EDITORIAL published: 30 November 2020 doi: 10.3389/fpls.2020.615346 Editorial: Translational Research for Cucurbit Molecular Breeding: Traits, Markers, and Genes Yiqun Weng 1*, Jordi Garcia-Mas 2,3 , Amnon Levi 4 and Feishi Luan 5 1 United States Department of Agriculture, Agriculture Research Service, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, United States, 2 Center for Research in Agricultural Genomics (CRAG) Consejo Superior de Investigaciones Científicas - Institut de Recerca i Tecnologia Agroalimentàries - Universitat Autònoma de Barcelona - Universitat de Barcelona, Barcelona, Spain, 3 Genomics and Biotecnology Program, Institut de Recerca i Tecnologia Agroalimentáries (IRTA), Barcelona, Spain, 4 US Vegetable Laboratory, United States Department of Agriculture, Agriculture Research Service, Charleston, SC, United States, 5 Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China Keywords: cucurbits, molecular breeding, QTL mapping, translational genomics, marker-assisted selection Editorial on the Research Topic Translational Research for Cucurbit Molecular Breeding: Traits, Markers, and Genes INTRODUCTION Cucurbits (family Cucurbitaceae) are economically important vegetable crops. Major cucurbits Edited by: growing globally include cucumber, melon, watermelon, and squash/pumpkin. Other cucurbits Herman Silva, like bitter melon, bottle gourd, winter melon, and luffa are popular in many Asian and African University of Chile, Chile countries. The last decade has witnessed a rapid development of genetic and genomics resources Reviewed by: including draft genome assemblies, and high-density genetic maps in a dozen cucurbit crops, Špela Baebler, making it possible to accelerate translational research for cucurbit breeding. This Research Topic National Institute of Biology (NIB), Slovenia is a collection of 21 Original Research articles or Reviews highlighting the achievements and Igor Pacheco, future directions in cucurbit translational research. These articles cover a variety of topics ranging University of Chile, Chile from improvement of the cucurbit genome assemblies to identification and molecular mapping of *Correspondence: horticulturally important genes or QTL for horticultural traits, and the use of such knowledge in Yiqun Weng marker-assisted selection for cucurbit improvement. Major findings from these investigations are yiqun.weng@usda.gov summarized below. Specialty section: IMPROVEMENT OF MELON DRAFT GENOME ASSEMBLY This article was submitted to Plant Breeding, Draft genomes of nearly a dozen cucurbit crops are now available (https://www.cucurbitgenomics. a section of the journal org/) and are constantly being revised using new technologies and experimental data. Castanera Frontiers in Plant Science et al. reported a further improvement of the melon reference genome using PacBio single-molecule Received: 08 October 2020 real time (SMRT) sequencing, which produced melon genome version v4.0 (DHL92). The melon Accepted: 05 November 2020 reference genome v3.5.1 (Garcia-Mas et al., 2012) was obtained using 454 technology and the Published: 30 November 2020 genome assembly was further improved using optical mapping to produce v3.6.1 (Ruggieri et al., Citation: 2018). However, v3.6.1 still contained 19% of gaps and more than 40 Mb unassigned sequences, Weng Y, Garcia-Mas J, Levi A and Luan F (2020) Editorial: Translational probably missing complex repeat regions. DHL92 melon assembly v4.0 had an increase of the Research for Cucurbit Molecular melon genome pseudomolecule size by 40 Mb with 90% of the v3.5.1 gaps being filled, and Breeding: Traits, Markers, and Genes. the completeness was improved mainly in non-genic regions. Specifically, 40% more full-length Front. Plant Sci. 11:615346. LTR retrotransposons were identified in the new assembly, mainly located in centromeric and doi: 10.3389/fpls.2020.615346 pericentromeric regions, and a burst of these repetitive elements was found to occur less than two Frontiers in Plant Science | www.frontiersin.org 1 November 2020 | Volume 11 | Article 615346 Weng et al. Editorial: Cucurbit Molecular Breeding million years ago. Some of these elements are polymorphic Two other articles reported microRNA (miRNA)-regulated among melon varieties and sit in the upstream regions of genes; resistance to target leaf spot (TLS, causal agent Corynespora however, their potential regulatory roles are unknown. cassiicola) and