S01 - Session O2 - Genetic information from phased SNP array data can improve assemblies of whole genome sequences

Authors: Stijn Vanderzande *, Cameron Peace

Whole genome sequence (WGS) assemblies for horticultural crops are a valuable resource to improve our understanding of key horticultural traits. The last decade has seen a rise in the availability, quality and use of WGSs, yet issues with aligning contigs and resolving haplotypes remain. SNP arrays have also become commonly available and large data sets of high-quality, phased SNP genotypic data have been generated. These data sets contain information on linkages among SNPs, allele presence in germplasm individuals and allele germplasm origins, and could therefore be a valuable additional resource to improve WGS assemblies n but are not fully exploited yet. To evaluate the quality of the haplotype-resolved WGS of 'Gala' and to demonstrate how SNP array data can contribute to WGS assemblies, phased 'Gala' SNP array data were compared to the WGS as follows. Genomic locations for the 8K SNP array SNPs were determined for each haploid WGS of 'Gala'. Then, SNP genotypes of the 'Gala' SNP array data were compared with those of the WGS and parental origin ('Kidd's Orange Red' or 'Golden Delicious') was assigned to the alleles on each WGS homolog. Genomic positions of a small proportion of SNPs were inconsistent between the two haploid WGSs, with the position for one homolog consistent with genetic maps. Furthermore, homologs in the 'Gala' WGS were expected to exclusively contain either maternal or paternal haplotypes, yet numerous homologs were composed of both. Also, several homologous regions were both composed of the same parental haplotype, with the expected other one missing. These results indicate that some contigs of the WGS were misassembled and that maternal and paternal haplotypes were not correctly resolved. We propose that available high-quality phased SNP array data, pedigree records, and extended shared haplotypes among individuals, which rely on inheritance-based genetics principles, are employed to improve WGS assemblies.