M. Oliver

Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon

Abstract Three different types of molecular markers, RAPD, AFLP and RFLP were used to measure genetic diversity among six genotypes of Cucumis melo L. Each line represented a different melon genotype: Piel de Sapo, Ogen, PI161375, PI414723, Agrestis and C105. A number of polymorphic RAPD, AFLP and RFLP bands were scored on all materials and the genetic similarity measured. Clustering analysis performed with the three types of markers separated the genotypes into two main groups: (1) the sweet type, cultivated melons and (2) the exotic type, not cultivated melons. While the data obtained suggest that all three types of markers are equally informative, AFLPs showed the highest efficiency in detecting polymorphism.

Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.).

A set of 118 simple sequence repeat (SSR) markers has been developed in melon from two different sources: genomic libraries (gSSR) and expressed sequence-tag (EST) databases (EST-SSR). Forty-nine percent of the markers showed polymorphism between the ‘Piel de Sapo’ (PS) and PI161375 melon genotypes used as parents for the mapping populations. Similar polymorphism levels were found in gSSR (51.2%) and EST-SSR (45.5%). Two populations, F2 and a set of double haploid lines (DHLs), developed from the same parent genotypes were used for map construction. Twenty-three SSRs and 79 restriction fragment length polymorphisms (RFLPs), evenly distributed through the melon genome, were used to anchor the maps of both populations. Ten cucumber SSRs, 41 gSSRs, 16 EST-SSR, three single nucleotide polymorphism (SNP) markers, and the Nsv locus were added in the DHL population. The maps developed in the F2 and DHL populations were co-linear, with similar lengths, except in linkage groups G1, G9, and G10. There was segregation distortion in a higher proportion of markers in the DHL population compared with the F2, probably caused by selection during the construction of DHLs through in vitro culture. After map merging, a composite genetic map was obtained including 327 transferable markers: 226 RFLPs, 97 SSRs, three SNPs, and the Nsv locus. The map length is 1,021 cM, distributed in 12 linkage groups, and map density is 3.11 cM/marker. SSR markers alone cover nearly 80% of the map length. This map is proposed as a basis for a framework melon map to be merged with other maps and as an anchor point for map comparison between species of the Cucurbitaceae family.

Identification of quantitative trait loci involved in fruit quality traits in melon (Cucumis melo L.)

Two populations [an F2 and a set of 77 double haploid lines (DHLs)] developed from a cross between a ‘Piel de Sapo’ cultivar (PS) and the exotic Korean accession PI 161375 were used to detect QTLs involved in melon fruit quality traits: earliness (EA), fruit shape (FS), fruit weight (FW) and sugar content (SSC); and loci involved in the colour traits: external colour (ECOL) and flesh colour (FC). High variation was found, showing transgressive segregations for all traits. The highest correlation among experiments was observed for FS and the lowest for FW and SSC. Correlations among traits within experiments were, in general, not significant. QTL analysis, performed by Composite Interval Mapping, allowed the detection of nine QTLs for EA, eight for FS, six for FW and five for SSC. Major QTLs (R2>25%) were detected for all traits. QTLs for different traits were no clearly co-localised, suggesting low pleiotropic effects at QTLs. Sixty-one per cent of them were detected in two or more experiments. QTLs for FS were detected in more trials than QTLs for FW and SSC, confirming that FS is under highly hereditable polygenic control. ECOL segregated as yellow:green in both experimental populations. The genetic control of ECOL was found to be complex, probably involving more than two loci with epistatic interactions. One of these loci was mapped on linkage group 9, but the other loci could not be clearly resolved. FC segregated as white:green:orange. The locus responsible for the green FC was mapped on linkage group 1, and it was proposed to correspond to the previously described locus gf. The genetic control of orange FC was complex: two loci in linkage groups 2 and 12 were associated with orange flesh, but larger population sizes would be necessary to elucidate completely the genetic control of orange flesh in this cross. Exotic alleles from PI161375 showed beneficial effects on EA, FW and SSC, indicating the usefulness of PI 161375 as a new source of genetic variability to improve European and American cultivars.

A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.).

BackgroundA number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS).ResultsUnder the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm.ConclusionsEven though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection).