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SUMMARY: Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome‐wide association study of natural cucumber populations, along with map‐based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow‐brown fruit skin) and Zaoer‐N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator‐like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow‐brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow‐colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C‐terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3′H, which encodes flavonoid 3′‐hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs. Significance Statement: Genome‐wide association study and map‐based cloning revealed that CsMYB60 regulates mature cucumber fruit skin coloring, which is promising for cucumber breeding. Two loss‐of‐function mutations of CsMYB60 provided color variations in the natural cucumber population. [ABSTRACT FROM AUTHOR]

SUMMARY: The formation of adventitious roots (ARs) derived from hypocotyl is the most important morphological adaptation to waterlogging stress in Cucumis sativus (cucumber). Our previous study showed that cucumbers with the gene CsARN6.1, encoding an AAA ATPase domain‐containing protein, were more tolerant to waterlogging through increased AR formation. However, the apparent function of CsARN6.1 remained unknown. Here, we showed that the CsARN6.1 signal was predominantly observed throughout the cambium of hypocotyls, where de novo AR primordia are formed upon waterlogging treatment. The silencing of CsARN6.1 expression by virus‐induced gene silencing and CRISPR/Cas9 technologies adversely affects the formation of ARs under conditions of waterlogging. Waterlogging treatment significantly induced ethylene production, thus upregulating CsEIL3 expression, which encodes a putative transcription factor involved in ethylene signaling. Furthermore, yeast one‐hybrid, electrophoretic mobility assay and transient expression analyses showed that CsEIL3 binds directly to the CsARN6.1 promoter to initiate its expression. CsARN6.1 was found to interact with CsPrx5, a waterlogging‐responsive class‐III peroxidase that enhanced H2O2 production and increased AR formation. These data provide insights into understanding the molecular mechanisms of AAA ATPase domain‐containing protein and uncover a molecular mechanism that links ethylene signaling with the formation of ARs triggered by waterlogging. Significance Statement: The AAA ATPase domain‐containing protein CsARN6.1 is required for waterlogging stress tolerance, where it regulates adventitious root (AR) formation. However, the functional relevance of this gene remained unknown. Our results reveal that in cucumber, a CsEIL3‐CsARN6.1 regulatory module confers AR formation through H2O2 production, mediated by CsPrx5. [ABSTRACT FROM AUTHOR]

SUMMARY: Occupation of living space is one of the main driving forces of adaptive evolution, especially for aquatic plants whose leaves float on the water surface and thus have limited living space. Euryale ferox, from the angiosperm basal family Nymphaeaceae, develops large, rapidly expanding leaves to compete for space on the water surface. Microscopic observation found that the cell proliferation of leaves is almost completed underwater, while the cell expansion occurs rapidly after they grow above water. To explore the mechanism underlying the specific development of leaves, we performed sequences assembly and analyzed the genome and transcriptome dynamics of E. ferox. Through reconstruction of the three sub‐genomes generated from the paleo‐hexaploidization event in E. ferox, we revealed that one sub‐genome was phylogenetically closer to Victoria cruziana, which also exhibits gigantic floating leaves. Further analysis revealed that while all three sub‐genomes promoted the evolution of the specific leaf development in E. ferox, the genes from the sub‐genome closer to V. cruziana contributed more to this adaptive evolution. Moreover, we found that genes involved in cell proliferation and expansion, photosynthesis, and energy transportation were over‐retained and showed strong expression association with the leaf development stages, such as the expression divergence of SWEET orthologs as energy uploaders and unloaders in the sink and source leaf organs of E. ferox. These findings provide novel insights into the genome evolution through polyploidization, as well as the adaptive evolution regarding the leaf development accomplished through biased gene retention and expression sub‐functionalization of multi‐copy genes in E. ferox. Significance Statement: Through the separation, reconstruction and evolutionary dissection of the three sub‐genomes of Euryale ferox, we reveal that the three sub‐genomes have different origins, with one sub‐genome showing a closer phylogenetic relationship to Victoria cruziana, which shows a similar adult leaf development process as that in E. ferox. Further analysis revealed that while all three sub‐genomes promoted the evolution of the specific leaf development process in E. ferox, the genes from the sub‐genome closer to V. cruziana contributed more to this adaptive evolution. Moreover, we found that genes involved in cell proliferation and expansion, photosynthesis, and energy transportation were over‐retained in multi‐copies and showed strong expression association with the different leaf development stages in E. ferox. [ABSTRACT FROM AUTHOR]

Summary: In plants, the formation of hypocotyl‐derived adventitious roots (ARs) is an important morphological acclimation to waterlogging stress; however, its genetic basis remains fragmentary. Here, through combined use of bulked segregant analysis‐based whole‐genome sequencing, SNP haplotyping and fine genetic mapping, we identified a candidate gene for a major‐effect QTL, ARN6.1, that was responsible for waterlogging tolerance due to increased AR formation in the cucumber line Zaoer‐N. Through multiple lines of evidence, we show that CsARN6.1 is the most possible candidate for ARN6.1 which encodes an AAA ATPase. The increased formation of ARs under waterlogging in Zaoer‐N could be attributed to a non‐synonymous SNP in the coiled‐coil domain region of this gene. CsARN6.1 increases the number of ARs via its ATPase activity. Ectopic expression of CsARN6.1 in Arabidopsis resulted in better rooting ability and lateral root development in transgenic plants. Transgenic cucumber expressing the CsARN6.1Asp allele from Zaoer‐N exhibited a significant increase in number of ARs compared with the wild type expressing the allele from Pepino under waterlogging conditions. Taken together, these data support that the AAA ATPase gene CsARN6.1 has an important role in increasing cucumber AR formation and waterlogging tolerance. [ABSTRACT FROM AUTHOR]