A roadmap to Durable BCTV Resistance Using Long-Read Genome Assembly of Genetic Stock KDH13

Beet Curly Top (BCT) is a viral disease which negatively impacts crop productivity for sugar beet growers and the sugar beet industry in the western USA and dry regions worldwide. Current varieties exhibit little genetic resistance to the Beet Curly Top Virus (BCTV), suggesting there is a large potential for improvement. KDH13 (PI 663862) is a double-haploid line created from a population (C762-17/PI 560130) which segregates for resistance to BCTV and was identified as genetic stock for the improvement of sugar beet varieties. PacBio sequences were generated and assembled to better define the content and organization of variation within the KDH13 genome and to provide resources to identify specific variation underpinning durable genetic resistance. Using ab initio predicted proteins as anchors, the assembled KDH13 contigs were placed in a more contiguous order using the EL10.1 reference genome, which leveraged Bio-Nano optical maps and Hi-C proximity information for chromosome level scaffolding. In total, 4681 (75%) of the 6245 contigs were placed in the order and orientation of the EL10.1 genome. The anchored contigs represented 502,929,268 bp (87.7%), the KDH13 genome assembly. An F₁ hybrid and parental lines KDH13 (resistant) and KDH19-17 (susceptible) were sequenced using Illumina technology in order to characterize the SNP, indel, and structural variation between parental lines and allow for a more detailed investigation into causal variation linked to important phenotypes. In total, 3,086,720 variants were detected, including 2,259,324 single-nucleotide polymorphisms, 191,448 insertions, 198,057 deletions, 268,090 complex substitutions, 90,004 multi allelic variants, and 79,797 structural variants. Of the total variation, 1,158,491 were informative in the F1 and were able to discriminate between the two parents. This information represents a high-density marker dataset distributed globally across the sugar beet genome and can be used to track genomic segments in populations where KDH13 is used as parental material to improve BCTV resistance.