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Current nomenclature for the taxonomic classification of melon cultivars (Cucumis melo L.) at the horticultural group level relies on morphological variation in certain key characters. However, the reliability of current infraspecific classification scheme in considering horticultural groups as botanical taxa was not fully understood. In the present study, the information of horticultural group classification in melon was assessed at the molecular level using genome-wide single nucleotide polymorphisms (SNPs). A total of 143 melon accessions of 15 horticultural groups in two subspecies, subsp. melo and subsp. agresti were collected and genotyped by using Genotyping-By-Sequencing (GBS). From the filtering of resultant sequence variants, 10,949 SNPs were selected and used for downstream genetic analysis including population structure, principle component analysis, and hierarchical clustering of 143 melon accessions. Our genetic analyses indicated that the distribution of accessions at the molecular level generally matched the subspecies classification and no substantial contradictions existed between the division of accessions based on horticultural group information and genetic relatedness revealed by the GBS. However, the distinction between horticultural groups was not clear-cut, implying the limitation of considering horticultural groups as botanical taxa. To improve the resolution of horticultural group classification in melon, our SNP data may be useful as supporting information in conjunction with morphological characters.

Genetic diversity analysis and cultivar identification were performed using a core set of single nucleotide polymorphisms (SNPs) in cucumber (Cucumis sativus L.). For the genetic diversity study, 280 cucumber accessions collected from four continents (Asia, Europe, America, and Africa) by the National Agrobiodiversity Center of the Rural Development Administration in South Korea and 20 Korean commercial F1 hybrids were genotyped using 151 Fluidigm SNP assay sets. The heterozygosity of the SNP loci per accession ranged from 4.76 to 82.76%, with an average of 32.1%. Population genetics analysis was performed using population structure analysis and hierarchical clustering (HC), which indicated that these accessions were classified mainly into four subpopulations or clusters according to their geographical origins. The subpopulations for Asian and European accessions were clearly distinguished from each other (FST value = 0.47), while the subpopulations for Korean F1 hybrids and Asian accessions were closely related (FST = 0.34). The highest differentiation was observed between American and European accessions (FST = 0.41). Nei’s genetic distance among the 280 accessions was 0.414 on average. In addition, 95 commercial F1 hybrids of three cultivar groups (Baekdadagi-, Gasi-, and Nakhap-types) were genotyped using 82 Fluidigm SNP assay sets for cultivar identification. These 82 SNPs differentiated all cultivars, except seven. The heterozygosity of the SNP loci per cultivar ranged from 12.20 to 69.14%, with an average of 34.2%. Principal component analysis and HC demonstrated that most cultivars were clustered based on their cultivar groups. The Baekdadagi- and Gasi-types were clearly distinguished, while the Nakhap-type was closely related to the Baekdadagi-type. Our results obtained using core Fluidigm SNP assay sets provide useful information for germplasm assessment and cultivar identification, which are essential for breeding and intellectual right protection in cucumber.

Most melon (Cucumis melo L.) breeding lines in South Korea display andromonoecious sex expression, which necessitates laborious hand emasculation during F1 hybrid seed production. Thus, there is a need to develop monoecious sex types in elite germplasm to obviate self-pollination. Sex expression is associated with floral ethylene production, which, in monecious melon plants, is associated with the A locus. Our study was conducted to develop molecular markers for selection of monoecious plants based on sequence variation inherent in the CmACS-7 gene [encoding 1-aminocyclopropane-1-carboxylic acid synthase (ACS)] that is associated with ethylene production. Full-length CmACS-7 sequences were cloned from a monoecious (MO23) and an andromonoecious (AM24) line. The alignment of those CmACS-7 sequences revealed a single nucleotide polymorphism (SNP; C170T) in exon 1 and an 18 bp indel in the 3′-untranslated region (UTR) of between MO23 and AM24, which was then used to develop a cleaved amplified polymorphic sequence (CAPS) (EX1-C170T) and a sequence characterized amplified region (SCAR) marker (T1ex), respectively. The sex expression and the T1ex SCAR-based genotype of 442 F2 plants derived from a MO23 × AM24 cross was determined. Monoecy and andromonoecy segregated in a 3:1 ratio in F2 progeny, where the sex type of 429 plants (13 plants not classified) co-segregated with the SCAR marker, demonstrating that sex expression regulated by CmACS-7 is controlled by a single dominant gene and that it confers monoecy in line MO23. Allelic variation in 112 geographically diverse melon lines for CmACS-7 as accessed by CAPS EX1-C170T and SCAR T1ex markers indicated that the: 1) exon 1 of CmACS-7 is highly conserved and the SNP/sex expression association detected is highly predictable making it potentially useful for marker-based selection of monoecious plants, and; 2) 18 bp indel mutation in the 3′-UTR was present in various lengths depending on different monoecious melon germplasm.

