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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #417840
Research Project: Enabling Mechanistic Allele Mining to Accelerate Genomic Selection for New Agro-Ecosystems

Location: Plant, Soil and Nutrition Research

Title: Transposable element abundance subtly contributes to lower fitness in maize

Author
item STITZER, MICHELLE - Cornell University
item KHAIPHO-BURCH, MERRITT - Cornell University
item HUDSON, ASHER - North Carolina State University
item SONG, BAOXING - Peking University
item VALDEZ-FRANCO, JOSE ARCADIO - Cornell University
item RAMSTEIN, GUILLAUME - Aarhuis University
item FESCHOTTE, CEDRIC - Cornell University
item Buckler, Edward - Ed

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 9/18/2023
Publication Date: 9/18/2023
Citation: Stitzer, M.C., Khaipho-Burch, M.B., Hudson, A.L., Song, B., Valdez-Franco, J., Ramstein, G., Feschotte, C., Buckler Iv, E.S. 2023. Transposable element abundance subtly contributes to lower fitness in maize. bioRxiv. https://doi.org/10.1101/2023.09.18.557618.
DOI: https://doi.org/10.1101/2023.09.18.557618

Interpretive Summary: This study explores the impact of transposable elements (TEs) on maize fitness. TEs are DNA sequences that can move around the genome, potentially causing harmful mutations. Researchers used data from nearly 5,000 maize inbred lines to measure TE content and its effect on grain yield, an important indicator of reproductive success. They found that higher TE content is associated with slightly lower yield, suggesting that while TEs contribute to genetic diversity, they also impose a small fitness cost. This research provides valuable insights into the balance between genetic variation and fitness in crop plants.

Technical Abstract: Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants.