Summary: Potato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day‐dependent tuber development. Herein, we present a high‐quality, chromosome‐scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein‐coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome‐wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.

The areca palm (Areca catechu L.) is one of the most economically important palm trees in tropical areas. To inform areca breeding programs, it is critical to characterize the genetic bases of the mechanisms that regulate areca fruit shape and to identify candidate genes related to fruit-shape traits. However, few previous studies have mined candidate genes associated with areca fruit shape. Here, the fruits produced by 137 areca germplasms were divided into three categories (spherical, oval, and columnar) based on the fruit shape index. A total of 45,094 high-quality single-nucleotide polymorphisms (SNPs) were identified across the 137 areca cultivars. Phylogenetic analysis clustered the areca cultivars into four subgroups. A genome-wide association study that used a mixed linear model identified the 200 loci that were the most significantly associated with fruit-shape traits in the germplasms. In addition, 86 candidate genes associated with areca fruit-shape traits were further mined. Among the proteins encoded by these candidate genes were UDP-glucosyltransferase 85A2, the ABA-responsive element binding factor GBF4, E3 ubiquitin-protein ligase SIAH1, and LRR receptor-like serine/threonine-protein kinase ERECTA. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the gene that encoded UDP-glycosyltransferase, UGT85A2, was significantly upregulated in columnar fruits as compared to spherical and oval fruits. The identification of molecular markers that are closely related to fruit-shape traits not only provides genetic data for areca breeding, but it also provides new insights into the shape formation mechanisms of drupes.

Plant height is an important characteristic, the modification of which can improve the ability of stress adaptation as well as the yield. In this study, genome-wide association analysis was performed for plant height traits in 370 potato cultivars using the tetraploid potato genome as a reference. A total of 92 significant single nucleotide polymorphism (SNP) loci for plant height were obtained, which were particularly significant in haplotypes A3 and A4 on chromosome 1 and A1, A2, and A4 on chromosome 5. Thirty-five candidate genes were identified that were mainly involved in the gibberellin and brassinolide signal transduction pathways, including the FAR1 gene, methyltransferase, ethylene response factor, and ubiquitin protein ligase. Among them, PIF3 and GID1a were only present on chromosome 1, with PIF3 in all four haplotypes and GID1a in haplotype A3. This could lead to more effective genetic loci for molecular marker-assisted selection breeding as well as more precise localization and cloning of genes for plant height traits in potatoes.

The Australian native plant finger lemon (Citrus australasica) is well-known for its distinct flavor and high economic and medicinal value. 'YaoJi' is a typical purple variety of finger lemon, but its genome has not been analyzed yet. In this study, we used three-generation nanopore sequencing technology to sequence and assemble the genome of the finger lemon and combined it with the transcriptome analysis of different varieties with different colors of rinds at the same developmental period to investigate the mechanism of the differences in the color of the rinds of finger lemons. According to the results, the finger lemon genome was built and has nine chromosomes and a size of 314.63 Mb (Contig N50, 6.60 Mb; Scaffold N50, 32.81 Mb). By using homologous protein comparison and gene annotation, a total of 21,154 protein-coding genes and 164.7 Mb (52.35%) of repetitive sequences have been identified. The phylogenetic evolutionary tree shows that 10 Mya years ago finger lemon diverged from sweet orange (Citrus sinensis (L.) Osbeck) and Cremantine red orange (Citrus × clementina). Presumably it's a whole genome duplication (WGD) event according to the synonymous substitution rates (KS). Transcriptome analysis showed that the differences in the rind color of finger lemon were associated with higher expression of PAL, 4CL, and ANS genes in flavonoid biosynthesis and VDE and PSY genes in carotenoid synthesis. Transcription factors regulating flavonoid biosynthesis, such as bHLH, MYB, WD40, and NAC were also identified, which provides insights into the origin and evolution of finger lemon species and functional gene mining.

The color change in the peel of Jaboticaba (Myrciaria cauliflora Berg) ‘Essart’ is primarily driven by the spatiotemporal regulation of anthocyanin biosynthesis, but its molecular mechanism remains unclear. This study employed a multi-omics integrated analysis approach, combining targeted metabolomics, transcriptomics, and small RNA sequencing, to systematically elucidate the regulatory mechanism underlying color change during Jaboticaba fruit peel development. The results showed that during the color-turning stage, the content of most anthocyanins tended to decrease, while the content of Cyanidin significantly increased during the fully ripe stage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the brown module as a highly relevant module for anthocyanin accumulation, which includes a co-expression network of 98 transcription factors and 6 structural genes (F3H, CHI, ANS, CHS). Furthermore, small RNA sequencing results discovered a novel regulatory relationship: plant-MIR408-4—McMYB88. This regulatory relationship exhibited precise temporal dynamics: during the green fruit stage, plant-MIR408-4 was highly expressed and McMYB88 was lowly expressed, thereby inhibiting anthocyanin synthesis; however, during the fully ripe stage, plant-MIR408-4 expression decreased and McMYB88 expression increased, promoting anthocyanin accumulation. In summary, this study revealed the molecular regulatory mechanism of color formation in Jaboticaba fruit peel, providing an important theoretical basis for its color improvement and molecular breeding.

Root and tuber crops (RTCs), such as potato, cassava, and sweet potato, are globally critical staple foods and exhibit substantial potential for carbon sequestration. Their unique source-sink-flow synergy, high photosynthetic efficiency, and underground carbon storage capacity make them pivotal for climate change mitigation. However, RTCs face inherent bottlenecks: inefficient C3 photosynthesis with photorespiratory losses, source-sink imbalance, and inadequate low-carbon management practices. To address these limitations, this review synthesizes genetic engineering strategies (e.g., optimizing Rubisco function, introducing C4/CAM pathway elements, enhancing sink strength via AGPase and sugar transporters), and improved field management (e.g., balanced fertilization, crop rotation, biochar application, and IoT-based precision agriculture). These integrated approaches synergistically boost carbon fixation, optimize carbon allocation, and strengthen soil carbon sinks. RTCs thus represent a promising avenue to reconcile food security with carbon neutrality goals, providing actionable pathways for developing climate-resilient and sustainable agricultural systems globally.