Vegetable biology and breeding in the genomics era

Li, Hongbo; Yang, Xueyong; Shang, Yi; Zhang, Zhonghua; Huang, Sanwen

doi:10.1007/s11427-022-2248-6

Cited by 15 publications

(4 citation statements)

References 248 publications

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“…SVs play important roles in driving plant genome evolution and trait adaptation in crops ( Li et al 2023 ). To assess CO patterns within SVs, we examined the enrichment of COs relative to SVs.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber

Wang,

Dong,

et al. 2023

Plant Physiology

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Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed two F2 populations from crosses between a semi-wild and two domesticated cucumber (Cucumis sativus) accessions and examined CO events. COs mainly occurred around genes and differed unevenly along chromosomes between the two hybrids. Fine-scale CO distributions were suppressed in regions of heterozygous structural variations (SVs) and were accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 tri-methylation (H3K4me3) modification, chromatin accessibility, and hypomethylation were positively associated with global CO landscapes and in local DNA double-strand break (DSB) hotspots and genes. The frequency and suppression of COs could be roughly predicted based on multi-omic information. Differences in CO events between hybrids could be partially traced to distinct genetic and epigenetic features and were significantly associated with specific DSB hotspots and heterozygous SVs. Our findings identify the genomic and epigenetic features that contribute to CO formation and hybrid-specific divergence in cucumber and provide theoretical support for selecting parental combinations and manipulating recombination events at target genomic regions during plant breeding.

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Section: Resultsmentioning

confidence: 99%

Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber

Wang,

Dong,

et al. 2023

Plant Physiology

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“…These changes in CsTOE3 expression pattern also seem to contribute to its functional differentiation in spine formation regulation in cucumber. Genetic studies of vegetable crops lag behind major food crops such as wheat, maize and rice, thus limiting the application of molecular breeding (Li et al., 2023). The functional analysis of CsTOE3 gene will greatly promote the germplasm improvement and quality breeding of spines as the target trait in cucumber.…”

Section: Discussionmentioning

confidence: 99%

TARGET OF EAT3 (TOE3) specifically regulates fruit spine initiation in cucumber (Cucumis sativus L.)

et al. 2023

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SUMMARY The presence or absence of spines is an important economic trait of cucumber fruit. Spines are believed to be a type of specialized trichome on the fruit surface, and all the identified cucumber trichome‐less mutants lack fruit spines. However, genes that specifically regulate fruit spine initiation remain to be identified. Here, we found that knocking out cucumber TARGET OF EAT3 homolog (CsTOE3), belonging to the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family, affected flower development and, more interestingly, inhibited cucumber fruit spine initiation. On analyzing expression patterns by quantitative reverse transcriptase‐polymerase chain reaction and in situ hybridization assay, CsTOE3 was found to be highly expressed in male and female flowers, and its mRNA accumulated in the tips of sepal and petal primordia and in the cells of fruit spines and peels. Biochemical analyses indicated that CsTOE3 directly interacts with GLABRA1 (CsGL1) and TRANSPARENT TESTA GLABRA1 (CsTTG1), which are positive regulators of trichome formation. In addition, RNA‐seq showed that the transcription levels of eight ERFs were significantly upregulated in CsTOE3 knockout lines. Phytohormone content analysis also revealed a significant increase in the amount of ethylene released by CsTOE3 knockout line, and treatment with the ethylene synthesis inhibitor aminoethoxyvinyl‐glycine partly restored the spineless phenotype. Our results suggest that CsTOE3 specifically regulates fruit spine initiation but does not affect the formation of trichomes on other organs in cucumber. Our findings may have a far‐reaching significance for cucumber germplasm improvement and quality breeding using fruit spines as the target trait.

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“…A high spermidine content was produced in chilling-treated cucumber; this metabolite also contributes to chilling tolerance [ 10 ]. Metabolites can bridge genotypes and phenotypes, and their presence and levels produce important clues to explore complex biological processes [ 11 ]. Multi-omics analysis revealed the regulatory network of steroidal glycoalkaloids in tomato fruit over the course of tomato domestication [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated Full-Length Transcriptome and Metabolome Profiling Reveals Flavonoid Regulation in Response to Freezing Stress in Potato

Zhu

Lingling

Guo

et al. 2023

Plants

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Cold stress impairs plant growth and development, resulting in crop failure. Cultivated potato (Solanum tuberosum L.) is sensitive to freezing, while its wild relative, S. commersonii, has a strong freezing tolerance. To decipher the anti-freezing mechanism of CM, we carried out a transcriptomic and metabolomic analysis of an anti-freezing variety of CM (a type of S. commersonii) and a freeze-sensitive variety of DM (a type of Solanum tuberosum L.). A total of 49,232 high-quality transcripts from 12,811 gene loci, including 46,772 coding sequences and 2018 non-coding RNAs, were identified. KEEG enrichment analysis of differentially expressed genes (DEGs) between the two varieties showed that the flavonoid biosynthesis pathway was strongly induced by freezing stress, which was proven by flavonoid metabolome analysis. Consistent with the accumulation of more flavonoids, nearly all the pathway genes were significantly upregulated in CM than those in DM. The transcript levels of two chalcone synthase (CHS-1) isoforms and four isoforms of flavonoid 3′-hydroxylase (F3′H-1) were confirmed by qRT-PCR. Co-expression analysis identified one Myb-related and three UGTs (UDP-glycosyltransferase) that were significantly upregulated in CM during freezing stress. Our findings support that the flavonoid pathway was significantly enhanced by freezing stress and the greater accumulation ofglycosylatedflavonoids in resistant types than that of sensitive types, maybe accounting for the increased freezing tolerance of freeze-resistant potato varieties.

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Vegetable biology and breeding in the genomics era

Cited by 15 publications

References 248 publications

Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber

Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber

TARGET OF EAT3 (TOE3) specifically regulates fruit spine initiation in cucumber (Cucumis sativus L.)

Integrated Full-Length Transcriptome and Metabolome Profiling Reveals Flavonoid Regulation in Response to Freezing Stress in Potato

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