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Plant cytochrome P450 (CYP) superfamily, the largest enzyme metabolism family, has been identified in many species and plays a vital role in plant development and stress response via secondary metabolite biosynthesis. A comprehensive identification and functional investigation of CYPs in tomato plants would contribute to deeper understanding of their biological significance. In this study, 268 tomato CYP genes were identified and found to be unevenly located on 12 chromosomes. Based on the phylogenetic analysis, these 268 SlCYPs were classed into two distinct clades (A‐type and non‐A‐type) and nine clans, including 48 families. Moreover, 67 tandem and 22 WGD (whole genome duplication)/segmental duplication events were detected, of which 12 SlCYP genes experienced both WGD/segmental and tandem duplication events, indicating that tandem duplication plays a major role in the expansion of the SlCYP family. Besides, 48 pairs containing 41 SlCYP and 44 AtCYP genes were orthologous, while 216 orthologous pairs were obtained between tomato and potato. The expression level of all SlCYP genes in tomato tissues at different development stages was analyzed, and most expressed SlCYPs showed a tissue‐specific pattern. Meanwhile, 143 differentially expressed SlCYPs were identified under cold stress. Furthermore, the RT‐qPCR results indicated that SlCYPs may be involved in fruit ripening and cold tolerance in tomato seedlings. These findings provide valuable insights into the evolutionary relationships and functional characteristics of SlCYPs, which can be utilized for further investigation of fruit metabolic pathways and cold tolerance in tomato. [ABSTRACT FROM AUTHOR]

Summary: B‐box (BBX) proteins are an important class of zinc finger transcription factors that play a critical role in plant growth and stress response. However, the mechanisms of how BBX proteins participate in the cold response in tomato remain unclear.Here, using approaches of reverse genetics, biochemical and molecular biology we characterized a BBX transcription factor, SlBBX17, which positively regulates cold tolerance in tomato (Solanum lycopersicum).Overexpressing SlBBX17 enhanced C‐repeat binding factor (CBF)‐dependent cold tolerance in tomato plants, whereas silencing SlBBX17 increased plant susceptibility to cold stress. Crucially, the positive role of SlBBX17 in CBF‐dependent cold tolerance was dependent on ELONGATED HYPOCOTYL5 (HY5). SlBBX17 physically interacted with SlHY5 to directly promote the protein stability of SlHY5 and subsequently increased the transcriptional activity of SlHY5 on SlCBF genes under cold stress. Further experiments showed that cold‐activated mitogen‐activated protein kinases, SlMPK1 and SlMPK2, also physically interact with and phosphorylate SlBBX17 to enhance the interaction between SlBBX17 and SlHY5, leading to enhanced CBF‐dependent cold tolerance.Collectively, the study unveiled a mechanistic framework by which SlMPK1/2‐SlBBX17‐SlHY5 regulated transcription of SlCBFs to enhance cold tolerance, thereby shedding light on the molecular mechanisms of how plants respond to cold stress via multiple transcription factors. [ABSTRACT FROM AUTHOR]

Summary: Plants adapt to cold stress at the physiological and biochemical levels, thus enabling them to maintain growth and development. However, the molecular mechanism of fine‐tuning cold signals remains largely unknown.We addressed the function of SlSEC1–SlC3H39 module in cold tolerance by using SlSEC1 and SlC3H39 knockout and overexpression tomato lines.A tandem CCCH zinc‐finger protein SlC3H39 negatively modulates cold tolerance in tomato. SlC3H39 binds to AU‐rich elements in the 3′‐untranslated region (UTR) to induce mRNA degradation and regulates gene expression post‐transcriptionally. We further validate that SlC3H39 participates in post‐transcriptional regulation of a variety of cold‐responsive genes. An O‐linked N‐acetylglucosamine transferase SlSEC1 physically interacts with SlC3H39 proteins and negatively regulates cold tolerance in tomato. Further study shows that SlSEC1 is essential for SlC3H39 protein stability and maintains SlC3H39 function in cold tolerance. Genetic analysis shows that SlC3H39 is epistatic to SlSEC1 in cold tolerance.The findings indicate that SlC3H39 negatively modulates plant cold tolerance through post‐transcriptional regulation by binding to cold‐responding mRNA 3′‐UTR and reducing those transcripts. SlSEC1 promotes the O‐GlcNAclation status of SlC3H39 and maintains SlC3H39 function in cold tolerance. Taken together, we propose a SlSEC1–SlC3H39 module, which allows plants to balance defense responses and growth processes. [ABSTRACT FROM AUTHOR]

Summary: High‐density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high‐resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra‐high‐density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole‐genome sequencing‐based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map‐based cloning data indicated that the R2R3‐MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish. [ABSTRACT FROM AUTHOR]