The responses to chilling temperature of 12 Korean cucumber varieties was compared to those of two U.S.A. (previously determined cold tolerant NC76 and ‘Chipper’), and Chinese and Japanese germplasms. Seedlings of each entry were exposed to 4°C (Experiment 1) and 1°C (Experiments 2 and 3) at the first-true leaf stage for eight and nine hours, respectively, under 80% relative humidity (RH) and 149 μmoles?m -2 ?s -1 photosynthetic photon flux (PPF). The chilling response [damage rating (DR)] of each accession was based on visual ratings (1 to 5) after treatment, where 1 = no damage, 2 = slight, 3 = moderate, 4 = advanced, and 5 = severe damage. Predictably the cumulative average DR of chilling tolerant line NC76 and ‘Chipper’ after chilling w as 1 a nd 1 .1, respectively . Korean ‘Nacdongchungjang’ w as m ost sensitive to c hilling temperatures [DR = 2 .3] when compared to the other entries examined. The sensitivity to chilling of ‘Nacdongchungjang’ was followed by Chinese ‘Dongguan’ [DR = 1.7]. In contrast, ‘Saeronchungjang’ (DR = 1) and ‘Janghyungnachap’ (DR = 1) were the most chilling tolerant of the Korean accessions examined and equivalent to the response of line NC76 and ‘Chipper’. Nevertheless, chloroplast type genotyping of these accessions with known chilling-linked sdCAPS genomic markers revealed genotypic differences between chilling tolerant lines (NC76 and ‘Chipper’) and all Korean lines examined.

Compact and dwarfing vining habits in melon (Cucumis melo L.; 2n = 2x = 24) may have commercial importance since they can contribute to the promotion of concentrated fruit set and can be planted in higher plant densities than standard vining types. A study was designed to determine the genetics of dwarfism associated with a diminutive (short internodes) melon mutant line PNU-D1 (C. melo ssp. cantalupensis). PNU-D1 was crossed with inbred wild-type melon line PNU-WT1 (C. melo ssp. agrestis), and resultant F1 progeny were then self-pollinated to produce an F2 population that segregated as dwarf and vining plant types. Primary stem length of F2 progeny assessed under greenhouse conditions indicated that a single recessive gene, designated mdw1, controlled dwarfism in this population. To identify the chromosomal location associated with mdw1, an simple sequence repeat (SSR)-based genetic linkage map was constructed using 94 F2 progeny. Using 76 SSR markers positioned on 15 linkage groups spanning 462.84 cM, the location of mdw1 was localized to Chromosome 7. Using the putative dwarfing-associated genes, fine genetic mapping of the mdw1 genomic region was facilitated with 1,194 F2 progeny that defined the genetic distance between mdw1 and cytokinin oxidase gene, a candidate gene for compact growth habit (cp) in cucumber, to be 1.7 cM. The candidate gene ERECTA (serin/threonine kinase) and UBI (ubiquitin) were also mapped to genomic regions flanking mdw1 at distances of 0.6 and 1.2 cM, respectively.

Chilling temperatures (

DNA markers can determine the genotype of many species. Single nucleotide polymorphism (SNP) detection is difficult without sequencing but it becomes easier with sdCAPS method. Here an experiment was performed for developing molecular markers using two SNPs, CSatpB-SNP and CSycf1-SNP, of chloroplast in cucumber plants. Properly designed primers with nucleotide sequences for restriction enzymes proved success of PCR and efficacy of digestion by the restriction enzymes. Then these markers were used to study the genotyping of cucumber breeding lines and cultivars obtained from various sources in respect of their chilling stress response. We confirmed that a U.S. cucumber line, 'NC76' known to possess a nuclear factor for the chilling tolerance showed the chloroplast genotypes related to chilling tolerance. However all Korean cucumber cultivars tested in this study showed the chloroplast genotypes related to chilling susceptibility. In conclusion, to develop chilling tolerant cucumber, both maternal and a nuclear factors related to chilling tolerance should be transferred from 'NC76' when 'NC76' is used as a female source and other elite lines as recurrent parents.

