A roadmap to durable BCTV resistance using long-read genome assembly of genetic stock KDH13

Submitted to: Plant Molecular Biology Reporter
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/18/2021
Publication Date: 8/13/2021
Citation: Galewski, P.J., Eujayl, I.A. 2021. A roadmap to durable BCTV resistance using long-read genome assembly of genetic stock KDH13. Plant Molecular Biology Reporter. https://doi.org/10.1007/s11105-021-01307-5.
DOI: https://doi.org/10.1007/s11105-021-01307-5

Interpretive Summary: 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 US and dry regions worldwide. The development of sequence from biological samples which contain agronomic traits of interest such as disease resistance has the potential to uncover the genome variation responsible. A fundamental understanding of the molecular mechanisms (e.g., genome variation, genes, and pathways) could allow for the development of a genome informed approach to improve resistance and increase the speed which varieties are developed in order to address this long-standing challenges to sugar beet cultivation. PacBio sequences were generated and assembled to better define the content and organization of variation within the KDH13 genome. Additionally, 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 BCTV resistance phenotypes segregating within F2 derived populations.

Technical Abstract: 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 US 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 BCT resistance and was identified as genetic stock for the improvement of sugar beet resistance to BCTV. 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-inito 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, 4,681 (75%) of the 6,245 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, 11,675,321 variants were detected, 3,377,004 SNP and 602,704 indels contained the ability to discriminate between the two parents. KDH13 contained 1,642,083 SNP and 308,615 indels identified as unique. This information represents a high-density marker dataset distributed across the beet genome and can be used to track genomic segments in populations where KDH13 is used as parental material to improve BCTV resistance.