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BackgroundWatermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important crop with an attractive ripe fruit that has colorful flesh. Fruit ripening is a complex, genetically programmed process.ResultsIn this study, a comparative transcriptome analysis was performed to identify the regulators and pathways that are involved in the fruit ripening of pale-yellow-flesh cultivated watermelon (COS) and red-flesh cultivated watermelon (LSW177). We first identified 797 novel genes to extend the available reference gene set. Second, 3958 genes in COS and 3503 genes in LSW177 showed at least two-fold variation in expression, and a large number of these differentially expressed genes (DEGs) during fruit ripening were related to carotenoid biosynthesis, plant hormone pathways, and sugar and cell wall metabolism. Third, we noted a correlation between ripening-associated transcripts and metabolites and the key function of these metabolic pathways during fruit ripening.ConclusionThe results revealed several ripening-associated actions and provide novel insights into the molecular mechanisms underlying the regulation of watermelon fruit ripening.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3442-3) contains supplementary material, which is available to authorized users.

Lycopene content is an important factor for determining watermelon fruit quality. However, the low DNA polymorphism among cultivated watermelon (Citrullus lanatus) has hindered the ability to establish high quality genetic maps and study the quantitative trait loci (QTL) controlling the lycopene content trait. In this study, we successfully constructed a genetic map of watermelon to determine lycopene content and other horticultural fruit traits using a F 2 population developed from a cross between the two lines of watermelon LSW-177 and Cream of Saskatchewan. The genetic map contained 16 linkage groups covering a total length of 2,039.5 cM, which included 37 SSRs (Simple Sequence Repeat) and 107 CAPSs (Cleaved Amplified Polymorphic Sequences), with all of the CAPS markers developed from high-throughput re-sequencing of data from this study. Three CAPS markers (WII04E07-33,WII04E07-37,WII04E07-40) caused the F 2 population to perfectly co-segregate for each F 2 population plants. We also obtained 12 QTLs for all of the traits measured. Only one QTL (LCYB4.1) was detected with a high value of trait variation (83.50 %) that related to lycopene content and mapped on Chromosome 4 between CAPS markers WII04E07-33 and WII04E07-40, which could nearly account for all of the differences in lycopene content between the two parental strains. In this study, we highlighted 2,458 CAPS loci that were suitable for primer design with a polymorphism of 48.9 %, which is approximately a 12-fold increase from previous studies. The present map and QTLs will facilitate future studies on determining lycopene content related genes and cloning watermelon genes, while also providing for useful markers for breeding for lycopene content.

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Domestication and improvement are two important stages in crop evolution. Melon (Cucumis melo L.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long-term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high-quality SNPs. Population structure and genetic diversity analyses revealed independent and two-step selections in two subspecies of melon: ssp. melo and ssp. agrestis during melon breeding. We detected 233 (~18.35 Mbp) and 159 (~17.71 Mbp) novel potential selective signals during the improvement stage in ssp. agrestis and spp. melo, respectively. Two alcohol acyltransferase genes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp. agrestis for the characteristic aroma as compared with other cucurbits. Genomewide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thinskinned ssp. agrestis, thickskinned ssp. melo has undergone a stronger selection for thicker flesh. In most melon accessions, CmCLV3 has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding. classified into two subspecies (C. melo ssp. melo and ssp. agrestis) based on the presence of ovary hairs (Jeffrey, 1980; Kirkbride, 1993). The ssp. agrestis is distributed mainly in Africa, Asia and Australia with momordica, acidulus, conomom, makuwa and chinensis groups, in Africa with the tibish group and in Central America with the chito group. The ssp. melo including the cantalupensis, inodorus, chandalak, ameri, flexuosus, chate or dudaim groups is distributed mainly in India, central and western

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Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.

Lycopene content and flesh color are important traits determined by a network of carotenoid metabolic pathways in watermelon. Based on our previous study of genetic inheritance and initial mapping using F2 populations of LSW-177 (red flesh) × cream of Saskatchewan (pale yellow flesh), red flesh color was controlled by one recessive gene regulating red and pale yellow pigmentation, and a candidate region related to lycopene content was detected spanning a 392,077-bp region on chromosome 4. To obtain a more precise result for further study, three genetic populations and a natural panel of 81 watermelon accessions with different flesh colors were used in this research. Herein, we narrowed the preliminary mapping region to 41,233 bp with the linkage map generated from F2 populations of LSW-177 (red flesh) × cream of Saskatchewan (pale yellow flesh) with 1,202 individuals. Two candidate genes, Cla005011 and Cla005012, were found in the fine mapping region; therein Cla005011 was a key locus annotated as a lycopene β-cyclase gene. Phylogenetic tree analysis showed that Cla005011 was the closest relative gene in gourd. LSW-177 × PI 186490 (white flesh) and another BC1 population derived from garden female (red flesh) × PI 186490 were generated to verify the accuracy of the red flesh candidate gene region. By analyzing the expression levels of candidate genes in different developmental stages of different color watermelon varieties, Cla005011 for the expression differences was not the main reason for the flesh color variation between COS and LSW-177. This indicated that the LCYB gene might regulate fruit color changes at the protein level. A new marker-assisted selection system to identify red and yellow flesh colors in watermelon was developed with flesh color–specific CAPS markers and tested in 81 watermelon accessions.