Cucumber (Cucumis sativus L. var. sativus; 2n = 2x = 14), has a narrow genetic base (3% to 8% polymorphism). Nevertheless, several genetic maps exist for this species. It is important to know the degree of colinearity among these maps. Thus, the positions of random amplified polymorphic DNAs, sequenced characterized amplified regions, simple sequence repeat, restriction fragment length polymorphisms, and fluorescent amplified fragment length polymorphism markers were compared in four maps. A previously unreported map was constructed in a narrow cross (processing line 2A × Gy8; C. s. var. sativus; ≈7% polymorphism) and compared with the three published maps [two narrow-based (processing type; C. s. var. sativus; 8% to 12% polymorphism) and a broad-based (C. s. var. sativus × C. s. var. hardwickii (R.) Alef. ≈12%)]. Common makers were identified in seven linkage groups, providing evidence for microsynteny. These common markers were used as anchor markers for map position comparisons of yield component quantitative trait loci. The relative order of anchor markers in each of six linkage groups (linkage groups 1, 2, and 4–7) that had two or more anchor markers within each group was colinear, and instances of microsynteny were detected. Commonalities in the position of some yield component quantitative trait loci exist in linkage groups 1 and 4 of the maps examined, and the general synteny among these maps indicates that identification and mapping of additional anchor markers would lead to successful map merging to increase cucumber map saturation for use in cucumber breeding.

Parthenocarpy (seedless fruit) is an economically important yield-related trait in cucumber (Cucumis sativus L.; 2n = 2x = 14). However, the genomic locations of factors controlling parthenocarpic fruit development in this species are not known. Therefore, an F 2: 3 mating design was utilized to map quantitative trait loci (QTL) for parthenocarpy using a narrow cross employing two gynoecious, indeterminate and normal leaf lines [2A (parthenocarpic) and Gy8 (non-parthenocarpic)]. QTL detection was performed employing 2A- and Gy8-coupling phase data using the parthenocarpic yield of 126 F 3 families grown at two locations at Hancock, WI in 2000. The QTLs detected in this study were compared with the map locations of QTLs conditioning first-harvest yield of seeded cucumber characterized in a previous study. There were 10 QTLs for parthenocarpy detected defining four genomic regions, in which three QTLs also mapped to the same genomic regions as QTLs detected for fruit yield at first-harvest as reported in a previous study. The eight fluorescence amplified fragment length polymorphism (AFLP) markers linked to parthenocarpy through QTL mapping defined herein (four each in linkage groups I and 4) are candidates for use in marker-assisted selection programmes where breeding for increased levels of parthenocarpy is an objective in the elite-processing cucumber populations.

The origins of wild melon (Cucumis melo) populations in the New World have been in question since their initial description in the mid-nineteenth century by Charles Naudin. Typically, these populations have been assumed to represent escaped forms of cultivated vars. chito or dudaim, and have been labelled accordingly, or more rarely as var. agrestis. To clarify the origins of New World melons, North American, chito, and dudaim accessions were studied with respect to 45 quantitative and 10 qualitative morphological and physiological characters. Also collected were RAPD and SSR data for 42 North American populations, 10 cultivar accessions of vars. chito and dudaim, 10 other small-fruited Old World accessions, and 4 other varieties of C. melo – vars. conomon, flexuosus, inodorus, and cantalupensis. All data revealed that New World populations are distinct, and should be classified as ssp. agrestis var. texanus Naudin. This variety showed the greatest genetic affinities to var. chito and to cultivars from Eastern Asia, including var. conomon.

Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.

