High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize.

Maize (Zea mays) is one of the most important crops in the world. However, few agronomically important maize genes have been cloned and used for trait improvement, due to its complex genome and genetic architecture. Here, we integrated multiplexed CRISPR/Cas9-based high-throughput targeted mutagenesis with genetic mapping and genomic approaches to successfully target 743 candidate genes corresponding to traits relevant for agronomy and nutrition. After low-cost barcode-based deep sequencing, 412 edited sequences covering 118 genes were precisely identified from individuals showing clear phenotypic changes. The profiles of the associated gene-editing events were similar to those identified in human cell lines and consequently are predictable using an existing algorithm originally designed for human studies. We observed unexpected but frequent homology-directed repair through endogenous templates that was likely caused by spatial contact between distinct chromosomes. Based on the characterization and interpretation of gene function from several examples, we demonstrate that the integration of forward and reverse genetics via a targeted mutagenesis library promises rapid validation of important agronomic genes for crops with complex genomes. Beyond specific findings, this study also guides further optimization of high-throughput CRISPR experiments in plants.

De novo domestication: a new way for crop design and breeding.

The impending global climate change presents significant challenges to agricultural production. It is imperative to find approaches to ensure sustained growth in food production while reducing agricultural input, in order to meet the needs of worldwide people for nutritious food supply. One of the effective strategies to address this challenge is still the development of new crop varieties with high yield, stable yield, environmental friendliness and rich nutrition. The creation of new crop cultivars depends largely on the expansion of genetic resources and the innovation of breeding techniques. De novo domestication is an innovative breeding strategy for developing new crop varieties. It involves utilizing undomesticated or semi-domesticated plants with desirable traits as founder species for breeding. The process involves rapid domestication of wild plants through the redesign of agronomic traits and the introduction of domestication genes to meet diverse human needs. In this review, we overview the history of crop domestication and genetic improvement, clarify the necessity of enriching crop diversity, and emphasize the significance of wild plants' genetic diversity in expanding the scope for crop redesign. Breeding strategy innovation is the key to accelerate crop breeding. We also discuss the feasibility and prospects of rapid developing new crops through de novo domestication.

De Novo Domestication in the Multi-Omics Era.

Most cereal crops were domesticated within the last 12,000 years and subsequently spread around the world. These crops have been nourishing the world by supplying a primary energy and nutrient source, thereby playing a critical role in determining the status of human health and sustaining the global population. Here, we review the major challenges of future agriculture and emphasize the utilization of wild germplasm. De novo domestication is one of the most straightforward strategies to manipulate domestication-related and/or other genes with known function, and thereby introduce desired traits into wild plants. We also summarize known causal variations and their corresponding pathways in order to better understand the genetic basis of crop evolution, and how this knowledge could facilitate de novo domestication. Indeed knowledge-driven de novo domestication has great potential for the development of new sustainable crops that have climate-resilient high yield with low resource input and meet individual nutrient needs. Finally, we discuss current opportunities for and barriers to knowledge-driven de novo domestication.

Genetic variation in YIGE1 contributes to ear length and grain yield in maize.

Ear length (EL), which is controlled by quantitative trait loci (QTLs), is an important component of grain yield and as such is a key target trait in maize breeding. However, very few EL QTLs have been cloned, and their molecular mechanisms are largely unknown. Here, using a genome wide association study (GWAS), we identified a QTL, YIGE1, which encodes an unknown protein that regulates EL by affecting pistillate floret number. Overexpression of YIGE1 increased female inflorescence meristem (IM) size, increased EL and kernel number per row (KNPR), and thus enhanced grain yield. By contrast, CRISPR/Cas9 knockout and Mutator insertion mutant lines of YIGE1 displayed decreased IM size and EL. A single-nucleotide polymorphism (SNP) located in the regulatory region of YIGE1 had a large effect on its promoter strength, which positively affected EL by increasing gene expression. Further analysis shows that YIGE1 may be involved in sugar and auxin signal pathways to regulate maize ear development, thus affecting IM activity and floret production in maize inflorescence morphogenesis. These findings provide new insights into ear development and will ultimately facilitate maize molecular breeding.

The genetic architecture of the dynamic changes in grain moisture in maize.

Low grain moisture at harvest is crucial for safe production, transport and storage, but the genetic architecture of this trait in maize (Zea mays) remains elusive. Here, we measured the dynamic changes in grain moisture content in an association-mapping panel of 513 diverse maize inbred lines at five successive stages across five geographical environments. Genome-wide association study (GWAS) revealed 71 quantitative trait loci (QTLs) that influence grain moisture in maize. Epistatic effects play vital roles in the variability in moisture levels, even outperforming main-effect QTLs during the early dry-down stages. Distinct QTL-environment interactions influence the spatio-temporal variability of maize grain moisture, which is primarily triggered at specific times. By combining genetic population analysis, transcriptomic profiling and gene editing, we identified GRMZM5G805627 and GRMZM2G137211 as candidate genes underlying major QTLs for grain moisture in maize. Our results provide insights into the genetic architecture of dynamic changes in grain moisture, which should facilitate maize breeding.

The Kernel Size-Related Quantitative Trait Locus qKW9 Encodes a Pentatricopeptide Repeat Protein That Aaffects Photosynthesis and Grain Filling.

In maize (Zea mays), kernel weight is an important component of yield that has been selected during domestication. Many genes associated with kernel weight have been identified through mutant analysis. Most are involved in the biogenesis and functional maintenance of organelles or other fundamental cellular activities. However, few quantitative trait loci (QTLs) underlying quantitative variation in kernel weight have been cloned. Here, we characterize a QTL, qKW9, associated with maize kernel weight. This QTL encodes a DYW motif pentatricopeptide repeat protein involved in C-to-U editing of ndhB, a subunit of the chloroplast NADH dehydrogenase-like complex. In a null qkw9 background, C-to-U editing of ndhB was abolished, and photosynthesis was reduced, resulting in less maternal photosynthate available for grain filling. Characterization of qKW9 highlights the importance of optimizing photosynthesis for maize grain yield production.

Genome sequencing reveals evidence of adaptive variation in the genus Zea.

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding.

CUBIC: an atlas of genetic architecture promises directed maize improvement.

BACKGROUND: Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders. RESULTS: Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait. We find epistasis contributes to phenotypic variance widely. Integrative cross-population analysis and cross-omics mapping allow effective and rapid discovery of underlying genes, validated here with a case study on leaf width. CONCLUSIONS: Through the integration of experimental genetics and genomics, our study provides useful resources and gene mining strategies to explore complex quantitative traits.