Epigenomic landscape and epigenetic regulation in maize

Epigenetic variation in maize agronomical traits for breeding and trait improvement

Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.

Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization

In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.

Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.

Activating stress memory: eustressors as potential tools for plant breeding

Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.

Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts

Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.