Abstract
Melon (Cucumis melo L.) genetic maps were compiled by the International Cucurbit Genomics Initiative (ICuGI) before the release of the melon genome. However, due to the use of different marker sets, the position of ICuGI markers in the genome remained unknown, complicating the integration of previous genetic mapping studies in the genome. We looked for the genome position of 870 simple sequence repeat and single nucleotide polymorphism (SNP) markers from the ICuGI map, locating 836 of them in the melon pseudochromosomes v3.5.1, and integrating them with previously available SNPs to reach a total of 1850 markers mapped in the genome sequence. The number of markers per scaffold ranged from 1 to 105, with an average of 13, thus improving on the previous studies in melon. Twenty-three of the markers mapped on virtual chromosome “0”, twelve of them being included in the ICuGI map, which could assist in the anchoring of some unanchored contigs and scaffolds. Genetic and physical distance comparison showed a good collinearity between them, confirming the quality of the ICuGI map. A higher recombination rate was also usually found at the ends of the chromosomes, whereas a drastic reduction was observed in the putative pericentromeric regions. Quantitative trait loci (QTL) previously located in the ICuGI map were also anchored in the genome. This work offers the opportunity to supplement the genetic maps available up to now with the genomic resources resulting from the melon genome sequencing to facilitate comparative mapping in melon between past and new studies, and to overcome some of the current limitations in QTL gene identification.
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Acknowledgments
This work was funded in part by the project AGL2012-40130-C02-02 from Spanish Ministry of Economy and Competitiveness (MINECO) to AJM.
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11032_2015_381_MOESM1_ESM.xlsx
Online Resource 1. ESM_1. DNA sequences of the original clones and primers used for anchoring. Each spreadsheet includes markers from a specific paper. (XLSX 231 kb)
11032_2015_381_MOESM2_ESM.xlsx
Online Resource 2. ESM_2. Physical positions of the markers included in the integrated map (name and coordinate in the scaffold and pseudomolecule). The positions in the original genetic maps are also indicated as well as a commentary on the markers that showed discrepancies between genetic and genome positions. (XLSX 166 kb)
11032_2015_381_MOESM3_ESM.pdf
Online Resource 3. ESM_3. Relationship between genetic (cM) and physical (Mb) distance for 1850 markers in the 12 melon pseudomolecules (PM). The vertical segments of the curves correspond to putative pericentromeric regions as they represent portions of the chromosomes with few recombination events. (PDF 171 kb)
11032_2015_381_MOESM4_ESM.xls
Online Resource 4. ESM_4. Anchoring of QTL located in the ICuGI map on the melon genome. QTL names are according to Diaz et al. (2011), followed by the chromosome where they were mapped, the flanking markers in the ICuGI map and their position on the genome (estimated in the case of markers different from SSRs or SNPs). The references of the original QTL mapping studies are listed in the “experiment” spreadsheet. (XLS 78 kb)
11032_2015_381_MOESM5_ESM.pdf
Online Resource 5. ESM_5. Anchoring of markers and QTL on the melon genome. QTLs are located in the center of the confidence interval of their respective position. Marker color codes are according to Fig. 1: SSRs (blue), indels (black) and SNPs (green). (PDF 561 kb)
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Diaz, A., Forment, J., Argyris, J.M. et al. Anchoring the consensus ICuGI genetic map to the melon (Cucumis melo L.) genome. Mol Breeding 35, 188 (2015). https://doi.org/10.1007/s11032-015-0381-7
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DOI: https://doi.org/10.1007/s11032-015-0381-7