The inheritance of yield-related traits in melon (Cucumis melo L.; 2n = 2x = 24) is poorly understood, and the mapping of quantitative trait loci (QTL) for such traits has not been reported. Therefore, a set of 81 recombinant inbred lines (RIL) was developed from a cross between the monoecious, highly branched line USDA 846-1 and a standard vining, andromonoecious cultivar, 'Top Mark'. The RIL, parental lines, and three control cultivars ('Esteem', 'Sol Dorado', and 'Hales Best Jumbo') were grown at Hancock, WI and El Centro, CA in 2002, and evaluated for primary branch number (PB), fruit number per plant (FN), fruit weight per plant (FW), average weight per fruit (AWF), and percentage of mature fruit per plot (PMF). A 190-point genetic map was constructed using 114 RAPD, 43 SSR, 32 AFLP markers, and one phenotypic trait. Fifteen linkage groups spanned 1,116 cM with a mean marker interval of 5.9 cM. A total of 37 QTL were detected in both locations (PB = 6, FN = 9, FW = 12, AWF = 5, and PMF = 5). QTL analyses revealed four location-independent factors for PB (pb1.1, pb1.2, pb2.3, and pb10.5), five for FN (fn1.1, fn1.2, fn1.3, fn2.4, and fn8.8), four for FW (fw5.8, fw6.10, fw8.11, and fw8.12), two for AWF (awf1.3 and awf8.5), and one for PMF (pmf10.4). The significant (P/= 0.05) positive phenotypic correlations observed among PB, FN, and FW, and negative phenotypic correlations between PB and AWF and between FN and AWF were consistent with the genomic locations and effects (negative vs. positive) of the QTL detected. Results indicate that genes resident in highly branched melon types have potential for increasing yield in US Western Shipping type germplasm via marker-assisted selection.

Genetic variation among 378 melon (Cucumis melo L.) germplasm accessions collected in India in 1992 and 26 accessions in China in 1994 was evaluated with 19 isozyme loci. ʻTop Markʼ and ʻGreen Flesh Honeydewʼ, which represented two distinct C. melo ssp. melo L. groups, Cantalupensis and Inodorus, respectively, were used as reference cultivars. Genetic distances among accessions were calculated, and an initial cluster analysis using these distances re- sulted in 148 groups of varying size, ranging from two to 47 accessions. One accession from each of the 148 groups was chosen at random and used in a second cluster analysis that identifi ed 11 accession groups. Group 1 was unique and consisted of only two C. melo ssp. agrestis (Naudin) Pangalo accessions. Two large branches were detected at cluster node 2. One branch was comprised of three groups of 3, 12, and 34 accessions, while the other branch contained seven groups of 2, 3, 14, 16, and 47 accessions, and the reference cultivars. Of the 148 accessions, 132 were from 41 sites in Rajasthan and Madhya Pradesh, India, which were distributed unequally across the 11 groups. The 14 Chinese ac- cessions originating from seven provinces were also dispersed unequally in the four major cluster groups. ʻTop Markʼ and ʻGreen Flesh Honeydewʼ were genetically distinct and uniquely clustered in the same group. These results indicate that additional collections of melon germplasm should be made in eastern and southern India. Cucumis melo is a morphologically diverse crop species consisting of two subspecies that are differentiated on the basis of ovary pubescence (Kirkbride Jr., 1993), C. melo ssp. agrestis and C. melo ssp. melo. Six subspecifi c groups of cultivated and wild types have long been recognized in the western literature (Robinson and Decker-Walters, 1997). A more recent treatment of melon taxonomy by Pitrat et al. (2000) using literature and analysis of melon germplasm available to western taxonomists and newly available germplasm from the former Soviet Union resulted in the provisional, albeit testable, classifi cation of melon into 16 groups, fi ve in subspecies agrestis and 11 in subspecies melo. Upon more rigorous analysis, these groups might be more accurately defi ned as "cultivar-groups" according to Spooner et al. (2003). Melon is a tropical, old world species that probably originated in Africa (Kerje and Grum, 2000). Afghanistan, China, India, Iran, Saudi Arabia, southern Russia, and Turkey were important second- ary gene centers that gave rise to cultivated melons (Jeffrey, 1980; Pangalo, 1930; Whitaker and Bemis, 1976; Whitaker and Davis, 1962). The primary center for diversity in melon is southwestern and central Asia, mainly Turkey, Syria, Iran, Afghanistan, north and central India and Transcaucasia, Turkmenistan, Tadjikistan, and Uzbekistan (Esquinas-Alcazar and Gulick, 1983). Second- ary centers of diversity for cultivated melons are found in China, Korea, Portugal, and Spain (Esquinas-Alcazar and Gulick, 1983). Today, melons are grown in many countries worldwide for local, national, and export markets (Robinson and Decker-Walters