The Genetic Regulation of Alternative Splicing in Populus deltoides

Jerald D Noble; Kelly M Balmant; Christopher Dervinis; Gustavo de Los Campos; Márcio F R Resende Jr; Matias Kirst; William Brad Barbazuk

doi:10.3389/fpls.2020.00590

The Genetic Regulation of Alternative Splicing in Populus deltoides

Front Plant Sci. 2020 Jun 5:11:590. doi: 10.3389/fpls.2020.00590. eCollection 2020.

Authors

Jerald D Noble¹, Kelly M Balmant², Christopher Dervinis², Gustavo de Los Campos^{3

4}, Márcio F R Resende Jr^{1

5}, Matias Kirst^{1

2

6}, William Brad Barbazuk^{1

6

7

8}

Affiliations

¹ Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States.
² School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States.
³ Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States.
⁴ Department of Statistics and Probability, Michigan State University, East Lansing, MI, United States.
⁵ Department of Horticultural Science, University of Florida, Gainesville, FL, United States.
⁶ Genetics Institute, University of Florida, Gainesville, FL, United States.
⁷ Department of Biology, University of Florida, Gainesville, FL, United States.
⁸ Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States.

Abstract

Alternative splicing (AS) is a mechanism of regulation of the proteome via enabling the production of multiple mRNAs from a single gene. To date, the dynamics of AS and its effects on the protein sequences of individuals in a large and genetically unrelated population of trees have not been investigated. Here we describe the diversity of AS events within a previously genotyped population of 268 individuals of Populus deltoides and their putative downstream functional effects. Using a robust bioinformatics pipeline, the AS events and resulting transcript isoforms were discovered and quantified for each individual in the population. Analysis of the AS revealed that, as expected, most AS isoforms are conserved. However, we also identified a substantial collection of new, unannotated splice junctions and transcript isoforms. Heritability estimates for the expression of transcript isoforms showed that approximately half of the isoforms are heritable. The genetic regulators of these AS isoforms and splice junction usage were then identified using a genome-wide association analysis. The expression of AS isoforms was predominately cis regulated while splice junction usage was generally regulated in trans. Additionally, we identified 696 genes encoding alternatively spliced isoforms that changed putative protein domains relative to the longest protein coding isoform of the gene, and 859 genes exhibiting this same phenomenon relative to the most highly expressed isoform. Finally, we found that 748 genes gained or lost micro-RNA binding sites relative to the longest protein coding isoform of a given gene, while 940 gained or lost micro-RNA binding sites relative to the most highly expressed isoform. These results indicate that a significant fraction of AS events are genetically regulated and that this isoform usage can result in protein domain architecture changes.

Keywords: alternative splicing; isoform; poplar; population; protein domain; splicing QTL; transcriptome.