Stylosanthes scabra, a legume native to the Brazilian semiarid region, exhibits remarkable drought tolerance and represents a valuable model for studying molecular adaptation in legumes. Transcription factors of the AP2/ERF superfamily play central roles in plant development and stress response. This study aimed to identify and characterize AP2/ERF genes in Stylosanthes scabra and to analyze their transcriptional response to root dehydration. Candidate genes were identified through a Hidden Markov Model (HMM) search using the AP2 domain profile (PF00847), followed by validation of conserved domains, physicochemical characterization, prediction of subcellular localization, phylogenetic and structural analyses, and functional annotation. A total of 295 AP2/ERF proteins were identified and designated as SscAP2/ERF, most of which were predicted to be localized in the nucleus. These proteins exhibited a wide range of molecular weights and isoelectric points, reflecting structural diversity, and were classified into four subfamilies: AP2, ERF, DREB, and RAV. Functional annotation revealed predominant roles in DNA binding and transcriptional regulation, while promoter analysis identified numerous stress-related cis-elements. A total of 32 transcripts were differentially expressed under 24 h of water deficit, and four selected genes had their expression patterns validated by qPCR. These findings provide new insights into the AP2/ERF gene subfamily in Stylosanthes scabra and lay the groundwork for future biotechnological approaches to enhance stress tolerance in legumes.

Objective: This study aimed to align genetic linkage groups (LGs) with the mango physical map by comparing single nucleotide polymorphism (SNP) sequences in the 'Alphonso' mango genome. Theoretical Framework: Few studies have evaluated the impact of linkage group (LG) formation and marker ordering on quantitative trait loci (QTL) estimates for marker-assisted selection (MAS). Method: SNPs from the mango linkage groups (n=20) were aligned on the chromosomes of the genome sequence of the 'Alphonso' mango (n=20), evaluating the correspondence between the genetic linkage map and the physical map. Results and Discussion: Four major aberrations were identified: (a) chromosome 1 was divided into LGs 9 and 14; (b) chromosome 4 was split between LGs 1 and 3; (c) LG 8 was formed by combining SNPs from chromosomes 9 and 17 of 'Alphonso'; and (d) chromosome 18 was not represented in any of the 20 LGs. All remaining LGs, except LGs 11, 14 and 20, contained at least one SNP from non-corresponding reference chromosomes. Significant discrepancies in SNP ordering were observed across the 20 LGs, particularly in 12 LGs. Research Implications: For species with available genome sequences, physical maps, created through SNP sequence Blast alignment, yield better results for quantitative trait mapping aimed at marker-assisted selection. Originality/Value: QTLs utilization in MAS remains limited. Insufficient attention has been given to limitations in linkage group formation and marker ordering compared to physical mapping as sources of spurious QTL estimates.

Transposable elements (TEs), which were once relegated to the status of genomic parasites, are today accepted as important agents of plant genome evolution and adaptation. This review integrates evidence pointing to their dual function as drivers of genetic diversity and instability, with a focus on their contribution to phenotypic innovation, stress tolerance, and crop trait control. TEs create structural and regulatory diversity by insertional mutagenesis, cis ‐regulatory sequence donation, and epigenetic interactions, facilitating fast adaptation to environmental stress. Advances in omics technologies have unraveled TE dynamics, showing insertion bias toward genic and regulatory regions and stress‐responsive activation patterns. The influence of the mobilome on crop improvement is emphasized by TE‐derived molecular markers, clustered regularly interspaced short palindromic repeats‐mediated TE regulation, and epigenome editing that minimizes risks of genome instability while tapping TE‐driven diversity. Rice ( Oryza sativa L.) mPing and maize ( Zea mays L.) Hopscotch , for instance, demonstrate TE potential in trait enhancement and domestication. Moreover, multi‐omics integration has defined TEs’ input into stress response and genome plasticity, offering new targets for precision breeding. Challenges remain in modeling TE behavior and weighing adaptive potential against harmful effects, requiring sophisticated computational models and synthetic biology strategies. Interdisciplinary approaches integrating machine learning and synthetic TE design should be prioritized in future research to maximize TE‐mediated crop resilience. With the integration of TE biology and cutting‐edge biotechnologies, global food security issues, fueled by climate change, can be mitigated by the scientific community. This overview situates TEs not merely as genomic leftovers but as essential next‐generation crop requirements, necessitating their strategic location in sustainable agro‐innovation.