SAMBA controls cell division rate during maize development

The genomic and epigenetic footprint of local adaptation to variable climates in kiwifruit

A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates. Actinidia eriantha is a shade-tolerant species, widely distributed in the southern tropical region of China, occurring in spatially heterogeneous environments. In the present study we combined population genomic, epigenomic, and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient, and to assess genomic offset to climatic change for A. eriantha. The population structure is strongly shaped by geography and influenced by restricted gene flow resulting from isolation by distance due to habitat fragmentation. In total, we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation, which were enriched in functional categories related to development processes and stress response; both temperature and precipitation are important factors driving adaptive variation. In addition to single-nucleotide polymorphisms (SNPs), a total of 27 single-methylation variants (SMVs) had significant correlation with at least one of four climatic variables and 16 SMVs were located in or adjacent to genes, several of which were predicted to be involved in plant response to abiotic or biotic stress. Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change. Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation. Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.

BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize

Ensuring food security for an ever-growing global population while adapting to climate change is the main challenge for agriculture in the 21st century. Although new technologies are being applied to tackle this problem, we are approaching a plateau in crop improvement using conventional breeding. Recent advances in CRISPR/Cas9-mediated gene engineering have paved the way to accelerate plant breeding to meet this increasing demand. However, many traits are governed by multiple small-effect genes operating in complex interactive networks. Here, we present the gene discovery pipeline BREEDIT, which combines multiplex genome editing of whole gene families with crossing schemes to improve complex traits such as yield and drought tolerance. We induced gene knockouts in 48 growth-related genes into maize (Zea mays) using CRISPR/Cas9 and generated a collection of over 1,000 gene-edited plants. The edited populations displayed (on average) 5%-10% increases in leaf length and up to 20% increases in leaf width compared with the controls. For each gene family, edits in subsets of genes could be associated with enhanced traits, allowing us to reduce the gene space to be considered for trait improvement. BREEDIT could be rapidly applied to generate a diverse collection of mutants to identify promising gene modifications for later use in breeding programs.

Genome-wide identification and expression analysis of anaphase promoting complex/cyclosome (APC/C) in rose

The anaphase promoting complex/cyclosome (APC/C) is a large multi-subunit complex, regulating plant development and cell cycle. In plants, the APC/C gene family has been identified in Arabidopsis, rice, and maize. The APC/Cs in rose has not yet been reported. In this study, a total of 19 APC/C genes were identified in rose. Furthermore, we also investigated phylogenetic relationships, chromosomal distribution, gene structure, motif analysis, promoter sequence analysis and expression pattern of RhAPC/C genes. Synteny analysis indicated that AtAPC/Cs and RhAPC/Cs show a high degree of conservation. RhAPC/C promoters contains numerous cis-elements involved in plant morphogenesis, hormone response and stress response. Based on the transcription of RhAPC/Cs in different tissues and developmental stages, it appears that RhAPC/Cs may play a variety of roles in rose growth and development. RhAPC/Cs have limitations in the time and space during which they respond to hormones and abiotic stress. RhAPC5, RhAPC11d, RhAPC13a and RhAPC13c may play a role in rose responding to abiotic stress. The expression of RhAPC10 was altered by infection with fungal pathogen. Our study will serve as a basis for determining the functional role of APC/C genes in roses and help future research on woody plants.

The translatability of genetic networks from model to crop species: lessons from the past and perspectives for the future

Comparative analyses of growth-regulatory mechanisms between Arabidopsis and maize revealed that even when the gene space is conserved, the translation of knowledge from model species to crops is not trivial. Based on these insights, we formulate future opportunities to improve the interpretation of curiosity-driven research towards crop improvement.

The role of APC/C in cell cycle dynamics, growth and development in cereal crops

Cereal crops can be considered the basis of human civilization. Thus, it is not surprising that these crops are grown in larger quantities worldwide than any other food supply and provide more energy to humankind than any other provision. Additionally, attempts to harness biomass consumption continue to increase to meet human energy needs. The high pressures for energy will determine the demand for crop plants as resources for biofuel, heat, and electricity. Thus, the search for plant traits associated with genetic increases in yield is mandatory. In multicellular organisms, including plants, growth and development are driven by cell division. These processes require a sequence of intricated events that are carried out by various protein complexes and molecules that act punctually throughout the cycle. Temporal controlled degradation of key cell division proteins ensures a correct onset of the different cell cycle phases and exit from the cell division program. Considering the cell cycle, the Anaphase-Promoting Complex/Cyclosome (APC/C) is an important conserved multi-subunit ubiquitin ligase, marking targets for degradation by the 26S proteasome. Studies on plant APC/C subunits and activators, mainly in the model plant Arabidopsis, revealed that they play a pivotal role in several developmental processes during growth. However, little is known about the role of APC/C in cereal crops. Here, we discuss the current understanding of the APC/C controlling cereal crop development.

Mini-Review: Transgenerational CRISPR/Cas9 Gene Editing in Plants

CRISPR/Cas9 genome editing has been used extensively in a wide variety of plant species. Creation of loss-of-function alleles, promoter variants and mutant collections are a few of the many uses of genome editing. In a typical workflow for sexually reproducing species, plants are generated that contain an integrated CRISPR/Cas9 transgene. After editing of the gene of interest, T-DNA null segregants can be identified in the next generation that contain only the desired edit. However, maintained presence of the CRISPR/Cas9 transgene and continued editing in the subsequent generations offer a range of applications for model plants and crops. In this review, we define transgenerational gene editing (TGE) as the continued editing of CRISPR/Cas9 after a genetic cross. We discuss the concept of TGE, summarize the current main applications, and highlight special cases to illustrate the importance of TGE for plant genome editing research and breeding.