Molecular Horticulture最新文献

The colored calla lily, a member of the genus Zantedeschia in the Araceae family native to South Africa, is a valuable ornamental plant. However, the lack of a high-quality genome has hindered genetic analysis and the identification of key trait-related genes. We successfully assembled a haplotype-resolved genome of the colored calla lily, revealing extensive heterozygosity between homologous chromosomes. Comparative genomics analyses demonstrated that transposon insertions have led to significant differences in genome size among Araceae species. Notably, Araceae species experienced two closely-spaced whole-genome duplication (WGD) events before species divergence. Further analysis revealed that in terrestrial True Araceae species, genes associated with lignin synthase, cellulose synthase, expansin, and sugar transport proteins have undergone expansion, likely contributing to environmental adaptation and tuber starch accumulation. Additionally, we identified a key MIKC^C gene that may play a crucial role in spathe development. This study not only elucidates the evolutionary history of Araceae species but also provides valuable data to support functional genomics research and breeding efforts for the colored calla lily.

The high-quality chromosomal-level genome assembly (627.72 Mb, contig N50 1.80 Mb) of Uncaria rhynchophylla, a Chinese herb used for hypertension and Alzheimer's disease. Integrated genomic and transcriptomic analyses identified 46,909 genes, including 72 UrWRKY transcription factors. Sixty-four candidate genes for monoterpenoid indole alkaloid (MIA) biosynthesis were screened. Functional validation confirmed UrTDC6 catalyzes tryptamine formation and UrLAMT1/UrLAMT2 catalyze loganin production. Correlation analysis linked MIA content with UrWRKY expression, identifying UrWRKY37 as a key regulator. UrWRKY37 directly activates UrTDC and UrSGD transcription. Overexpression in hairy roots upregulated MIA pathway genes and significantly increased accumulation of isocorynoxeine, corynoxeine, and isorhynchophylline. This work elucidates MIA biosynthesis and its transcriptional regulation in U. rhynchophylla.

Prunus mume originated from China and is highly valued for its remarkable combination of ornamental blossoms and high economic value. Previously published P. mume genomes contain unanchored genetic regions and excessive gaps. Here, we report the P. mume f. viridicalyx gap-free telomere-to-telomere (T2T) haplotype genome. The LE_hap1 and LE_hap2 genomes were 229.29 and 228.36 Mb in length, respectively, with an N50 length of the contig between 27.65 and 27.79 Mb and 24,318 and 24,316 protein-coding genes, respectively. The completeness, continuity, and accuracy of the P. mume f. viridicalyx genome was significantly improved over the previous P. mume genomes. The key mutated genes during P. mume f. viridicalyx cultivar domestication were identified by comparative genomic, population evolution, and selective sweep analyses to be significantly enriched in the anthocyanin metabolism process, glutathione metabolism process, and carotenoid biosynthesis. Further analysis revealed that early codon termination of the PmGSTF2 gene, which is the key gene for the characteristic production of P. mume f. viridicalyx, reduced anthocyanin accumulation. We assembled a complete T2T gap-free haplotype P. mume genome, which provides a reference for gene mining and genome evolution of the anthocyanin deficiency phenotype in P. mume.

Flowering time is crucial for plant adaptation to regional climate conditions and for reproduction in agricultural production. Turnip (Brassica rapa ssp. rapa) is a traditional adaptive vegetable cultivated on the Qinghai-Xizang Plateau. However, little is known about the potential molecular mechanisms underlying the adaptive evolution of flowering time in turnip in different regions, especially on the Qinghai-Xizang Plateau. In this study, the key adaptive trait of flowering time, which is positively correlated with altitude, was analyzed in 104 turnip accessions grown worldwide. Whole-genome resequencing and Sanger sequencing discovered that the FRIa gene, a key regulator of flowering time in turnip, had sequence variations, with five distinct alleles and eight genotypes being defined. By combining the association analyses of FRIa genotypes and flowering time as well as genetic validation, FRIa1 was identified as a highly functional allele that contributes to delayed flowering of turnip for adaptation to the Qinghai-Xizang Plateau. Four specific SNP variations were determined to be critical for the strong function of FRIa in turnip. Our results provide new insights into the adaptation of flowering time in turnip along altitudinal gradients and shed light on the adaptive evolution of FRIa in turnip on the Qinghai-Xizang Plateau.

