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SUMMARY: Ear length (EL) is a key trait that greatly contributes to yield in maize. Although dozens of EL quantitative trait loci have been mapped, very few causal genes have been cloned, and the molecular mechanisms remain largely unknown. Our previous study showed that YIGE1 is involved in sugar and auxin pathways to regulate ear inflorescence meristem (IM) development and thus affects EL in maize. Here, we reveal that YIGE2, the paralog of YIGE1, regulates maize ear development and EL through auxin pathway. Knockout of YIGE2 causes a significant decrease of auxin level, IM length, floret number, EL, and grain yield. yige1 yige2 double mutants had even shorter IM and ears implying that these two genes redundantly regulate IM development and EL. The genes controlling auxin levels are differential expressed in yige1 yige2 double mutants, leading to lower auxin level. These results elucidated the critical role of YIGE2 and the redundancy between YIGE2 and YIGE1 in maize ear development, providing a new genetic resource for maize yield improvement. [ABSTRACT FROM AUTHOR]

SUMMARY: Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple‐level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements. Significance Statement: This review emphasizes the progress made toward the applications and perspectives of omics technologies in the exploration of key genes involved in oil and fatty acid accumulation in major oilseed, thereby providing targets for genetically engineered oil plants. [ABSTRACT FROM AUTHOR]

The Plant Journal has published a collection of Resource Articles over the past decade, which cover a wide range of topics in plant biology. These articles provide valuable databases and research-based information on subjects such as genome assembly, gene function prediction, and stress responses in plants. The authors highlight the significance of these articles in advancing plant biology and encourage the submission of future articles in these areas. These resources are beneficial for researchers studying various plant species and biological processes. [Extracted from the article]

SUMMARY: Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high‐quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome‐wide association and transcriptome‐wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes. Significance Statement: This article reviews how sequencing technology has boosted pangenomics, promoted analysis of more complex genetic variations and single‐cell omics, and driven recent advances in studying plant physiology and evolution. [ABSTRACT FROM AUTHOR]

SUMMARY: Global agriculture is dominated by a handful of species that currently supply a huge proportion of our food and feed. It additionally faces the massive challenge of providing food for 10 billion people by 2050, despite increasing environmental deterioration. One way to better plan production in the face of current and continuing climate change is to better understand how our domestication of these crops included their adaptation to environments that were highly distinct from those of their centre of origin. There are many prominent examples of this, including the development of temperate Zea mays (maize) and the alteration of day‐length requirements in Solanum tuberosum (potato). Despite the pre‐eminence of some 15 crops, more than 50 000 species are edible, with 7000 of these considered semi‐cultivated. Opportunities afforded by next‐generation sequencing technologies alongside other methods, including metabolomics and high‐throughput phenotyping, are starting to contribute to a better characterization of a handful of these species. Moreover, the first examples of de novo domestication have appeared, whereby key target genes are modified in a wild species in order to confer predictable traits of agronomic value. Here, we review the scale of the challenge, drawing extensively on the characterization of past agriculture to suggest informed strategies upon which the breeding of future climate‐resilient crops can be based. Significance Statement: In this article we summarize recent advances in the understanding of the genetic basis of crop domestication and how this knowledge, combined with state‐of‐the‐art and future tools for gene editing or classical breeding, could open new avenues for establishing crops better suited to future climate conditions. [ABSTRACT FROM AUTHOR]

SUMMARY: Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates. However, it is unclear how evolution contributes to metabolic variation in plants. Here, we investigated the metabolomics data from leaf and seed tissues in maize and rice. Using principal components analysis based on leaf metabolites but not seed metabolites, metabolomics data could be clearly separated for rice Indica and Japonica accessions, while two maize subgroups, temperate and tropical, showed more visible admixture. Rice and maize seed exhibited significant interspecific differences in metabolic variation, while within rice, leaf and seed displayed similar metabolic variations. Among 10 metabolic categories, flavonoids had higher variation in maize than rice, indicating flavonoids are a key constituent of interspecific metabolic divergence. Interestingly, metabolic regulation was also found to be reshaped dramatically from positive to negative correlations, indicative of the differential evolutionary processes in maize and rice. Moreover, perhaps due to this divergence significantly more metabolic interactions were identified in rice than maize. Furthermore, in rice, the leaf was found to harbor much more intense metabolic interactions than the seed. Our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice. Significance Statement: Metabolites are the intermediate and final products of metabolism, which play essential roles in plant growth, evolution and adaptation to changing climates, but it is unclear how evolution contributes to metabolic variation in plants. We investigated the metabolomics data from leaf and seed tissues in maize and rice, and our result suggests that metabolomes are valuable for tracking evolutionary history, thereby complementing and extending genomic insights concerning which features are responsible for interspecific differentiation in maize and rice. [ABSTRACT FROM AUTHOR]

