Published August 4, 2022 | Version v1
Dataset Open

Data from: Unravelling cucumber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs

Creators

  • 1. 1 INRAE, Génétique et Amélioration des Fruits et Légumes, 84143, Montfavet, France 2 Bayer Crop Science, 13670, Saint-Andiol, France
  • 2. Bayer Crop Science, 13670, Saint-Andiol, France
  • 3. 1 INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Université Paris-Saclay, 91190, Gif-sur-Yvette, France 2 Mathématiques et Informatique Appliquées (MIA)-Paris, INRAE, AgroParisTech, Université Paris-Saclay, 91120 Palaiseau, France
  • 4. INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
  • 5. Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
  • 6. Bayer Crop Science, 2661 CZ, Bergschenhoek, The Netherlands
  • 7. INRAE, Génétique et Amélioration des Fruits et Légumes, 84143, Montfavet, France

Description

The mapping and introduction of sustainable resistance to viruses in crops is a major challenge in modern breeding, especially regarding vegetables. We hence assembled a panel of cucumber elite lines and landraces from different horticultural groups for testing with six virus species. We mapped 18 quantitative trait loci (QTL) with a multiloci genome wide association studies (GWAS), some of which have already been described in the literature. We detected two resistance hotspots, one on chromosome 5 for resistance to the cucumber mosaic virus (CMV), cucumber vein yellowing virus (CVYV), cucumber green mottle mosaic virus (CGMMV) and watermelon mosaic virus (WMV), colocalizing with the RDR1 gene, and another on chromosome 6 for resistance to the zucchini yellowing mosaic virus (ZYMV) and papaya ringspot virus (PRSV) close to the putative VPS4 gene location. We observed clear structuring of resistance among horticultural groups due to plant virus coevolution and modern breeding which have impacted linkage disequilibrium (LD) in resistance QTLs. The inclusion of genetic structure in GWAS models enhanced the GWAS accuracy in this study. The dissection of resistance hotspots by local LD and haplotype construction helped gain insight into the panel’s resistance introduction history. ZYMV and CMV resistance were both introduced from different donors in the panel, resulting in multiple resistant haplotypes at same locus for ZYMV, and in multiple resistant QTLs for CMV.

Notes

Leaf samples from three plants were bulked for each accession of a cucumber diversity panel composed by 257 lines/landrace. Samples were sequenced with Illumina 150 bp pair-end to 20x coverage. The Cornell Chinese Long v3.0 public genome (Li et al. 2019) was used for sequence alignment and variant calling. Variant discovery performed using GATK4 Best Practices (Van der Auwera et O'Connor 2020), first by calling individual sample SNPs, followed by joint genotyping on the population. All biallelic SNP with a depth equal or superior to 20X and a Phred score superior to 20 for each accession were collected, resulting in a genetic dataset of 2,081,122 biallelic SNPs, 28,162 multiallelic SNPs and 30,557 InDels. The SNPs were then filtered for QD (Quality by Depth) >18. SNPs exhibiting a missing rate above 10%, a heterozygous rate above 20% and a minor allele frequency (MAF) under 3,25% (~8 homozygous accessions), were discarded. InDels and multi-allelic SNPs were also discarded. The final matrix is composed by 257 accessions and 1,384,889 biallelic SNPs.

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SNPmatrix_CUC_GWASvirus_M10.txt

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