园艺研究(英文)最新文献

Centromeres are essential for centromere-specific histone H3 (CENH3) recruitment and kinetochore assembly, ensuring accurate chromosome segregation and maintaining genome stability in plants. Although extensively studied in model species, the structural organization of centromeres in nonmodel plants, such as fruit trees, remains poorly explored. Our previous study revealed that jujube centromeres lack the typical tandem repeat (TR)-rich structure, complicating their precise identification. In this study, we updated the genome assembly of jujube (Ziziphus jujuba Mill. 'Dongzao') to a haplotype-resolved T2T version, enabling accurate mapping and comparison of centromeres between haplotypes using CENH3 ChIP-seq. These centromeres, ranging from 0.75 to 1.40 Mb, are largely conserved between haplotypes, except for a localized inversion on chromosome 10. Unlike the TR-rich centromeres found in many plant species, jujube centromeres are predominantly composed of Gypsy-type long-terminal repeat retrotransposons (LTR-RTs). Among these, we identified a centromere-enriched LTR family, centromeric retrotransposons of jujube (CRJ), which is particularly abundant in terminal LTRs compared to the internal transposon regions. Comparative analysis across plant species revealed that centromeric retrotransposons primarily fall into three subfamilies-CRM, Tekay, and Athila-highlighting strong subfamily specificity. Notably, early insertions of CRJ-derived LTR segments contributed to the formation of TR-like structures, suggesting a mechanistic link between transposable elements and the evolution of centromeric tandem repeats. This work provides the first in-depth characterization of a TE-dominated centromere architecture in a fruit tree, offering new insights into the diversity and evolution of plant centromeres.

Vegetable and grain soybeans are typically distinguished by harvest time and pod size, yet their nutritional differences are often overlooked in breeding programs. This study compared 10 varieties each of vegetable and grain soybeans to find key nutritional markers distinguishing them. Results showed that vegetable soybeans have higher concentrations of sucrose, total soluble sugar, and crude protein, along with lower concentrations of crude oil and total fatty acid. Specifically, vegetable soybeans contain a relatively higher amount of unsaturated fatty acids, particularly oleic acid, at green edible stages. Principal component analysis of 12 nutritional components revealed clear distinctions between vegetable and grain soybeans. Additionally, machine learning algorithms identified sucrose as the most critical nutritional marker for distinguishing these two types. Dynamic RNA-seq analysis combined with weighted gene co-expression network analysis identified a sucrose-related module, highlighting GmSPS17 as a predominant sucrose phosphate synthase encoding gene involved in sucrose accumulation in soybean seeds. Furthermore, we identified GmZF-HD1 as an upstream transcription factor regulating GmSPS17. Yeast one-hybrid, luciferase, and electrophoretic mobility shift assays confirmed that GmZF-HD1 directly activates GmSPS17 transcription. Overexpression experiments in hairy roots validated that GmZF-HD1 enhances GmSPS17 expression, thereby increasing sucrose accumulation. In summary, this study establishes sucrose as a key nutritional marker for distinguishing vegetable soybeans from grain soybeans and elucidates the GmZF-HD1-GmSPS17 regulatory pathway, providing valuable insights into sugar accumulation mechanisms and offering guidance for breeding high-sugar vegetable soybean varieties.

The MYB transcription factor (TF) family, which is involved in plant growth and development, is large and diverse. Previous studies on MYB family in Cucurbitaceae were mostly based on a single genome or focused on the R2R3 subfamily. Here, we analyzed 91 genomes of 11 Cucurbitaceae species and identified a total of 15 858 MYB genes. According to phylogenetic relationships, these genes were divided into 27 subgroups. The identified MYB genes were further classified into 121 MYB orthologous gene groups (OGGs), including 25 core, 57 softcore, 19 shell and 20 line-specific/cloud groups. Whole-genome duplication was the most common mechanism of MYB genes expansion. In core group, the higher proportions of MYB genes were found to be in the coexpression network constructed by the RNA-seq data. Through the comprehensive analysis including phylogeny and gene expression profile of cucumber MYB genes, as well as genetic variations in 103 cucumber germplasms, we identified a MYB gene CsRAX5, which may be related to cucumber plant height. We used gene editing technology to knockout and overexpress CsRAX5. In the knockout lines, Csrax5, the height was significantly increased compared with wild type (WT), whereas after overexpression the height of CsRAX5-OE plants was significantly decreased compared with WT. These results indicated that MYB gene CsRAX5 negatively regulated cucumber plant height. The large-scale analysis of MYB genes in Cucurbitaceae in this study provides insights for further investigating the evolution and function of MYB genes in Cucurbitaceae crops.