Summary: Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance‐heterogeneity genome‐wide association study to examine the contribution of variance heterogeneity to oil‐related quantitative traits. We identified 79 unique variance‐controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance‐heterogeneity genes for 21 oil‐related traits using the Levene test (P < 1.0 × 10−5). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean‐effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two‐hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high‐oil maize (Zea mays L.). Significance Statement: This work validated the additive manner in which oil concentration is inherited, and can be used to guide the selection of haplotypes for improvement of oil concentration even with low phenotypic variability. However, gene × gene interaction plays a major role in the formation of variance heterogeneity of fatty acid compositional traits, which will allow modification of breeding selection plans to achieve the most efficient means of creating maize lines with the desired fatty acids. [ABSTRACT FROM AUTHOR]

Summary: The nutritional traits of maize kernels are important for human and animal nutrition, and these traits have undergone selection to meet the diverse nutritional needs of humans. However, our knowledge of the genetic basis of selecting for kernel nutritional traits is limited. Here, we identified both single and epistatic quantitative trait loci (QTLs) that contributed to the differences of oil and carotenoid traits between maize and teosinte. Over half of teosinte alleles of single QTLs increased the values of the detected oil and carotenoid traits. Based on the pleiotropism or linkage information of the identified single QTLs, we constructed a trait–locus network to help clarify the genetic basis of correlations among oil and carotenoid traits. Furthermore, the selection features and evolutionary trajectories of the genes or loci underlying variations in oil and carotenoid traits revealed that these nutritional traits produced diverse selection events during maize domestication and improvement. To illustrate more, a mutator distance–relative transposable element (TE) in intron 1 of DXS2, which encoded a rate‐limiting enzyme in the methylerythritol phosphate pathway, was identified to increase carotenoid biosynthesis by enhancing DXS2 expression. This TE occurs in the grass teosinte, and has been found to have undergone selection during maize domestication and improvement, and is almost fixed in yellow maize. Our findings not only provide important insights into evolutionary changes in nutritional traits, but also highlight the feasibility of reintroducing back into commercial agricultural germplasm those nutritionally important genes hidden in wild relatives. Significance Statement: The identification and selection‐feature characterization of genetic loci contributing to nutritional trait variation between maize and teosinte is of fundamental importance in understanding the evolutionary interface between plant and human. Most favorable alleles associated with nutritional traits exist in teosinte and are not fixed in modern maize, underscoring the potential benefit of introducing teosinte alleles during maize breeding regimens to yield hybrids with desirable nutritional traits. [ABSTRACT FROM AUTHOR]

Summary: Phytol is one of the key precursors for tocopherol synthesis in plants, however, the underlying mechanisms concerning the accumulation of tocopherol remain poorly understood. In this study, qVE5, a major QTL affecting tocopherol accumulation in maize kernels was identified via a positional cloning approach. qVE5 encodes a protochlorophyllide oxidoreductase (ZmPORB2), which localizes to the chloroplast. Overexpression of ZmPORB2 increased tocopherol content in both leaves and kernels. Candidate gene association analysis identified a 5/8‐bp insertion/deletion (InDel058) in the 5′ untranslated region (UTR) as the causal polymorphism in affecting ZmPORB2 expression and being highly associated with tocopherol content. We showed that higher expression of ZmPORB2 correlated with more chlorophyll metabolites in the leaf following pollination. RNA‐sequencing and metabolic analysis in near isogenic lines (NILs) support that ZmPORB2 participates in chlorophyll metabolism enabling the production of phytol, an important precursor of tocopherol. We also found that the tocopherol content in the kernel is mainly determined by the maternal genotype, a fact that was further confirmed by in vitro culture experiments. Finally, a PCR‐based marker based on Indel058 was developed in order to facilitate the high tocopherol (vitamin E) maize breeding. Significance Statement: Known as vitamin E, tocopherol is a lipid‐soluble antioxidant required for plant growth and human health. In this study, characterization of ZmPORB2 involved in chlorophyll metabolism revealed that this gene affects tocopherol content in maize by the maternal genotype and has applicable potential in breeding. [ABSTRACT FROM AUTHOR]

Summary: It is generally recognized that many favorable genes which were lost during domestication, including those related to both nutritional value and stress resistance, remain hidden in wild relatives. To uncover such genes in teosinte, an ancestor of maize, we conducted metabolite profiling in a BC2F7 population generated from a cross between the maize wild relative (Zea mays ssp. mexicana) and maize inbred line Mo17. In total, 65 primary metabolites were quantified in four tissues (seedling‐stage leaf, grouting‐stage leaf, young kernel and mature kernel) with clear tissue‐specific patterns emerging. Three hundred and fifty quantitative trait loci (QTLs) for these metabolites were obtained, which were distributed unevenly across the genome and included two QTL hotspots. Metabolite concentrations frequently increased in the presence of alleles from the teosinte genome while the opposite was observed for grain yield and shape trait QTLs. Combination of the multi‐tissue transcriptome and metabolome data provided considerable insight into the metabolic variations between maize and its wild relatives. This study thus identifies favorable genes hidden in the wild relative which should allow us to balance high yield and quality in future modern crop breeding programs. Significance Statement: A large scale QTL mapping of primary metabolite traits in a teosinte‐maize population reveals robust advantages existing in teosinte primary metabolism. [ABSTRACT FROM AUTHOR]

