Editorial: Translational research for cucurbit molecular breeding: Traits, markers, and genes

Cucurbits (family Cucurbitaceae) are economically important vegetable crops. Major cucurbits growing globally include cucumber, melon, watermelon, and squash/pumpkin. Other cucurbits like bitter melon, bottle gourd, winter melon, and luffa are popular in many Asian and African countries. The last decade has witnessed a rapid development of genetic and genomics resources including draft genome assemblies, and high-density genetic maps in a dozen cucurbit crops, making it possible to accelerate translational research for cucurbit breeding. This Research Topic is a collection of 21 Original Research articles or Reviews highlighting the achievements and future directions in cucurbit translational research. These articles cover a variety of topics ranging from improvement of the cucurbit genome assemblies to identification and molecular mapping of horticulturally important genes or QTL for horticultural traits, and the use of such knowledge in marker-assisted selection for cucurbit improvement. Major findings from these investigations are summarized below.info:eu-repo/semantics/publishedVersio

Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis

In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1–AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., 2009, Nat. Genet. 41, 1275–1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the mechanisms of dysploid chromosome reduction that has not been achieved previously.This research was supported by US Department of Agriculture Current Research Information System Project 3655-21000-048-00D and a US Department of Agriculture Specialty Crop Research Initiative grant (project number 2011-51181-30661) to Y.W.Peer reviewe

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. (2n = 2 × = 14) and melon, <it>C. melo </it>L. (2n = 2 × = 24) are two important vegetable species in the genus <it>Cucumis </it>(family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes.</p> <p>Results</p> <p>Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F₂- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.</p> <p>Conclusions</p> <p>Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of <it>Cucumis </it>species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.</p

Isolation and Activity Analysis of Phytoene Synthase (<i>ClPsy1</i>) Gene Promoter of Canary-Yellow and Golden Flesh-Color Watermelon

Watermelon (Citrullus lanatus) is an economically important cucurbit crop. Its pulp is rich in antioxidant carotenoids, which confer a variety of flesh colors. ClPsy1 (Phytoene Synthase) is the rate-limiting enzyme for carotenoid synthesis; however, the promoter activity of ClPsy1 is still unknown. In the present study, promoter sequences were isolated from four watermelon accessions: Cream of Saskatchewan pale yellow (COS), canary yellow flesh (PI 635597), golden flesh (PI 192938), and red flesh (LSW-177), all of which express ClPsy1 at extremely high levels. Sequence alignment and cis-element analysis disclosed six SNPs between the four lines all in COS, two of which (at the 598th and 1257th positions) caused MYC and MYB cis-element binding sequence variations, respectively. To confirm ClPsy1 gene promoter activity, full-length and deletion fragments of the promoter were constructed and connected to a β-D-glucosidase (GUS) vector and transferred into tomato fruits. GUS staining was performed to analyze the key segment of the promoter. The activity of the PI 192938 ClPsy1 full-length promoter exceeded that of COS. The deletion fragment from −1521 bp to −1043 bp exhibited strong promoter activity, and contained a MYB transcription factor-binding site mutation. We combined RNA-seq with qRT-PCR to analyze the gene expression pattern between the MYB transcription factor Cla97C10G196920 and ClPsy1 gene and found that Cla97C10G196920 (ClMYB21) showed the same expression trend with ClPsy1, which positively regulates carotenoid synthesis and metabolism

Editorial: Translational research for cucurbit molecular breeding: Traits, markers, and genes

This work in YW's lab was supported by the Agriculture and Food Research Initiative Competitive Grant 2015-51181-24285 from the USDA NIFA (National Institute of Food and Agriculture).Work in FL's lab was supported by the China Agriculture Research System fund (CARS-25). Work in JG-M's lab was supported by the Spanish Ministry of Economy and Competitiveness grant AGL2015-64625-C2-1-R, the Severo Ochoa Programme for Centres of Excellence in R&D 2016-2020 (SEV-2015-0533), and the CERCA Programme/Generalitat de Catalunya.Peer reviewe

The complete chloroplast genome sequence of the Sechium edule (Jacq.) Swartz. (Cucurbitaceae)

Sechium edule (Jacq.) Swartz is an important vegetable with both food and medicinal values. The complete chloroplast genome sequence of S. edule has been reported in this study. The total genome size is 154,558 bp in length and contains a pair of inverted repeats (IRs) of 19,128 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 98,806 and 17,496 bp, respectively. A total of 122 genes were predicted including 78 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. Further, the phylogenetic analysis confirmed that S. edule belongs to the family Cucurbitaceae. The complete chloroplast genome of S. edule would play a significant role in the development of molecular markers for plant phylogenetic and population genetic studies

DNA Fingerprinting of Chinese Melon Provides Evidentiary Support of Seed Quality Appraisal