QTL mapping of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. cucumerinum) resistances in cucumber. Wang X. et al. studied the association of four QTL MAPPING OF DISEASE RESISTANCES miRNAs, miR164d, miR396b, Novel-miR1, and Novel- IN CUCURBITS miR7, with TLS resistance. The four miRNAs inhibit their target genes NAC transcription factor, APE (for anthranilate Cucurbits are susceptible to a number of common pathogens. phosphoribosyltransferase), 4CL (coding for 4-coumarate: CoA Identification of disease resistances and associated molecular ligase), and PAL (coding for phenylalanine ammonia-lyase), markers is often a priority in most cucurbit breeding programs. respectively. Transient expression of the four miRNAs and Three articles reported molecular mapping of host resistances the corresponding four target genes in cucumber cotyledons, against viral pathogens. Pascual et al. describe a general strategy resulted in reduced and enhanced TLS resistance, respectively. for virus resistance in melon, conferred by the vacuolar protein Overexpression of 4CL, PAL, and novel-miRNA1/7 down- sorting 41 (CmVPS41) gene, which is responsible for the regulated lignin synthesis suggesting that the two miRNAs are restriction of the virus to the bundle sheath cells and preventing associated with TLS resistance through regulating flavonoid phloem entry. VPS41 is a protein involved in intracellular biosynthesis. In another article, Dong J. et al. conducted QTL trafficking of proteins and vesicles from late Golgi to the vacuole. mapping of FW resistance in the cucumber line “Rijiecheng.” A A previous study (Giner et al., 2017) found that the cmv1 locus in major-effect QTL, fw2.1 was detected in a 1.91-Mb-long region melon accession PI 161375 for resistance against the Cucumber of cucumber Chr2. Further linkage analysis narrowed the QTL Mosaic Virus (CMV) was due to a mutation in CmVPS41. Pascual into a 600 kb region containing ∼80 annotated genes. RNA-Seq et al. sequenced the CmVPS41 locus in 52 melon accessions revealed five genes in this region which were up-regulated in the and identified 16 new haplotypes, 12 protein variants, and nine FW resistant parental line. This QTL was adjacent to two FW new resistant accessions. Only two non-synonymous mutations, resistance QTL previously detected in this region. L348R carried by PI 161375 and G85E, resulted in CMV resistance. In both cases, the virus was able to replicate and move from cell to cell but was unable to reach the phloem. The authors QTL MAPPING FOR ABIOTIC STRESS suggest that resistance to viral entrance to the phloem seems to TOLERANCES IN CUCUMBER AND be a general strategy in melon. This opens up new possibilities MELON for using different breeding approaches based on genes, which control different steps of the viral cycle to promote resistances to Two articles in this Research Topic report on QTL mapping of different viruses. abiotic stress tolerances. Dong S. et al. conducted QTL mapping The cucumber vein yellowing virus (CVYV) causes severe for low temperature tolerance (LTT) in cucumber seedlings. yield losses in cucurbit crops across Mediterranean countries. Phenotyping was performed in replicated trials using an F2 : 3 Pujol et al. identified CsCvy-1, a monogenic locus with population and a low-temperature injury index (LTII) that was incomplete dominance for CVYV resistance, in a long Dutch of quantitative inheritance. Three QTL, qLTT5.1, qLTT6.1, and cucumber, which can explain more than 80% of the variance. qLTT6.2 were detected, with the major-effect QTL qLTT6.2 A BSA (bulked segregant analysis)-Seq and an additional accounting for ∼25% of the observed phenotypic variance. linkage analysis placed CsCvy-1 in a 625 kb region of cucumber In silico BSA and qPCR (quantitative real-time PCR) in a Chromosome 5 (Chr5). There are 24 annotated genes in this re-sequenced cucumber core collection identified a 42-kb region region including two RNA-dependent RNA polymerase (RDR1a of the qLTT6.2 locus with Csa6G445210 (coding for an auxin and RDR1b) genes as potential candidates for CsCvy-1. RDRs response factor), and Csa6G445230 (coding for an ethylene- are critical players in RNA silencing pathways involved in the responsive transmembrane protein) being the most possible process of amplification of double-stranded RNAs that activate candidates for this QTL. gene silencing after nuclease processing. In