In the context of rapidly increasing population and diversified market demands, the steady improvement of yield and quality in horticultural crops has become an urgent challenge that modern breeding efforts must tackle. Heterosis, a pivotal theoretical foundation for plant breeding, facilitates the creation of superior hybrids through crossbreeding and selection among a variety of parents. However, the vast number of potential hybrids presents a significant challenge for breeders in efficiently predicting and selecting the most promising candidates. The development and refinement of effective hybrid prediction methods have long been central to research in this field. This article systematically reviews the advancements in hybrid prediction for horticultural crops, including the roles of marker-assisted breeding and genomic prediction in phenotypic forecasting. It also underscores the limitations of some predictors, like genetic distance, which do not consistently offer reliable hybrid predictions. Looking ahead, it explores the integration of phenomics with genomic prediction technologies as a means to elevate prediction accuracy within actual breeding programs.

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.

Cucumber (Cucumis sativus L.), a globally significant horticultural crop, requires substantial nitrogen inputs due to its high nutrient demand. However, the prevalent issues of low nitrogen use efficiency (NUE) in cultivars and excessive fertilizer application have led to increased production costs and environmental burdens. To identify quantitative trait nucleotides (QTNs) and genes associated with low-nitrogen tolerance, we conducted a genome-wide association study (GWAS) on a basis of three low-nitrogen tolerance traits and 594,066 single nucleotide polymorphisms (SNPs) of a natural population of 107 cucumber accessions. The transcriptome of low-nitrogen tolerant genotype (F005) and low-nitrogen sensitive genotype (F027) were sequenced between low and normal nitrogen treatments. Through GWAS, we identified 29 QTNs harboring 196 candidate genes, while RNA sequencing (RNA-seq) revealed 3,765 differentially expressed genes (DEGs). 24 were identified by both methods. Among these 24 genes, 20 genes showed significant phenotype differences among different haplotypes. These 20 genes were defined as more valuable candidate genes for low-nitrogen tolerance. Furthermore, functional validation of the candidate gene CsaV3_7G035390 (encoding a GATA9 transcription factor) was performed using virus-induced gene silencing (VIGS), which demonstrated that silencingn this gene significantly enhanced soil plant analysis development (SPAD) and leaf of nitrogen accumulation in cucumber, indicating its negative regulatory role in low-nitrogen tolerance. Collectively, this study provides novel genetic resources for improving NUE in cucumber breeding programs.

The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit β-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with β-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced β-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, β-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces β-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.

Cucumber is one of the most important vegetables, and nitrogen is essential for the growth and fruit production of cucumbers. It is crucial to develop cultivars with nitrogen limitation tolerance or high nitrogen efficiency for green and efficient development in cucumber industry. To reveal the genetic basis of cucumber response to nitrogen starvation, a genome-wide association study (GWAS) was conducted on a collection of a genetically diverse population of cucumber (Cucumis sativus L.) comprising 88 inbred and DH accessions including the North China type, the Eurasian type, the Japanese and South China type mixed subtype, and the South China type subtype. Phenotypic evaluation of six traits under control (14 mM) and treatment (3.5 mM) N conditions depicted the presence of broad natural variation in the studied population. The GWAS results showed that there were significant differences in the population for nitrogen limitation treatment. Nine significant loci were identified corresponding to six LD blocks, three of which overlapped. Sixteen genes were selected by GO annotation associated with nitrogen. Five low-nitrogen stress tolerance genes were finally identified by gene haplotype analysis: CsaV3_3G003630 (CsNRPD1), CsaV3_3G002970 (CsNRT1.1), CsaV3_4G030260 (CsSnRK2.5), CsaV3_4G026940, and CsaV3_3G011820 (CsNPF5.2). Taken together, the experimental data and identification of candidate genes presented in this study offer valuable insights and serve as a useful reference for the genetic enhancement of nitrogen limitation tolerance in cucumbers.

Cucumber (Cucumis sativus L.) is a crucial vegetable crop, requiring significant nitrogen fertilizer inputs. However, excessive nitrogen application not only impairs growth but also poses severe environmental risks. Thus, enhancing nitrogen use efficiency (NUE) in cucumber is imperative. For the identification of genes associated with NUE in cucumber, roots of high NUE and low NUE lines were analyzed under high nitrogen conditions. Using transcriptome sequencing through WGCNA, a total of 15,180 genes were categorized into 35 co-expression modules, with 5 modules being highly correlated with NUE. Based on differential expression within the five modules and the results of GO and KEGG enrichment analyses, 25 genes were identified as potentially related to NUE. Among these, CsaV4_1G002492 (GLR22), CsaV4_2G003460 (GLR35), CsaV4_3G000307 (NRT1.1), and CsaV4_7G001709 (UPS2) were homologous to genes in Arabidopsis known to directly participate in NUE related process. These four genes were chosen as key genes for further analysis. qRT-PCR analysis revealed that CsaV4_3G000307 and CsaV4_7G001709 were more active during the early stages of the high nitrogen treatment in the high NUE line. Conversely, CsaV4_1G002492 and CsaV4_2G003460 were more active in the low NUE line. Using transcriptomic analysis, a frameshift INDEL mutation was observed in CsaV4_3G000307 in the low NUE line, which impacted the compactness of the protein structure, potentially altering its function. Analysis of protein interactions of these four key genes predicted some potential interaction networks. This research offers critical insights into the genetic factors influencing NUE in cucumber, presenting potential targets for genetic modification or breeding programs.