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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #402793
Research Project: Grapevine Genetics, Genomics and Molecular Breeding for Disease Resistance, Abiotic Stress Tolerance, and Improved Fruit Quality

Location: Grape Genetics Research Unit (GGRU)

Title: Multiple-tiered haplotype marker system for chromosome-level phasing correction and QTL fine-mapping of a novel locus for resistance to grapevine downy mildew

Author
item ZOU, CHENG - Cornell University
item SAPKOTA, SURYA - Cornell University
item FIGUEROA-BALDERAS, ROSA - Uc Davis Medical Center
item GLAUBITZ, JEFF - Cornell University
item CANTU, DARIO - Uc Davis Medical Center
item SUN, QI - Cornell University
item Cadle-Davidson, Lance

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/17/2023
Publication Date: 9/14/2023
Citation: Zou, C., Sapkota, S., Figueroa-Balderas, R., Glaubitz, J., Cantu, D., Sun, Q., Cadle Davidson, L.E. 2023. Multiple-tiered haplotype marker system for chromosome-level phasing correction and QTL fine-mapping of a novel locus for resistance to grapevine downy mildew. Plant Physiology. https://doi.org/10.1093/plphys/kiad494.
DOI: https://doi.org/10.1093/plphys/kiad494

Interpretive Summary: DNA markers help plant breeders locate the genetic basis of traits. Here we developed a new DNA marker strategy to increase the accuracy of trait mapping. Our approach enabled construction of a chromosome-level genome, accurate detection of meiosis recombination sites, and quantification of gene expression for each version of each gene. We used this approach to dissect a novel locus we call RPV33 conferring resistance to grapevine downy mildew. Our DNA markers narrowed the candidate region to only 400,000 base pairs. Gene expression analysis identified two resistance gene candidates in this region. These two candidate genes are not present in susceptible grapevines. Furthermore, our strategy corrected 16 errors in the genome assembly. This mapping strategy could be widely adopted for genetic mapping in highly heterozygous species.

Technical Abstract: Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here we employed a multi-tiered haplotypic marker system to increase the accuracy of fine mapping through construction of a chromosome-level, haplotype-solved parental genome, accurate detection of recombination sites, and allelic-specific characterization of the transcriptome. The pre-developed rhAmpSeq markers core genome detected the approximate region of the QTL, while accurate localization of recombination cross-over sites from Illumina skim-seq data was facilitated by the Viterbi algorithm. We used this approach to dissect a novel RPV33 locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.4 Mb. Allelic-specific RNA-seq analysis identified putative disease-resistance RPP13-like protein 3 genes located in a non-syntenic insertion as probable candidate genes. Furthermore, together with the rhAmpSeq core genome haplotype markers, the skim-seq-derived, high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana ‘PI 588149’ assembly, initially built solely from PacBio Hifi reads, and led to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs of interest, and could be widely adopted for QTL mapping in highly heterozygous species.