A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis meloL.)

Abstract

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).

Association of RGA-SSCP markers with resistance to downy mildew and anthracnose in grapevines

“…Several molecular marker systems such as random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), inter-simple sequence repeat (ISSR), and single-strand conformation polymorphism (SSCP) have been used in the analysis of marker-trait association (Roy et al, 2006;Wang et al, 2010;Bandyopadhyay, 2011;Diaz et al, 2011;Immanuel et al, 2011;Kalivas et al, 2011;Milad et al, 2011;Nisar and Ghafoor, 2011;Yu et al, 2011). The association of these molecular markers with different traits related to disease and insect resistance has been established in several plants (Lefebvre and Chèvre, 1995;Obert et al, 2000;Shalini et al, 2007).…”

Seeds morpho-colourimetric analysis as complementary method to molecular characterization of melon diversity

“…Moreover, the evidence of a non random 574 allelic distribution in large/small seed groups of accessions of SNPs located in 575 some genomic regions in which QTLs involved in fruit weight had been 576 previously located (Diaz et al, 2011) suggests that some of these regions 577 might also account for part of the observed variation in seed size. This non 578 random distribution of alleles could be also due to an effect of the structure of 579 the population, then associations of alleles to seed traits must be proved in 580 larger unstructured populations or in populations specifically designed, such 581 as introgression lines with which we are currently working.…”

“…This genetic position was used to check the allelic distribution in 204 the germplasm collection of SNPs located in regions of the genetic map in 205 which QTLs for fruit size were previously located (Diaz et al, 2011), and to 206 confirm if differential allelic distributions were also related with differences in 207 the seed traits measured in the present study. 208…”

Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.)

“…Markers were grouped at a minimum logarithm of odds (LOD) score of 4.0, and a recombination frequency value of 0.4. Linkage group (LG) designation was according to the recently merged melon map (Diaz et al 2011), which includes the 414xDul map. QTL analyses were performed by the MapQTL ® 5 software (Van Ooijen 2004), including: interval mapping (IM), multiple QTL model (MQM) and permutation analysis.…”