another study in melon, Branham et al. report QTL Sáez et al. conducted a QTL analysis for resistance to mapping for tolerance to sulfur phytotoxicity and the the Tomato leaf curl New Delhi virus (ToLCNDV) in two development of markers useful for melon breeding programs. pumpkin (Cucurbita moschata) accessions (PI 419083 and PI Sulfur is widely used in cucurbit cultivation to control powdery 604506). Allelism tests indicated that both lines carried the same mildew, although it is known that several accessions can develop monogenic, recessive locus. Consistent with this, QTL mapping a phytotoxicity reaction leading to plant death. The use of the identified a major-effect QTL for ToLCNDV resistance on Chr8, MR-1 ×AY RIL (recombinant inbred line) population that which was also confirmed in the interspecific C. moschata × C. segregates for sulfur tolerance allowed the identification of one pepo segregating populations, but the resistance level seemed to major (qSulf-1 on Chr1) and two minor (qSulf-8 on Chr8, and be affected by the C. pepo genetic background. A comparative qSulf-12 on Chr12) QTL. The authors also provided a set of analysis indicated that this major-effect QTL was located in a KASP (Competitive allele specific PCR© ) markers tightly linked syntenic region on melon Chr11 which was previously shown to to qSulf-1, which can immediately be incorporated into melon harbor a locus for ToLCNDV resistance. breeding programs. Frontiers in Plant Science | www.frontiersin.org 2 November 2020 | Volume 11 | Article 615346 Weng et al. Editorial: Cucurbit Molecular Breeding MOLECULAR MAPPING OF FRUIT YIELD allelic diversity, and gene function analyses identified the AND QUALITY-RELATED TRAITS transcription factor CsSHINE1/CsWIN1 (CsV3_1g030200) as a source of natural variation for cucumber fruit epidermal traits. For all cucurbits, fruit is the main target for breeding Pericarp wax on cucumber fruit skin may affect consumer improvement. Important attributes affecting cucurbit fruit yield, preference and marketability. Grafting of cucumber onto and quality may include fruit size/shape, fruit external (rind/skin pumpkin rootstock (Cucurbita moschata) often produces glossy color, stripe pattern, fruit spines, warts, and texture), and fruits. Zhang J. et al. conducted transcriptome profiling, genome- internal (flavor/taste, nutritional content, flesh color) qualities. wide DNA methylation sequencing, and wax metabolite analysis In this Research Topic, seven articles described studies on in the pericarps of self-rooted vs. grafted cucumbers, and fruit quality-related traits in cucumber, watermelon and bottle found that the AP2/ERF-type transcription factor gene CsWIN1 gourd. Lycopene content and flesh color are important fruit (Csa3G878210) was methylated and up-regulated in grafted nutritional and appearance attributes for watermelon. Wang C. compared to self-rooted scions. The increased expression of et al. conducted linkage analysis in a red × pale yellow flesh CsWIN1 was positively correlated with expression of several key F2 population and found that the red flesh color was controlled wax biosynthesis genes and the accumulation of wax esters in by a recessive gene, which was located in a 392 kb region grafted cucumber pericarp. The glossier appearance of grafted on Chr4. Further linkage and association analyses narrowed pericarp seemed to be the result of higher wax ester content the candidate gene down to a ∼41 kb region. Additional and higher integration of small trichomes in the pericarp. It is evidence supported the lycopene β-cyclase (LCYB, Cla005011) interesting to see that the two different members of the AP2/ERF- gene as the candidate that regulates flesh color changes at the type transcription factor gene family control different aspects of protein level. Cleaved amplified polymorphic sequence (CAPS) fruit epidermal features. markers were developed to differentiate red vs. yellow flesh The fruit spine is also an important external fruit colors in watermelon genotypes that could be used in marker- quality trait. The MYB transcription factor gene CsTRY assisted breeding. (Csa5G139610) is a negative regulator for fruit spine initiation. Bitter fruit is undesirable for consumption in bottle gourd Zhang L. et al. found that in plants overexpressing CsTRY, (Lagenaria siceraria). Wu et al. phenotyped an F2 : 3 population the expression of key genes in the flavonoid