The C-repeat binding factor (CBF)/dehydration-responsive element binding (DREB1) proteins play a prominent role in freezing tolerance and are highly conserved in higher plants. Here we performed a genome-wide search of the CBF/DREB1 gene family in lettuce (Lactuca sativa L.) and identified 14 members of the family with one member gene containing a non-sense mutation within the AP2 DNA-binding domain. A comprehensive phylogenetic analysis of the CBF/DREB1 family members in 20 plant species from the Asterid or Rosid clade provided evidence that tandem duplication played an important role in the expansion of the CBF/DREB1 family. Expression analysis showed that twelve of the lettuce CBF genes were responsive to low temperature (4 °C), and that three and six of them could also be responsive to salt and heat stresses, respectively. Unlike Arabidopsis thaliana whose members of the CBF/DREB1 family respond only to a particular stress, lettuce CBFs provide wider protection from combinations of abiotic stresses. A global transcriptome analysis revealed distinctive temporal expression patterns among the cold-regulated genes in lettuce plants exposed to low temperature. Genes induced throughout the cold treatment are enriched in functions associated with protection from UV and high-light intensity and the genes suppressed after 7 days of cold exposure are enriched in photosynthesis-associated functions. These results provide insight into the molecular evolutionary properties of the CBF/DREB1 gene family in lettuce and a reference for genetic improvement of the lettuce response to cold acclimation.

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.

Genetic diversity is an important resource in crop breeding to improve cultivars with desirable traits. Selective breeding can lead to a reduction of genetic diversity. However, our understanding on this subject remains limited in lettuce ( Lactuca sativa L.). Genotyping‐by‐sequencing (GBS) can provide a reduced version of the genome as a cost‐effective method to identify genetic variants across the genome. We genotyped a diverse set of 441 lettuce accessions using the GBS method. Phylogenetic and population genetic analyses indicated substantial genetic divergence among four horticultural types of lettuce: butterhead, crisphead, leaf, and romaine. Genetic‐diversity estimates between and within the four types indicated that the crisphead type was the most differentiated from other types, whereas its population was the most homogenous with the slowest linkage disequilibrium (LD) decay among the four types. These results suggested that crisphead lettuces had relatively less genetic variation across the genome as well as low gene flow from other types. We identified putative selective sweep regions that showed low genetic variation in the crisphead type. Genome‐wide association study (GWAS) and quantitative trait loci (QTL) analyses provided evidence that these genomic regions were, in part, associated with delayed bolting, implicating the positive selection of delayed bolting in reducing variation. Our findings enhance the current understanding of genetic diversity and the impacts of selective breeding on patterning genetic variation in lettuce.

Background: The APETALA2/ETHYLENE-RESPONSIVE FACTOR (AP2/ERF) transcription factor family plays a crucial role in plant development and stress responses. Characterized by the conserved AP2 DNA-binding domain, this family includes key subfamilies such as ERF, AP2, and RAV. Understanding the composition and evolutionary dynamics of the AP2/ERF family in coffee is essential for advancing the development of stress-resilient cultivars. Leveraging recent genomic resources for Coffea canephora (robusta coffee), Coffea arabica , and Coffea eugenioides , this study aims to provide a comprehensive genome-wide characterization and evolutionary analysis of the AP2/ERF family within these economically important species. Results: A total of 453 AP2/ERF genes were identified across the three Coffea species, constituting approximately 0.48% of their protein-coding genes. Chromosomal mapping and synteny analysis revealed a high degree of conservation among C. canephora , C. arabica , and C. eugenioides , reflecting their close evolutionary relationships. Gene duplication events were found to significantly contribute to the expansion of the AP2/ERF family, accounting for 16% of the total gene count. Subgroup IX, associated with disease resistance, exhibited substantial variation between the two parental species and their descendant subgenomes in C. arabica , indicating possible lineage-specific gene loss or expansion. Similarly, Subgroup III, linked to temperature tolerance, showed distinct expansion patterns among the coffee species, hinting at adaptive responses to varied environments. Conclusions: These comparative analyses of the AP2/ERF transcription factor family in Coffea species provide valuable insights into the adaptive evolution of this gene family under diverse environmental stresses. The observed subgroup-specific variations provide a basis for further functional studies and underscore potential candidates for breeding programs aimed at enhancing stress resilience and sustainability in coffee production.

Coffea stenophylla is a rare Coffea species boasting a flavor profile comparable to Arabica coffee (Coffea arabica) and has a good adaptability to lowland tropical climates. This species faces increasing threats from climate change, deforestation, and habitat fragmentation in its West African homeland. Using 1037 novel SNP markers derived from Genotyping-by-Sequencing (GBS), we revealed the presence of three distinct natural populations (mean Fst = 0.176) in Sierra Leone. Evidence of recent bottlenecks and small effective population size (118–140) was found across all three populations, reflecting the impact of recent anthropogenic disturbances on this species. Using a model-flexible inference approach, we unveiled a strong ancient bottleneck approximately 23,000 years ago, coinciding with the last glacial maximum (LGM), followed by post-glacial expansion and divergence into distinct genetic clusters. A comparative analysis between ex situ genebanks and natural populations detected a significant gap in genetic diversity, with two out of three natural populations missing from the ex situ genebank collection. These findings highlight the urgent need to improve conservation practices for C. stenophylla in Sierra Leone. The novel SNP markers developed in this study provided valuable tools to support future efforts in conservation and utilization of C. stenophylla genetic resources in West Africa.

Cacao ( Theobroma cacao ), the source of chocolate, is threatened by devastating diseases like frosty pod rot (FPR) and witches' broom disease (WBD), impacting global production and farmer livelihoods. Here, we employ a machine learning‐driven genome‐wide association study to dissect the genetic architecture of disease resistance and productivity in cacao. Upon analyzing phenotypic data for healthy pod rate along with FPR and WBD resistance across 102 diverse accessions, coupled with single nucleotide polymorphism (SNP) markers mapped to the Criollo and Matina reference genomes, we identified numerous novel candidate genes. These genes are implicated in various biological processes, including cell wall modification, stress response signaling, and defense‐related mechanisms. Notably, associations varied between the reference genomes, highlighting the genomic complexity of these traits. Our analyses, using Bootstrap Forest and Boosted Tree models, uncovered loci not previously reported, demonstrating the power of machine learning in uncovering complex genetic interactions. This study offers important insights into the polygenic nature of disease resistance in cacao and presents a genomic roadmap for developing disease‐resistant varieties.