Aimee J Schulz

Cornell University

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i-10 index

Research Trends

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Document Type

Co-Authors

Edward S. Buckler

Agricultural Research Service

M. Cinta Romay

Cornell University

Matthew B. Hufford

Iowa State University

Michelle C. Stitzer

Cornell University

Taylor AuBuchon‐Elder

Missouri Botanical Garden

Sheng‐Kai Hsu

Cornell University

Brandon Monier

Cornell University

Jeffrey Ross‐Ibarra

University of California, Davis

Thuy La

Cornell University

Elizabeth A. Kellogg

Donald Danforth Plant Science Center

Cooperative Institutions

Cornell University

Agricultural Research Service

Plant (United States)

University of California, Davis

United States Department of Agriculture

University of Missouri

Iowa State University

Corteva (United States)

Pioneer Hi-Bred

National Institute of Genomic Medicine

Author Statistics

Papers

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Contrasting Rhizosphere Nitrogen Dynamics in Andropogoneae Grasses: Implications for Sustainable Agriculture

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Sheng‐Kai Hsu Bryan D. Emmett Alexandria J Haffke Germano Costa‐Neto Aimee J Schulz

Background: Nitrogen (N) fertilization in crop production significantly impacts ecosystems, often disrupting natural plant-microbe-soil interactions and causing environmental pollution. Our research tested the hypothesis that phylogenetically related perennial grasses might preserve rhizosphere management strategies conducive to a sustainable N economy for crops. Method: We analyzed the N cycle in the rhizospheres of 36 Andropogoneae grass species related to maize and sorghum, investigating their impacts on N availability and losses. This assay is supplemented with the collection and comparison of native habitat environment data for ecological inference as well as cross-species genomic and transcriptomic association analyses for candidate gene discovery. Result: Contrary to our hypothesis, all examined annual species, including sorghum and maize, functioned as N "Conservationists," reducing soil nitrification potential and conserving N. In contrast, some perennial species enhanced nitrification and leaching ("Leachers"). Yet a few other species exhibited similar nitrification stimulation effects but limited NO3- losses ("Nitrate Keepers"). We identified significant soil characteristics as influential factors in the eco-evolutionary dynamics of plant rhizospheres, and highlighted the crucial roles of a few transporter genes in soil N management and utilization. Conclusion: These findings serve as valuable guidelines for future breeding efforts for global sustainability.

10.1101/2024.06.03.597142

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Muller’s Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Evan Long Michelle C. Stitzer Brandon Monier Aimee J Schulz M. Cinta Romay

Abstract Centuries of clonal propagation in cassava ( Manihot esculenta ) have engaged Muller’s Ratchet, leading to the accumulation of deleterious mutations due to the absence of sexual recombination. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of the Euphorbiaceae family, including notable species such as rubber tree (Hevea brasiliensis) and poinsettia (Euphorbia pulcherrima). Expanding upon preliminary draft genomes, we annotated 7 long-read genome assemblies and aligned a total of 52 genomes, to analyze selection across the genome and the phylogeny. Through this comparative genomic approach, we identified 48 genes under relaxed selection in cassava. Notably, we discovered an overrepresentation of floral expressed genes, especially focused at six pollen-related genes. Our results indicate that domestication and a transition to clonal propagation has reduced selection pressures on sexually reproductive functions in cassava leading to an accumulation of mutations in pollen-related genes. This relaxed selection and the genome-wide deleterious mutations responsible for inbreeding depression are potential targets for improving cassava breeding, where the generation of new varieties relies on recombining favorable alleles through sexual reproduction.

Manihot esculenta

Sexual reproduction

10.1101/2024.02.14.580345

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Fishing for a reelGene: evaluating gene models with evolution and machine learning

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Aimee J Schulz Jingjing Zhai Taylor AuBuchon‐Elder Mohamed El-Walid Taylor H. Ferebee

Abstract Assembled genomes and their associated annotations have transformed our study of gene function. However, each new assembly generates new gene models. Inconsistencies between annotations likely arise from biological and technical causes, including pseudogene misclassification, transposon activity, and intron retention from sequencing of unspliced transcripts. To evaluate gene model predictions, we developed reelGene, a pipeline of machine learning models focused on (1) transcription boundaries, (2) mRNA integrity, and (3) protein structure. The first two models leverage sequence characteristics and evolutionary conservation across related taxa to learn the grammar of conserved transcription boundaries and mRNA sequences, while the third uses conserved evolutionary grammar of protein sequences to predict whether a gene can produce a protein. Evaluating 1.8 million gene models in maize, reelGene found that 28% were incorrectly annotated or nonfunctional. By leveraging a large cohort of related species and through learning the conserved grammar of proteins, reelGene provides a tool for both evaluating gene model accuracy and genome biology.

