Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Verification of an introgression line, ‘IL10–1’, with M. incognita-resistance provides the opportunity to unravel the resistance mechanism of cucumber against M. incognita. In the present study, analyses of physiological responses and transcriptional events between IL10–1 (resistant line) and CC3 (susceptible line) were conducted after M. incognita infection. Physiological observations showed abnormal development of giant cells and M. incognita in IL10–1, which were the primary differences compared with CC3. Furthermore, Gene ontology (GO) analysis revealed that genes encoding cell wall proteins were up-regulated in IL10–1 and that the highly expressed lipid transfer protein gene (Csa6G410090) might be the principal regulator of this up-regulation. Simultaneously, analyses of gene expression profiles revealed more auxin-related genes were suppressed in IL10–1 than in those of CC3, which corresponded with the lower level of indole acetic acid (IAA) in the roots of IL10–1 than in those of CC3. Additionally, poor nucleus development as a clear indication of abnormal giant cells in IL10–1 was related to inhibition of the cell cycle. Of those genes related to the cell cycle, the F-box domain Skp2-like genes were down-regulated in IL10–1, whereas more of these genes were up-regulated in CC3. All of these findings indicate that suppressed expression of genes related to auxin and the cell cycle and highly expressed cell wall proteins play important roles in the abnormal development of giant cells, which hinders the development of M. incognita, thereby causing resistance to M. incognita in IL10–1. Knowledge from this research will provide a useful foundation for developing effective strategies in M. incognita-resistance breeding.

Carotenoids are indispensable to plants and essential for human nutrition and health. Carotenoid contents are strongly influenced by light through light-responsive genes such as B-Box (BBX) genes. BBX proteins, a class of zinc-finger transcription factors, mediate many light-signaling pathways, leading to the biosynthesis of important metabolites in plants. However, the identification of the BBX gene family and expression analysis in response to photoperiod-mediated carotenoid accumulation in cucumber remains unexplored. We performed a genome-wide study and determined the expression of cucumber BBX genes (hereafter referred to as CsaBBXs genes) in the endocarp of Xishuangbanna cucumber fruit (a special type of cucumber accumulating a high level of β-carotene in the endocarp) using an RNA-seq analysis of plants previously subjected to two photoperiodic conditions. Here, 26 BBX family genes were identified in the cucumber genome and named serially CsaBBX1 through CsaBBX26. We characterized CsaBBX genes in terms of their phylogenetic relationships, exon-intron structures, cis-acting elements, and syntenic relationships with Arabidopsis thaliana (L.) Heynh. RNA-seq analysis revealed a varied expression of CsaBBX genes under photoperiod treatment. The analysis of CsaBBXs genes revealed a strong positive correlation between CsaBBX17 and carotenoid biosynthetic pathway genes (phytoene synthase, ζ-carotene desaturase, lycopene ε-cyclase, β-carotene hydroxylase-1), thus suggesting its involvement in β-carotene biosynthesis. Additionally, nine CsaBBX genes (CsaBBX 4,5,7,9,11, 13,15,17 and 22) showed a significant positive correlation with β-carotene content. The selected CsaBBX genes were verified by qRT-PCR and confirmed the validity of RNA-seq data. The results of this study established the genome-wide analysis of the cucumber BBX family and provide a framework for understanding their biological role in carotenoid accumulation and photoperiodic responses. Further investigations of CsaBBX genes are vital since they are promising candidate genes for the functional analysis of carotenoid biosynthesis and can provide genetic tools for the molecular breeding of carotenoids in plants.

Xishuangbanna (XIS) cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan), is a botanical variety of cucumber cultivars native to southwest China that possesses excellent agronomic traits for cucumber improvement. However, breeding utilization of XIS cucumber is limited due to the current poor understanding of its photoperiod-sensitive flowering characteristics. In this study, genetic and transcriptomic analysis were conducted to reveal the molecular basis of photoperiod-regulated flowering in XIS cucumber. A major-effect QTL locus DFF1.1 was identified that controls the days to first flowering (DFF) of XIS cucumbers with a span of 1.38 Mb. Whole-genome re-sequencing data of 9 cucumber varieties with different flowering characteristics in response to photoperiod suggested that CsaNFYA1 was the candidate gene of DFF1.1, which harbored a single non-synonymous mutation in its fifth exon. Transcriptomic analysis revealed the positive roles of auxin and ethylene in accelerating flowering under short-day (SD) light-dark cycles when compared with equal-day/night treatment. Carbohydrate storage and high expression levels of related genes were important reasons explaining early flowering of XIS cucumber under SD conditions. By combining with the RNA-Seq data, the co-expression network suggested that CsaNFYA1 integrated multiple types of genes to regulate the flowering of XIS cucumber. Our findings explain the internal regulatory mechanisms of a photoperiodic flowering pathway. These findings may guide the use of photoperiod shifts to promote flowering of photoperiod-sensitive crops.

The CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

The Xishuangbanna (XIS) cucumber is an important botanical variety, accumulating high levels of β-carotene (700 μg/100 g) in the endocarp of mature fruit compared with normal green/white flesh types (25–50 μg/100 g, fresh weight). β-carotene is an essential precursor of provitamin A synthesis required for human health, thus XIS cucumber is an appealing germplasm for vitamin A breeding programs. In this review, we highlighted the molecular research progress of XIS cucumber as well as the bottlenecks undermining its utilization in genetic breeding. The XIS cucumber was first reported in 1983; thereafter, the literature on XIS cucumber was sporadic until 2012 and 2013 following QTL mapping of the Ore gene and subsequent cloning of the CsaBCH1 gene, respectively. Whereas QTL mapping studies underlying its flowering time and fruit quality related traits have been reported, fine mapping of their candidate genes remains unknown. Cucumber fruits are mainly consumed at fresh immature stage; however, XIS cucumber accumulates β-carotene at mature fruit state, thus limiting the utilization of β-carotene derived from it. In our opinion, we believe that the production and commercialization of immature orange-fleshed cucumber would gain wider acceptance among consumers. Additionally, we highlighted a comprehensive breeding strategy, precisely for enhanced β-carotene accumulation based on prior studies of XIS cucumber coupled with those from other crops. In MAS, we proposed schematic molecular backcross breeding strategy using lines possessing both ore and fft1.1 loci. This review, therefore, provides insights of XIS cucumber research and opportunities for further genetic breeding.

Allopolyploids undergo “genomic shock” leading to significant genetic and epigenetic modifications. Previous studies have mainly focused on nuclear changes, while little is known about the inheritance and changes of organelle genome in allopolyploidization. The synthetic allotetraploid Cucumis ×hytivus, which is generated via hybridization between C. hystrix and C. sativus, is a useful model system for studying cytonuclear variation. Here, we report the chloroplast genome of allotetraploid C. ×hytivus and its diploid parents via sequencing and comparative analysis. The size of the obtained chloroplast genomes ranged from 154 673 to 155 760 bp, while their gene contents, gene orders, and GC contents were similar to each other. Comparative genome analysis supports chloroplast maternal inheritance. However, we identified 51 indels and 292 SNP genetic variants in the chloroplast genome of the allopolyploid C. ×hytivus relative to its female parent C. hystrix. Nine intergenic regions with rich variation were identified through comparative analysis of the chloroplast genomes within the subgenus Cucumis. The phylogenetic network based on the chloroplast genome sequences clarified the evolution and taxonomic position of the synthetic allotetraploid C. ×hytivus. The results of this study provide us with an insight into the changes of organelle genome after allopolyploidization, and a new understanding of the cytonuclear evolution.