Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery.

Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding of development requires insight into the full diversity of cell types and developmental domains and the gene networks required to specify them. Until now, these were identified primarily by morphology and insights from classical genetics, which are limited by genetic redundancy and pleiotropy. Here, we investigated the transcriptional profiles of 12,525 single cells from developing maize ears. The resulting developmental atlas provides a single-cell RNA sequencing (scRNA-seq) map of an inflorescence. We validated our results by mRNA in situ hybridization and by fluorescence-activated cell sorting (FACS) RNA-seq, and we show how these data may facilitate genetic studies by predicting genetic redundancy, integrating transcriptional networks, and identifying candidate genes associated with crop yield traits.

Diversifying maize genomic selection models.

Genomic selection (GS) is one of the most powerful tools available for maize breeding. Its use of genome-wide marker data to estimate breeding values translates to increased genetic gains with fewer breeding cycles. In this review, we cover the history of GS and highlight particular milestones during its adaptation to maize breeding. We discuss how GS can be applied to developing superior maize inbreds and hybrids. Additionally, we characterize refinements in GS models that could enable the encapsulation of non-additive genetic effects, genotype by environment interactions, and multiple levels of the biological hierarchy, all of which could ultimately result in more accurate predictions of breeding values. Finally, we suggest the stages in a maize breeding program where it would be beneficial to apply GS. Given the current sophistication of high-throughput phenotypic, genotypic, and other -omic level data currently available to the maize community, now is the time to explore the implications of their incorporation into GS models and thus ensure that genetic gains are being achieved as quickly and efficiently as possible.

The regulatory landscape of early maize inflorescence development.

BACKGROUND: The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. RESULT: Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. CONCLUSIONS: These analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

Multi-Trait Genome-Wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture.

Maize inflorescence is a complex phenotype that involves the physical and developmental interplay of multiple traits. Given the evidence that genes could pleiotropically contribute to several of these traits, we used publicly available maize data to assess the ability of multivariate genome-wide association study (GWAS) approaches to identify pleiotropic quantitative trait loci (pQTL). Our analysis of 23 publicly available inflorescence and leaf-related traits in a diversity panel of n = 281 maize lines genotyped with 376,336 markers revealed that the two multivariate GWAS approaches we tested were capable of identifying pQTL in genomic regions coinciding with similar associations found in previous studies. We then conducted a parallel simulation study on the same individuals, where it was shown that multivariate GWAS approaches yielded a higher true-positive quantitative trait nucleotide (QTN) detection rate than comparable univariate approaches for all evaluated simulation settings except for when the correlated simulated traits had a heritability of 0.9. We therefore conclude that the implementation of state-of-the-art multivariate GWAS approaches is a useful tool for dissecting pleiotropy and their more widespread implementation could facilitate the discovery of genes and other biological mechanisms underlying maize inflorescence.

Genome-Wide Analysis and Prediction of Resistance to Goss's Wilt in Maize.

Goss's bacterial wilt and leaf blight is one of the most important foliar diseases of maize ( L.). To date, neither large-effect resistance genes, nor practical chemical controls exist to manage the disease. Thus, the importance of discovering durable host resistance necessitates additional genetic mapping for this disease. Unfortunately, because of the biology of the pathogen and the highly significant genotype-by-environment interaction effect observed with Goss's wilt, consistent phenotyping across multiple years poses a hurdle for genetic studies and conventional breeding methods. The objective of this study was to perform a genome-wide association study (GWAS) to identify regions of the genome associated with Goss's wilt resistance as well as to use genomic prediction models to evaluate the utility of genomic selection (GS) in predicting Goss's wilt phenotypes in a panel of diverse maize lines. Using genome-wide association mapping, we were unable to identify any variants significantly associated with Goss's wilt. However, using genomic prediction we were able to train a model with an accuracy of 0.69. Taken together, this suggests that resistance to Goss's wilt is highly polygenic. In addition, when evaluating the accuracy of our prediction model under reduced marker density, it was shown that only 10,000 single nucleotide polymorphisms (SNPs), or ∼20% of our total marker set, was necessary to achieve prediction accuracies similar to the full marker set. This is the first report of genomic prediction for a bacterial disease of maize, and these results highlight the potential of GS for disease resistance in maize.