QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)

Supplemental files

Supplementary table S1 Sequence information for the KASP markers, including: SNP ID, physical position of the SNP, primer sequences, SNP flanking sequence, and nucleotides of the sulfur tolerant (T) and sensitive (S) alleles.

Supplementary table S2 Phenotypic data used for QTL mapping: RIL means of percentage of damaged (chlorotic or necrotic) area after vaporized elemental sulfur treatment of cotyledons (cot) or leaves (leaf) in test 1 (_t1), in test 2 (_t2), and across tests (cot or leaf).

Supplementary table S3 Melon accession genotypes at KASP markers developed across qSulf-1. Markers are named according to physical position (bp) on chromosome 1. Genotypes are color coded, with individuals homozygous for the sulfur tolerance allele (B) in blue, sensitivity allele (A) in yellow, heterozygous (H) in gray and missing (NA) in white. The significance and magnitude of correlation between sulfur response and genotype are listed for each marker

Supplementary table S4 Chromosomal location and functional information for genes that collocated with the major QTL for sulfur tolerance, including the position of the start and stop codons within the chromosome (cs), gene ontology (GO) code and term, and conserved domains and features found within the gene (NCBI).

Supplementary table S5 Functional annotation of candidate gene polymorphisms between the parents in the QTL interval of qSulf-1, including the chromosome, physical position (in bp), parental alleles, polymorphism location relative to the gene (ie. upstream, exonic, downstream, etc.), distance from the gene (in bp), type of exonic mutation (synonymous or nonsynonymous), and detail (which exon and the nucleotide and amino acid changes).

Supplementary figure S1 Interaction plot showing evidence for epistasis between qSulf-1 and qSulf-12. Alleles from the sulfur sensitive parent (MR-1) are 'AA' and from the sulfur tolerant parent (AY) are 'BB'. The circle represents the mean percent damage of individuals in the population with the labelled genotypes. The plus signs indicate the standard error.

Supplementary figure S2 Logarithm of odds (LOD) scores for forward model selection of up to seven QTL associated with mean percentage of damaged (chlorotic or necrotic) area after vaporized elemental sulfur treatment of: (a) cotyledons in test 1, (b) cotyledons in test 2, (c) leaves in test 1 and (d) leaves in test 2. The initial scan shows the likelihood of the first QTL being located at each SNP in the genome (linkage group=chromosome) with subsequent scans showing the LOD of an additional QTL with the effects of the previous QTL(s) controlled for in the model. The dashed line marks the genome-wide significance threshold.

Supplementary figure S3 Interaction plot showing evidence for epistasis between qSulf-1 and qSulf-8. Alleles from the sulfur sensitive parent (MR-1) are 'AA' and from the sulfur tolerant parent (AY) are 'BB'. The circle represents the mean percent damage of individuals in the population with the labelled genotypes. The plus signs indicate the standard error.

sulfQ1_annovar.csv Functional annotation of all gene polymorphisms between the parents in the QTL interval of qSulf-1, including the chromosome, physical position (in bp), parental alleles, polymorphism location relative to the gene (ie. upstream, exonic, downstream, etc.), distance from the gene (in bp), type of exonic mutation (synonymous or nonsynonymous), and detail (which exon and the nucleotide and amino acid changes).

Funding provided by: U.S. Department of Agriculture
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000199
Award Number: 6080-22000-028-00

Funding provided by: U.S. Department of Agriculture
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000199
Award Number: 6080-21000-019-08