Plant V-ATPase serves as a primary active proton pump of the endomembrane system and is crucial for the stress response. However, the role of the C subunit of V-ATPase (VHA-C) in effector-triggered immunity remains poorly understood. Here, we reveal that Phytophthora infestans evolved a pair of RxLR effectors, AL3 and Avr2, which are expressed sequentially and both target the host VHA-C (StATP6V1C1) and StBSL1. In the early stage of P. infestans infection, AL3 promotes the assembly of StATP6V1C1 with subunits G and E, leading to increased V-ATPase activity and cytoplasmic acidification. Subsequently, Avr2 inhibits the StWNK10-catalyzed Ser-261 phosphorylation of StATP6V1C1, thereby retarding V-ATPase activity and causing intracellular alkalinization. In cultivars absence of two immune receptors, this pH shift facilitates the interactions of the two effectors with downstream susceptibility factors of StBSL1 at various stages of infection, which may promote the onset and development of the disease. As coping strategy, plants independently evolve two NLRs, R2 and Rpi-mcq1, guard both StATP6V1C1 and StBSLs to perceive effectors thereby mitigating the risk of late blight. Our findings establish a new arms race battlefield between plants and oomycetes, highlighting the role of intracellular pH homeostasis in both effector-triggered susceptibility (ETS) and effector-triggered immunity (ETI).

In most fruit-bearing plants, the growth and ripening of the fruit are highly coordinated with its seeds. In tomato (Solanum lycopersicum), fruit growth is regulated by a number of transcription factors. The WUSCHEL-RELATED HOMEOBOX (WOX) transcription factor COMPOUND INFLORESCENCE (S)/SlWOX9 is a key regulator of inflorescence branching and embryogenesis. In this study, we show that S activity is indispensable for fruit and seed development. Ectopic S expression led to a decrease in seed weight and markedly suppressed endoreduplication-associated fruit growth. Conversely, the s-classic allele promoted fruit growth in the small-fruited S. pimpinellifolium accession LA1781 though the promotion was offset by fruit overload and vegetative reversion of flowers in large-fruited cultivars. Through transcriptome profiling and DNA affinity purification sequencing (DAP-seq), we discovered that S targeted a set of genes involved in seed development. Moreover, we demonstrate that S regulates fruit and seed development mainly through direct transcriptional repression of the Mei2-like gene SlTEL1 (Solanum lycopersicum TERMINAL EAR-LIKE 1). These findings uncover a new aspect of transcription regulation of fruit growth and seed development by WOX transcription factors in tomato.

Parthenocarpy is an important target trait for the yield and quality of fruit crops. It has been used and selected in cucumber breeding for more than a hundred years, which has led to variation in parthenocarpic ability among different cucumber groups and thus resulted in a complex genetic basis. Here, we performed deep resequencing of 236 cucumbers from six cucumber groups and investigated parthenocarpic phenotypes over three years and six seasons to explore the genetic basis of parthenocarpy in cucumber. Among the 34 loci associated with parthenocarpy identified through a genome-wide association study (GWAS), 17 (50%) were correlated with reported quantitative trait loci (QTLs), and 27 (79.4%) were selected during cucumber domestication. We found that favorable parthenocarpic alleles continuously accumulated in cultivated cucumbers, and our data pinpoint that different favorable alleles were selected in the cucumber groups, leading to variations in parthenocarpic ability among them. To validate the favorable alleles detected by GWAS, we cloned three genes, CsACA10, CsCaM, and CsERT2, and verified their roles in the regulation of parthenocarpy for the first time. Our study elucidated the genetic basis and molecular mechanism of parthenocarpy, providing important germplasms for improving parthenocarpy in cucumber breeding.