Apple (Malus × domestica) is one of the most popular fruits grown and consumed worldwide, contributing to human health with significant amounts of polyphenols and other bioactive compounds, and providing positive impacts to the economy and society. Understanding the diversity and inheritance of health-active compounds in apple can provide novel selection criteria for future breeding and cultivar development, as consumers increasingly prioritize the health benefits of their food choices. We therefore conducted an untargeted metabolomic analysis using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS) to investigate thousands of semipolar chemicals, mainly phenolic compounds, in 439 diverse apple accessions, and quantified 2066 features in positive ion mode. To identify key areas of genetic control for apple metabolite abundance, we performed a metabolomic genome-wide association study (mGWAS) on the quantified mass features using ~280 000 single nucleotide polymorphisms (SNPs). The mGWAS revealed >630 significant loci with hotspots for various groups of known and unknown phenolic compounds including flavonols on Chromosome 1, dihydrochalcones on Chromosome 5, and flavanols on Chromosomes 15 and 16. The most significant hotspot on Chromosome 16 included bHLH and C2H2 transcription factors that may play a role in controlling the abundance and complexity of phenolic compounds through regulation of the flavonoid biosynthesis pathway. Our analysis links the apple metabolome with candidate genes and biosynthetic mechanisms and establishes a foundation for marker-assisted breeding and gene editing to improve and modify phenolic compounds in apple for marketability and the benefit of human health.

[This corrects the article DOI: 10.1093/hr/uhaf139.].

Amorphophallus konjac, as a significant representative of the Araceae family, demonstrates considerable potential for applications in medicine, healthcare, food, industry, and bioenergy due to its rich content of konjac glucomannan (KGM). However, the synthetic pathway of KGM remains largely unclear. Although genomic sequencing has been completed for various representative Araceae plants, including Amorphophallus konjac, a comprehensive data platform for deep analysis and exploration of the functions of these genes is lacking. In the current work, genomic and transcriptomic data from multiple Araceae species were integrated, and a database, AraceaeDB (http://www.araceaedb.com/), was constructed specifically for analyzing and comparing gene functions in Araceae plants. The gene functions in the database were annotated in detail, and their ortholog groups were identified and classified into different functional modules based on their expression patterns across various transcriptomic datasets. Multiple functional genomics analysis tools were developed, including OrthoGroup analysis, BLAST search, co-expression analysis, KEGG/GO enrichment analysis, and the JBrowse visualization tool. Moreover, the database incorporates several medicinally significant bioactive compounds traditionally important in the Araceae family, providing target prediction capabilities for these compounds. Furthermore, the major biosynthetic pathway of KGM has been successfully elucidated through these database resources, and a key gene AkCSL3 has been identified. It has been further confirmed that overexpression of AkCSL3 can significantly increase the content of KGM, suggesting its potential crucial role in the polymerization process of glucomannan in konjac corms.

Post-polyploid karyotype evolution represents a crucial cytological mechanism contributing to angiosperm diversification and speciation. Many polyploids show extensive karyotypic reshuffling relative to their pre-ancestors. However, karyotypic stasis is gaining popularity as an alternative evolutionary pathway following polyploidization, whose underlying cytological mechanisms remain poorly understood. Here, we successfully developed a set of enhanced oligo-painting (EOP) probes specific to 20 chromosomes of Cucurbita (2n = 40), a paleo-polyploid with very small chromosomes and rich genetic diversity. The probes generated robust fluorescence in situ hybridization (FISH) signals across six Cucurbita and one sister outgroup species. Cross-species EOP results confirmed that Cucurbita genomes originated from a paleo-allotetraploid and maintained remarkably conserved chromosomal synteny without chromosome reshuffling, indicating karyotypic structural stasis during post-polyploid diploidization. Repositioning and amplification/elimination of rDNA loci (45S and 5S) across species caused significant morphological variations on seven out of 20 chromosomes. Six predicted centromeric monomers showed dramatic variations in localization and copy number along the phylogenetic relationships, highlighting the rapid turnover of centromere-associated sequences. In conclusion, our results suggest that Cucurbita genomes maintain karyotypic structural stasis during post-polyploid diploidization, with karyotype evolution instead being driven by rDNA repositioning and centromere turnover events, which constitute the cytogenetic basis for species divergence in Cucurbita. This finding highlights the more refined cytological evolutionary mechanisms underlying karyotypic stasis, providing new insights into post-polyploid karyotype evolution.

[This corrects the article DOI: 10.1093/hr/uhac224.].