Summary: Maize (Zea mays mays) oil is a rich source of polyunsaturated fatty acids (FAs) and energy, making it a valuable resource for human food, animal feed, and bio‐energy. Although this trait has been studied via conventional genome‐wide association study (GWAS), the single nucleotide polymorphism (SNP)‐trait associations generated by GWAS may miss the underlying associations when traits are based on many genes, each with small effects that can be overshadowed by genetic background and environmental variation. Detecting these SNPs statistically is also limited by the levels set for false discovery rate. A complementary pathways analysis that emphasizes the cumulative aspects of SNP‐trait associations, rather than just the significance of single SNPs, was performed to understand the balance of lipid metabolism, conversion, and catabolism in this study. This pathway analysis indicated that acyl‐lipid pathways, including biosynthesis of wax esters, sphingolipids, phospholipids and flavonoids, along with FA and triacylglycerol (TAG) biosynthesis, were important for increasing oil and FA content. The allelic variation found among the genes involved in many degradation pathways, and many biosynthesis pathways leading from FAs and carbon partitioning pathways, was critical for determining final FA content, changing FA ratios and, ultimately, to final oil content. The pathways and pathway networks identified in this study, and especially the acyl‐lipid associated pathways identified beyond what had been found with GWAS alone, provide a real opportunity to precisely and efficiently manipulate high‐oil maize genetic improvement. Significance Statement: This pathway analysis provided insights into the genetic basis of lipid metabolism, beyond what could be detected via GWAS alone, and indicated specific opportunities to precisely and efficiently manipulate high‐oil maize genetic improvement. [ABSTRACT FROM AUTHOR]

Summary: With the advent of rapid genotyping and next‐generation sequencing technologies, genome‐wide association study (GWAS) has become a routine strategy for decoding genotype–phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype–phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many 'hits' obtained, this review summarizes recent efforts to increase our understanding of the genetic architecture of complex traits by focusing on non‐main effects including epistasis, pleiotropy, and phenotypic plasticity. We also discuss how these achievements and the remaining gaps in our knowledge will guide future studies. Synthetic association is highlighted as leading to false causality, which is prevalent but largely underestimated. Furthermore, validation evidence is appealing for future GWAS, especially in the context of emerging genome‐editing technologies. Significance Statement: This review summarizes the latest advances in generating an overall view of the genetic architecture associated with crop complex traits, and discusses how these updated insights will guide future studies. A multiple‐causal‐allele hypothesis was formulated to explain the increasingly common artifact/synthetic associations. [ABSTRACT FROM AUTHOR]

SUMMARY: Primary metabolism plays a pivotal role in normal plant growth, development and reproduction. As maize is a major crop worldwide, the primary metabolites produced by maize plants are of immense importance from both calorific and nutritional perspectives. Here a genome‐wide association study (GWAS) of 61 primary metabolites using a maize association panel containing 513 inbred lines identified 153 significant loci associated with the level of these metabolites in four independent tissues. The genome‐wide expression level of 760 genes was also linked with metabolite levels within the same tissue. On average, the genetic variants at each locus or transcriptional variance of each gene identified here were estimated to have a minor effect (4.4–7.8%) on primary metabolic variation. Thirty‐six loci or genes were prioritized as being worthy of future investigation, either with regard to functional characterization or for their utility for genetic improvement. This target list includes the well‐known opaque 2 (O2) and lkr/sdh genes as well as many less well‐characterized genes. During our investigation of these 36 loci, we analyzed the genetic components and variations underlying the trehalose, aspartate and aromatic amino acid pathways, thereby functionally characterizing four genes involved in primary metabolism in maize. [ABSTRACT FROM AUTHOR]

Summary: Maize is the cereal crop with the highest production worldwide, and its oil is a key energy resource. Improving the quantity and quality of maize oil requires a better understanding of lipid metabolism. To predict the function of maize genes involved in lipid biosynthesis, we assembled transcriptomic and lipidomic data sets from leaves of B73 and the high‐oil line By804 in two distinct time‐series experiments. The integrative analysis based on high‐dimensional regularized regression yielded lipid–transcript associations indirectly validated by Gene Ontology and promoter motif enrichment analyses. The co‐localization of lipid‐transcript associations using the genetic mapping of lipid traits in leaves and seedlings of a B73 × By804 recombinant inbred line population uncovered 323 genes involved in the metabolism of phospholipids, galactolipids, sulfolipids and glycerolipids. The resulting association network further supported the involvement of 50 gene candidates in modulating levels of representatives from multiple acyl‐lipid classes. Therefore, the proposed approach provides high‐confidence candidates for experimental testing in maize and model plant species. [ABSTRACT FROM AUTHOR]