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1. 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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2. A biphasic trajectory for maize stalk mechanics shaped by genetic, environmental, and biotic factors

   https://doi.org/10.1111/tpj.70342  

   Ikiriko, Irene_I; Hostetler, Ashley_N; Reneau, Jonathan_W; Betts, Alyssa_K; Sparks, Erin_E (July 2025, The Plant Journal)

   SUMMARY Stalk mechanical properties impact plant stability and interactions with pathogenic microorganisms. The evaluation of stalk mechanics has focused primarily on the end‐of‐season outcomes and defined differences among inbred and hybrid maize genotypes. However, there is a gap in understanding how these different end‐of‐season outcomes are achieved. This study measured stalk flexural stiffness in maize inbred genotypes across multiple environments and in maize commercial hybrid genotypes under different disease states. Under all conditions, stalk flexural stiffness followed a biphasic trajectory, characterized by a linear increase phase and a sustained phase. Within a genotype, the environment or disease state altered the rate of increase in the linear phase but did not impact the timing of transition to the sustained phase. Whereas between genotypes, the timing of transition between phases varied. Destructive 3‐point bend tests of inbred stalks showed that the trajectory of stalk mechanics is defined by the bending modulus, not the geometry. Together, these results define a biphasic trajectory of maize stalk mechanics that can be modulated by internal and external factors. This work provides a foundation for breeding programs to make informed decisions when selecting for optimized stalk mechanical trajectories, which are necessary for enhancing resilience to environmental stresses. 

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3. A key to totipotency: Wuschel‐like homeobox 2a unlocks embryogenic culture response in maize ( Zea mays L.)

   https://doi.org/10.1111/pbi.14098  

   McFarland, Frank L.; Collier, Ray; Walter, Nathalie; Martinell, Brian; Kaeppler, Shawn M.; Kaeppler, Heidi F. (June 2023, Plant Biotechnology Journal)

   Summary The ability of plant somatic cells to dedifferentiate, form somatic embryos and regenerate whole plantsin vitrohas been harnessed for both clonal propagation and as a key component of plant genetic engineering systems. Embryogenic culture response is significantly limited, however, by plant genotype in most species. This impedes advancements in both plant transformation‐based functional genomics research and crop improvement efforts. We utilized natural variation among maize inbred lines to genetically map somatic embryo generation potential in tissue culture and identify candidate genes underlying totipotency. Using a series of maize lines derived from crosses involving the culturable parent A188 and the non‐responsive parent B73, we identified a region on chromosome 3 associated with embryogenic culture response and focused on three candidate genes within the region based on genetic position and expression pattern. Two candidate genes showed no effect when ectopically expressed in B73, but the geneWox2awas found to induce somatic embryogenesis and embryogenic callus proliferation. Transgenic B73 cells with strong constitutive expression of the B73 and A188 coding sequences ofWox2awere found to produce somatic embryos at similar frequencies, demonstrating that sufficient expression of either allele could rescue the embryogenic culture phenotype. Transgenic B73 plants were regenerated from the somatic embryos without chemical selection and no pleiotropic effects were observed in theWox2aoverexpression lines in the regenerated T0 plants or in the two independent events which produced T1 progeny. In addition to linking natural variation in tissue culture response toWox2a, our data support the utility ofWox2ain enabling transformation of recalcitrant genotypes. 

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4. An Improved Agrobacterium-Mediated Transformation and Genome-Editing Method for Maize Inbred B104 Using a Ternary Vector System and Immature Embryos

   https://doi.org/10.3389/fpls.2022.860971  

   Kang, Minjeong; Lee, Keunsub; Finley, Todd; Chappell, Hal; Veena, Veena; Wang, Kan (May 2022, Frontiers in Plant Science)

   For maize genome-editing and bioengineering, genetic transformation of inbred genotypes is most desired due to the uniformity of genetic background in their progenies. However, most maize inbred lines are recalcitrant to tissue culture and transformation. A public, transformable maize inbred B104 has been widely used for genome editing in recent years. This is primarily due to its high degree of genetic similarity shared with B73, an inbred of the reference genome and parent of many breeding populations. Conventional B104 maize transformation protocol requires 16–22 weeks to produce rooted transgenic plants with an average of 4% transformation frequency (number of T0 plants per 100 infected embryos). In this Method paper, we describe an advanced B104 transformation protocol that requires only 7–10 weeks to generate transgenic plants with an average of 6.4% transformation frequency. Over 66% of transgenic plants carried CRISPR/Cas9-induced indel mutations on the target gene, demonstrating that this protocol can be used for genome editing applications. Following the detailed and stepwise procedure described here, this quick and simplified method using the Agrobacterium ternary vector system consisting of a T-DNA binary vector and a compatible helper plasmid can be readily transferable to interested researchers. 

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5. Identification of the expressome by machine learning on omics data

   https://doi.org/10.1073/pnas.1813645116  

   Sartor, Ryan C.; Noshay, Jaclyn; Springer, Nathan M.; Briggs, Steven P. (September 2019, Proceedings of the National Academy of Sciences)

   Accurate annotation of plant genomes remains complex due to the presence of many pseudogenes arising from whole-genome duplication-generated redundancy or the capture and movement of gene fragments by transposable elements. Machine learning on genome-wide epigenetic marks, informed by transcriptomic and proteomic training data, could be used to improve annotations through classification of all putative protein-coding genes as either constitutively silent or able to be expressed. Expressed genes were subclassified as able to express both mRNAs and proteins or only RNAs, and CG gene body methylation was associated only with the former subclass. More than 60,000 protein-coding genes have been annotated in the reference genome of maize inbred B73. About two-thirds of these genes are transcribed and are designated the filtered gene set (FGS). Classification of genes by our trained random forest algorithm was accurate and relied only on histone modifications or DNA methylation patterns within the gene body; promoter methylation was unimportant. Other inbred lines are known to transcribe significantly different sets of genes, indicating that the FGS is specific to B73. We accurately classified the sets of transcribed genes in additional inbred lines, arising from inbred-specific DNA methylation patterns. This approach highlights the potential of using chromatin information to improve annotations of functional genes. 

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