestica cultivar from the ‘Antonovka’ group known for its disease resistance and abiotic stress tolerance. However, reference-based assemblies have limited accuracy in candidate alleles identification along extended genomic loci, as these may contain contigs from different haplotypes. Here, we provide an improved high-quality version of the ‘Antonovka’ 172670B genome. This assembly is fully phased as it integrates chromosome conformation capture sequencing and parental SNP data binning for de novo scaffolding and post-assembly phasing of pseudochromosomes into haplotypes, respectively. It shows improved quality scores and completeness of 59.8 and 96.7%, respectively. A total of 21,740 structural variations larger than 50 bp and over 3 million SNPs were identified between the two haplomes and can be further validated for genetic mapping studies. This assembly identified new candidate alleles for apple scab resistance in the extended flanking region of the Rvi6 -linked marker Ch-Vf1 on linkage group 1 of haplotype 1. These alleles have kinase and transferase activity, and those that show high homology with the HcrVf scab resistance gene showed between 3.6- to 8.3-fold upregulation upon Venturia inaequalis inoculation, making them the prime candidates for future functional validation studies of ‘Antonovka’ scab resistance.