Pseudogene

Conserved sequence

Leverage (statistics)

Gene prediction

10.1101/2023.09.19.558246

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Allele-specific expression reveals multiple paths to highland adaptation in maize

bioRxiv (Cold Spring Harbor Laboratory) (2022)

Haixiao Hu Taylor M. Crow Saghi Nojoomi Aimee J Schulz Matthew B. Hufford

Abstract Maize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggests the maize’s adaptation to these regions occurred largely independently, providing a case study for parallel evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F 1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis- regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis- regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence. Our findings reveal a complex genetic architecture of cis -regulatory alleles underlying adaptation to highlands in maize. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.

Convergent evolution

Local adaptation

Genetic architecture

10.1101/2022.07.15.500250

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Citations (1)

Inbreeding depression leads to reduced fitness in declining populations of wild maize

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Aimee J Schulz David E. Hufnagel Paul Gepts Matthew B. Hufford

Abstract Crop wild relatives can serve as a source of variation for the genetic improvement of modern varieties. However, the realization of this genetic potential depends critically on the conservation of wild populations. In this study, five populations of Zea mays ssp. parviglumi s, the closest relative of domesticated maize, were collected in Jalisco, Mexico and planted in a common garden. Eleven traits related to plant fitness were measured and evaluated in the context of genetic diversity and genetic load. Plants whose seed were sourced from larger, less disturbed populations had greater genetic diversity, lower genetic load, and possessed phenotypes associated with higher fitness, while plants sourced from smaller, heavily impacted populations had traits characteristic of lower fitness and increased genetic load. For example, plants from larger populations germinated more quickly, reached anthesis sooner, demonstrated a higher level of photosynthetic activity, and produced more above-ground biomass, suggesting a direct correlation between the fitness of a population, genetic diversity, and genetic load. These results emphasize the importance of preserving the habitat of populations of Zea mays ssp. parviglumis to limit inbreeding depression and maintain the genetic diversity and adaptive potential of this germplasm.

Genetic load

Germ plasm

Genetic Variability

10.1101/2023.11.20.567972

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Extensive genome evolution distinguishes maize within a stable tribe of grasses

bioRxiv (Cold Spring Harbor Laboratory) (2025)

Michelle C. Stitzer Arun S. Seetharam Armin Scheben Sheng‐Kai Hsu Aimee J Schulz

Abstract Over the last 20 million years, the Andropogoneae tribe of grasses has evolved to dominate 17% of global land area. Domestication of these grasses in the last 10,000 years has yielded our most productive crops, including maize, sugarcane, and sorghum. The majority of Andropogoneae species, including maize, show a history of polyploidy – a condition that, while offering the evolutionary advantage of multiple gene copies, poses challenges to basic cellular processes, gene expression, and epigenetic regulation. Genomic studies of polyploidy have been limited by sparse sampling of taxa in groups with multiple polyploidy events. Here, we present 33 genome assemblies from 27 species, including chromosome-scale assemblies of maize relatives Zea and Tripsacum . In maize, the after-effects of polyploidy have been widely studied, showing reduced chromosome number, biased fractionation of duplicate genes, and transposable element (TE) expansions. While we observe these patterns within the genus Zea , 12 other polyploidy events deviate significantly. Those tetraploids and hexaploids retain elevated chromosome number, maintain nearly complete complements of duplicate genes, and have only stochastic TE amplifications. These genomes reveal variable outcomes of polyploidy, challenging simple predictions and providing a foundation for understanding its evolutionary implications in an ecologically and economically important clade.

Tribe

10.1101/2025.01.22.633974

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Evolutionary Signatures of The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)

G3 Genes Genomes Genetics (2024)

Evan Long Michelle C. Stitzer Brandon Monier Aimee J Schulz M. Cinta Romay

Abstract Centuries of clonal propagation in cassava (Manihot esculenta) have reduced sexual recombination, leading to the accumulation of deleterious mutations. This has resulted in both inbreeding depression affecting yield and a significant decrease in reproductive performance, creating hurdles for contemporary breeding programs. Cassava is a member of the Euphorbiaceae family, including notable species such as rubber tree (Hevea brasiliensis) and poinsettia (Euphorbia pulcherrima). Expanding upon preliminary draft genomes, we annotated 7 long-read genome assemblies and aligned a total of 52 genomes, to analyze selection across the genome and the phylogeny. Through this comparative genomic approach, we identified 48 genes under relaxed selection in cassava. Notably, we discovered an overrepresentation of floral expressed genes, especially focused at six pollen-related genes. Our results indicate that domestication and a transition to clonal propagation has reduced selection pressures on sexually reproductive functions in cassava leading to an accumulation of mutations in pollen-related genes. This relaxed selection and the genome-wide deleterious mutations responsible for inbreeding depression are potential targets for improving cassava breeding, where the generation of new varieties relies on recombining favorable alleles through sexual reproduction.

Sexual reproduction

Euphorbiaceae

10.1093/g3journal/jkae282

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Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize

Molecular Biology and Evolution (2022)

Haixiao Hu Taylor M. Crow Saghi Nojoomi Aimee J Schulz Juan M Estévez-Palmas

Maize is a staple food of smallholder farmers living in highland regions up to 4,000 m above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggest the maize's adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.

Convergent evolution

Local adaptation

Gene pool

10.1093/molbev/msac239

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Citations (11)