synthesis with a trained panel of sensory analysis and found two pathway was repressed, suggesting that CsTRY not only complementary genes underlying fruit bitterness in bottle gourd, regulates the development of fruit spines, but also functions which was consistent with the QTL mapping result in this in the synthesis of flavonoids, acting as the repressor of population. The two QTL, QBt.1 and QBt.2, were located in a anthocyanin synthesis. region of 1.6-Mbp and 1.9-Mbp on Chr6, and Chr7, respectively, Cucumber is consumed when still immature. Over ripe fruit which were validated in an advanced bulked segregant analysis affects its market value. Cheng et al. isolated and characterized a (A-BSA). Sequence-based comparative analysis suggested that MADS-box gene, Cucumis sativus SHATTERPROOF (CsSHP) in the causal genes underlying QBt.1 and QBt.2 may not be direct cucumber that may participate in fruit maturation through the orthologs of the reported bitterness genes in cucumber, melon ABA pathway and floral organ specification via interaction with and watermelon. CsSEPs (SEPALLATA). Among the four articles on cucurbit external fruit quality attributes, Liu et al. investigated the inheritance of rind (skin) colors in watermelon. BSA-Seq and fine mapping with a yellow QTL FOR SEED-RELATED TRAITS × green F2 population mapped the yellow rind (Clyr) locus in a 91.42 kb region on Chr4. The authors also conducted In many countries, seed are also the end products for comparative transcriptomic analysis in the two parental lines watermelon and pumpkin/squash (Cucurbita spp.) production. at different fruit development stages and identified genes and There is considerable variation in seed color, size, and shape pathways related to rind pigment metabolism. Rett-Cadman in these crops. Four articles reported on a genetic analysis and et al. studied developmental changes and natural variation development of molecular markers for seed color and size in of cucumber fruit surface properties. They first conducted a watermelon and pumpkin, and a comparative analysis QTL for microscopic investigation of the fruit surface in two cucumber seed size variation among cucurbits. Paudel et al. examined lines (CL9930 and Gy14) at different development stages and the previously established four-gene model (R, T1, W, and D) found significant differences in cuticle thickness, depth of wax explaining seed coat color variation in watermelon. QTL-seq and intercalation between epidermal cells, epidermal cell size and genotyping-by-sequencing (GBS) analyses mapped R, T1, W, and shape, and number and size of lipid droplets in the two lines. QTL D on Chr3, 5, 6, and 8, respectively. They also developed KASP mapping in the Gy14 × CL9930 RIL population revealed strong assays and SNP markers useful for incorporating each of these QTL for epidermal cell height, cuticle thickness, intercalation gene loci in watermelon breeding programs. In another study, Li depth, and diameter of lipid droplets co-localized on cucumber B. et al. conducted a genetic mapping analysis and identified a Chr1. Fine mapping combined with gene expression profiling polyphenol oxidase (PPO) gene (Cla019481) as the candidate for suggested a small number of candidate genes underlying these the ClCS1 locus controlling the black seed color in watermelon. traits. Tissue specificity, developmental analysis of expression, The black color was proposed to be due to a frameshift mutation Frontiers in Plant Science | www.frontiersin.org 3 November 2020 | Volume 11 | Article 615346 Weng et al. Editorial: Cucurbit Molecular Breeding in this PPO gene that is involved in melanin oxidation during important topic on how sex determination genes and their melanin biosynthesis. interactions determine sex in cucurbit crops. Six sex morphs In pumpkin (C. maxima), based on a high-density SNP-based could be found based on the distribution of female, male, genetic map, Wang Y. et al. identified 10 QTL for seed width or bisexual flowers on a plant. So far, five orthologous genes (SW), seed length (SL), and hundred-seed weight (HSW). Based involved in sex determination have been cloned, and their on gene annotation and non-synonymous SNPs in the major SL various combinations and expression patterns can explain all the and SW-associated regions, two genes coding for a VQ motif and identified sex types in cucurbits. The phytohormone ethylene an E3 ubiquitin-protein