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SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

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Abstract

Novel sequencing technologies were recently used to generate sequences from multiple melon (Cucumis melo L.) genotypes, enabling the in silico identification of large single nucleotide polymorphism (SNP) collections. In order to optimize the use of these markers, SNP validation and large-scale genotyping are necessary. In this paper, we present the first validated design for a genotyping array with 768 SNPs that are evenly distributed throughout the melon genome. This customized Illumina GoldenGate assay was used to genotype a collection of 74 accessions, representing most of the botanical groups of the species. Of the assayed loci, 91 % were successfully genotyped. The array provided a large number of polymorphic SNPs within and across accessions. This set of SNPs detected high levels of variation in accessions from this crop’s center of origin as well as from several other areas of melon diversification. Allele distribution throughout the genome revealed regions that distinguished between the two main groups of cultivated accessions (inodorus and cantalupensis). Population structure analysis showed a subdivision into five subpopulations, reflecting the history of the crop. A considerably low level of LD was detected, which decayed rapidly within a few kilobases. Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in melon. Since many of the genotyped accessions are currently being used as the parents of breeding populations in various programs, this set of mapped markers could be used for future mapping and breeding efforts.

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Acknowledgments

This project was carried out in the frame of the MELONOMICS project (2009–2012) of the Fundación Genoma España and with the contributions of the PLAT KKBE project PIM2010PKB-00691.

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Corresponding authors

Correspondence to Antonio J. Monforte or Belén Picó.

Additional information

Communicated by H. Nybom.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2013_2053_MOESM1_ESM.xls

Online Resource Table 1 Melon accessions analyzed in this study. Code used in the current study, common name, accession number from the respective genebanks, origin, seed bank/project donor (COMAV, Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Valencia, Spain; NPGS, USDA/ARS/NCRPIS, USA; MELRIP, ERA-PG project GEN2006-27773-C2-2-E; LA MAYORA, Experimental Station “La Mayora” (IHSM-UMA-CSIC), Málaga, Spain; IMIDRA, Madrilean Research Institute for Rural Development, Agriculture and Food, Madrid, Spain) and cultivar group are specified for each accession. The accessions included in each assay are indicated

122_2013_2053_MOESM2_ESM.xls

Online Resource Table 2 SNPs included in the GoldenGate platform. The SNP and the flanking sequence, the map and genome position, the annotation details of the corresponding unigenes, the custom oligos for the Illumina assay, as well as the Illumina score are listed for each marker. The number of reads of each allele in the sequenced genotypes (for the SNPs selected in silico by Blanca et al. (2011)) are indicated. The SNPs that failed in the GoldenGate assay due to different clustering or amplification problems are indicated in red. Those SNPs that were monomorphic in all varieties are in blue. Those that were monomorphic, heterozygous, or failed in one or both mapping parents and were not mapped are in orange. Markers in LG VII that were fixed in inodorus cultivars and were highly variable in cantalupensis and momordica are in yellow. In purple, loci with high Fst values (>0.75) between inodorus and cantalupesis. In green, SNPs found to be polymorphic in the ‘Piel de Sapo’ commercial group, but monomorphic in the group of ‘Piel de Sapo’ Spanish landraces and/or in the entire inodorus landraces group

122_2013_2053_MOESM3_ESM.xlsx

Online Resource Table 3 SNP genotyping results. Genotype of the 74 accessions analyzed with the GoldenGate array is included for the 698 working markers. Major allele frequency, gene diversity and PIC for each marker in the whole collection, and also in the different groups of varieties, are indicated. Also, Wright’s F-statistics (Fit, Fis and Fst) values for a set of SNPs, polymorphic in the inodorus and cantalupesis group, are included. Those SNPs that were monomorphic in all varieties are in blue. Those that were monomorphic, heterozygous, or failed in one or both mapping parents and were not mapped are in orange. Markers in LG VII that were fixed in inodorus cultivars and were highly variable in cantalupensis and momordica are in yellow. In purple, loci with high Fst values (>0.75) between inodorus and cantalupesis. In green, SNPs found to be polymorphic in the ‘Piel de Sapo’ commercial group, but monomorphic in the group of ‘Piel de Sapo’ Spanish landraces and/or in the entire inodorus landraces group

122_2013_2053_MOESM4_ESM.docx

Online Resource Table 4 Candidate loci under selection. Loci that show high Fst values between the two predefined groups of cultivated melons, inodorus and cantalupensis, are included. The values of the Fst, Fit and Fis, the position in the genetic map, the annotation of the corresponding genes in the melon genome sequence, and the allelic variation in each group are indicated

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Online Resource Fig. 1 Photographs of the melon accessions analyzed in this study. a Commercial Inodorus cultivars; b Spanish Inodorus landraces c Inodorus, ameri and other landraces from Eastern Europe, North of Africa and Asia d Cantalupensis and reticulatus accessions e Flexuosus, chate, dudaim, momordica and conomon accessions f Acidulus, tibish, chito and small-agrestis accessions

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Online Resource Fig. 2 Graphic genotype of each of the accessions analyzed with the GoldenGate platform. The variability of the SNPs along each LG is graphically represented for each genotype. Regions homozygous for the SC/T111 allele are in red/dark blue, and heterozygous in light blue

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Online Resource Fig. 3 First (a) and second (b) preliminary linkage disequilibrium analysis Linkage disequilibrium (r 2) among sequences included in Scaffold00003, Scaffold00011 and Scaffold00016 is plotted versus SNP physical distance in Kb for 20 selected C. melo subsp melo accessions. The black line indicates the fitted curve by second-degree LOESS. The 0.05 false discovery rate is indicated by a horizontal dashed line

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Esteras, C., Formisano, G., Roig, C. et al. SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium. Theor Appl Genet 126, 1285–1303 (2013). https://doi.org/10.1007/s00122-013-2053-5

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  • DOI: https://doi.org/10.1007/s00122-013-2053-5

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