<div><p>Melon, <em>Cucumis melo</em> L. is an important vegetable crop worldwide. At present, there are phenomena of homonyms and synonyms present in the melon seed markets of China, which could cause variety authenticity issues influencing the process of melon breeding, production, marketing and other aspects. Molecular markers, especially microsatellites or simple sequence repeats (SSRs) are playing increasingly important roles for cultivar identification. The aim of this study was to construct a DNA fingerprinting database of major melon cultivars, which could provide a possibility for the establishment of a technical standard system for purity and authenticity identification of melon seeds. In this study, to develop the core set SSR markers, 470 polymorphic SSRs were selected as the candidate markers from 1219 SSRs using 20 representative melon varieties (lines). Eighteen SSR markers, evenly distributed across the genome and with the highest contents of polymorphism information (PIC) were identified as the core marker set for melon DNA fingerprinting analysis. Fingerprint codes for 471 melon varieties (lines) were established. There were 51 materials which were classified into17 groups based on sharing the same fingerprint code, while field traits survey results showed that these plants in the same group were synonyms because of the same or similar field characters. Furthermore, DNA fingerprinting quick response (QR) codes of 471 melon varieties (lines) were constructed. Due to its fast readability and large storage capacity, QR coding melon DNA fingerprinting is in favor of read convenience and commercial applications.</p> </div

QTL-seq identifies major quantitative trait loci of stigma color in melon

Stigma color plays an important role in pollination. In nature, melon (Cucumis melo L.) stigmas are either yellow or green; however, a review of the literature found no report on how stigma color affects pollination and fruit development in melon. Here, we used an F2 melon population derived from a cross between ‘MR-1’ (P1, with green stigmas) and ‘M1–32’ (P2, with yellow stigmas), and performed genetic analysis and mapping. The results of bulked segregant analysis allowed the identification of genetic loci controlling stigma color on chromosomes 6 and 8. An F2 population consisting of 150 individuals was used for initial mapping. A genetic map of 304.17 cM was constructed using 37 cleaved amplified polymorphism sequence (CAPS) markers. We identified one major quantitative trait locus (QTL) and one minor QTL for stigma color. The major QTL GS8.1 was further mapped to a 4.13 cM interval between CAPS markers 8C-10 and 8C-16, which explained 27.04% of the phenotypic variation. In addition, GS6.1 was mapped between E-49 and 6A-7, explaining 18.6% of the phenotypic variation. This study provides a theoretical basis for the fine mapping and cloning of melon genes controlling stigma color

Functional Characterization and in Silico Analysis of Phytoene Synthase Family Genes Responsible for Carotenoid Biosynthesis in Watermelon (Citrullus lanatus L.)

Carotenoids are the main pigments in watermelon (Citrullus lanatus L.) fruit and contribute to its aesthetic and nutritional value. Phytoene synthase (PSY) is reported to be the first rate-limiting enzyme in carotenogenesis and controls the carotenoid flux. This study aimed to identify PSY genes responsible for carotenoid biosynthesis in the red-fleshed watermelon cultivar LSW-177. The PSY gene members ClPSY1, ClPSY2 and ClPSY3 were characterized and their catalytic activities were displayed in the heterologous complementation assay. The transcript levels of ClPSY genes at the different developmental stages of LSW-177 fruit and the promoter sequence of ClPSY1 were also analyzed. Transcription factors involved in regulating the ClPSY1 expression were scanned with previous RNA-seq data of the different stages during fruit ripening. Results showed that the PSY proteins from watermelon LSW-177 contained the conserved PSY domains and exhibited the ability to condense GGPP into phytoene in E. coli. ClPSY1 is the dominant carotenogenic gene during fruit ripening; and can be induced by light and hormones. Furthermore, Cla013914 and Cla007950 that, respectively encode the transcription factors WD40-like protein and bZIP, likely upregulate ClPSY1 during fruit ripening. In conclusion, ClPSY1 play a dominant role in carotenoid biosynthesis during watermelon fruit ripening and is regulated by complex light and hormone-responsive networks

The 18 core SSRs for DNA fingerprinting.

1<p>Zhu et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052431#pone.0052431-Zhu1" target="_blank">[41]</a>.</p>2<p>Gao et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052431#pone.0052431-Gao1" target="_blank">[42]</a>.</p>3<p>Diaz et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052431#pone.0052431-Diaz1" target="_blank">[43]</a> (ICUGI, <a href="http://www.icugi.org/" target="_blank">http://www.icugi.org/</a>).</p>4<p>Localization on melon genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052431#pone.0052431-GarciaMas2" target="_blank">[44]</a> using SSR primer sequences by BLAST.</p><p>–, not on the linkage group.</p