ligase were proposed to be the potential plays a critical role in sex expression in cucurbits. Two ethylene candidates influencing SL, while an F-box and leucine-rich repeat signaling components, CsERF110 and CsERF31, have recently (LRR) domain-containing protein is the potential regulator for been identified, which may help in exploring the ethylene SW in C. maxima. signaling-mediated interactions among sex-related genes. The Guo et al. conducted a literature review on seed size (SS) authors proposed a nomenclature to name genes and sex QTL identified in watermelon, pumpkin/squash, cucumber, morphs across different cucurbit crops, which is at present and melon, and inferred consensus SS QTL based on their rather confusing. physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), CONCLUSIONS two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were a major-effect, stable QTL for seed This Research Topic provides readers with updates of size and weight, which were located in syntenic regions across translational research in cucurbit crops, many updates of different genomes, suggesting possible structural, and functional which are not only of importance for cucurbit breeding, but also conservation of some important genes for seed size control in elucidate basic concepts of cucurbit development and response cucurbit crops. to biotic and abiotic stressors. The editors thank all contributors to this Research Topic. PLANT ARCHITECTURE IN WATERMELON AND SEX EXPRESSION IN CUCURBITS AUTHOR CONTRIBUTIONS Plant architecture is important for crop improvement. There All authors listed have made a substantial, direct and intellectual is great interest by breeders and growers in the development contribution to the work, and approved it for publication. of dwarf watermelon varieties useful for high plant density cultivation and high yield production. Zhu et al. conducted BSA- FUNDING Seq of F2 plants derived from a cross between a normal-height and dwarf watermelon inbred lines. They identified a gene This work in YW’s lab was supported by the Agriculture (Cla010337) coding for an ATP-binding cassette transporter and Food Research Initiative Competitive Grant 2015-51181- (ABC transporter) protein with two SNPs associated with the 24285 from the USDA NIFA (National Institute of Food and dwarfness. A derived CAPS (dCAPS) marker that co-segregates Agriculture).Work in FL’s lab was supported by the China with the dwarf trait was validated using the F2 population and a Agriculture Research System fund (CARS-25). Work in JG- germplasm collection of 165 watermelon accessions. This dCAPS M’s lab was supported by the Spanish Ministry of Economy marker can be used in a marker-assisted selection (MAS) for the and Competitiveness grant AGL2015-64625-C2-1-R, the Severo development of dwarf watermelon cultivars. Ochoa Programme for Centres of Excellence in R&D 2016- In cucurbits, sex determination is critically associated with 2020 (SEV-2015-0533), and the CERCA Programme/Generalitat fruit earliness, yield, and quality. Li D et al. reviewed this de Catalunya. REFERENCES Conflict of Interest: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois, M., Mir, B., González, V. potential conflict of interest. M., et al. (2012). The genome of melon (Cucumis melo L.). Proc. Natl. Acad. Sci. U.S.A. 109, 11872–11877. doi: 10.1073/pnas.1205415109 Copyright © 2020 Weng, Garcia-Mas, Levi and Luan. This is an open-access article Giner, A., Pascual, L., Bourgeois, M., Gyetvai, G., Rios, P., Picó, B., et al. (2017). A distributed under the terms of the Creative Commons Attribution License (CC BY). mutation in the melon vacuolar protein sorting 41 prevents systemic infection The use, distribution or reproduction in other forums is permitted, provided the of Cucumber mosaic virus. Sci. Rep. 7:10471. doi: 10.1038/s41598-017-10783-3 original author(s) and the copyright owner(s) are credited and that the original Ruggieri, V., Alexiou, K. G., Morata, J., Argyris, J., Pujol, M., Yano, R., et al. publication in this journal is cited, in accordance with accepted academic practice. (2018). An improved assembly and annotation of the melon (Cucumis melo No use, distribution or reproduction is permitted which does not comply with these L.) reference genome. Sci. Rep. 8:8088. doi: 10.1038/s41598-018-26416-2 terms. Frontiers in Plant Science | www.frontiersin.org 4 November 2020 | Volume 11 | Article 615346