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1. Elucidating the patterns of pleiotropy and its biological relevance in maize

   https://doi.org/10.1371/journal.pgen.1010664  

   Khaipho-Burch, Merritt; Ferebee, Taylor; Giri, Anju; Ramstein, Guillaume; Monier, Brandon; Yi, Emily; Romay, M. Cinta; Buckler, Edward S. (March 2023, PLOS Genetics)

   Qu, Li-Jia (Ed.)

   Pleiotropy—when a single gene controls two or more seemingly unrelated traits—has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56–32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low. 

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2. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

   https://doi.org/10.1371/journal.pgen.1011086  

   Munasinghe, Manisha; Read, Andrew; Stitzer, Michelle C.; Song, Baoxing; Menard, Claire C.; Ma, Kristy Yubo; Brandvain, Yaniv; Hirsch, Candice N.; Springer, Nathan (December 2023, PLOS Genetics)

   VITTE, Clémentine (Ed.)

   Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated forde novogenome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences. 

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3. Regulatory variation controlling architectural pleiotropy in maize

   https://doi.org/10.1038/s41467-025-56884-w  

   Bertolini, Edoardo; Rice, Brian R; Braud, Max; Yang, Jiani; Hake, Sarah; Strable, Josh; Lipka, Alexander E; Eveland, Andrea L (March 2025, Nature Communications)

   Abstract An early event in plant organogenesis is establishment of a boundary between the stem cell containing meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we use regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses. In addition to defining network plasticity around core pleiotropic loci, we identify new transcription factors that contribute to phenotypic variation in canopy architecture, and structural variation that contributes tocis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific developmental networks to pinpoint pleiotropic loci and theircis-regulatory components, which can be used to fine-tune plant architecture for crop improvement. 

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4. An ancient origin of the naked grains of maize

   https://doi.org/10.1073/pnas.2503748122  

   Fairbanks, Regina A; Ross-Ibarra, Jeffrey (June 2025, Proceedings of the National Academy of Sciences)

   Adaptation to novel environments requires genetic variation, but whether adaptation typically acts upon preexisting genetic variation or must wait for new mutations remains a fundamental question in evolutionary biology. Selection during domestication has been long used as a model to understand evolutionary processes, providing information not only on the phenotypes selected but also, in many cases, an understanding of the causal loci. For each of the causal loci that have been identified in maize, the selected allele can be found segregating in natural populations, consistent with their origin as standing genetic variation. The sole exception to this pattern is the well-characterized domestication locustga1(teosinte glume architecture1), which has long been thought to be an example of selection on a de novo mutation. Here, we use a large dataset of maize and teosinte genomes to reconstruct the origin and evolutionary history oftga1. We first estimated the age oftga1-maizeusing a genealogy-based method, finding that the allele arose approximately 42,000 to 49,000 y ago, predating the beginning of maize domestication. We also identifytga1-maizein teosinte populations, indicating that the allele can survive in the wild. Finally, we compare observed patterns of haplotype structure and mutational age distributions neartga1with simulations, finding that patterns neartga1in maize better resemble those generated under simulated selective sweeps on standing variation. These multiple lines of evidence suggest that maize domestication likely drew upon standing genetic variation attga1and cement the importance of standing variation in driving adaptation during domestication. 

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5. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time

   https://doi.org/10.1073/pnas.2100036119  

   Barnes, Allison C.; Rodríguez-Zapata, Fausto; Juárez-Núñez, Karla A.; Gates, Daniel J.; Janzen, Garrett M.; Kur, Andi; Wang, Li; Jensen, Sarah E.; Estévez-Palmas, Juan M.; Crow, Taylor M.; et al (July 2022, Proceedings of the National Academy of Sciences)

   Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time. 

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