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Original Research ARTICLE

Front. Plant Sci. | doi: 10.3389/fpls.2017.00694

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

Wenbin Mei1, Sanzhen Liu2, 3, James C. Schnable4, Cheng-Ting Yeh2, Nathan M. Springer5, Patrick S. Schnable2, 6 and William B. Barbazuk1, 7*
  • 1Department of Biology, University of Florida, USA
  • 2Agronamy, Iowa State University, USA
  • 3Plant Pathology, Kansas State University, USA
  • 4Agronomy and Horticulture, University of Nebraska-Lincoln, USA
  • 5Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, USA
  • 6Center for Plant Genomics, Iowa State University, USA
  • 7University of Florida Genetics Instiute, USA

Identifying and characterizing alternative splicing (AS) enables our understanding of the biological role of transcript isoform diversity. This study describes the use of publicly available RNA-Seq data to identify and characterize the global diversity of AS isoforms in maize using the inbred lines B73 and Mo17, and a related species, sorghum. Identification and characterization of AS within maize tissues revealed that genes expressed in seed exhibit the largest differential AS relative to other tissues examined. Additionally, differences in AS between the two genotypes B73 and Mo17 are greatest within genes expressed in seed. We demonstrate that changes in the level of alternatively spliced transcripts (intron retention and exon skipping) do not solely reflect differences in total transcript abundance, and we present evidence that intron retention may act to fine-tune gene expression across seed development stages. Furthermore, we have identified temperature sensitive AS in maize and demonstrate that drought-induced changes in alternative splicing involve distinct sets of genes in reproductive and vegetative tissues. Examining our identified AS isoforms within B73 x Mo17 recombinant inbred lines (RILs) identified splicing QTL (sQTL). 43.3% of cis-sQTL regulated junctions are actually identified as alternative spliced junctions in our analysis, while 10 Mb windows on each side of 48.2% of trans-sQTLs overlap with splicing related genes. Using sorghum as an out-group enabled direct examination of loss or conservation of AS between homeologous genes representing the two subgenomes of maize. We identify several instances where AS isoforms that are conserved between one maize homeologue and its sorghum orthologue are absent from the second maize homeologue, suggesting that these AS isoforms may have been lost after the maize whole genome duplication event. This comprehensive analysis provides new insights into the complexity of AS in maize.

Keywords: Alternative Splicing, Maize, Sorghum, seed development, abiotic stress, splicing QTL, Whole genome duplication

Citation: Mei W, Liu S, Schnable JC, Yeh C, Springer NM, Schnable PS and Barbazuk WB (2017). A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize. Front. Plant Sci. 8:694. doi: 10.3389/fpls.2017.00694

Received: 15 Nov 2016; Accepted: 18 Apr 2017.

Edited by:

Ann E. Stapleton, University of North Carolina at Wilmington, USA

Reviewed by:

Asa Ben-Hur, Colorado State University, USA
Stephen M. Mount, University of Maryland, College Park, USA
Paula Casati, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina  

Copyright: © 2017 Mei, Liu, Schnable, Yeh, Springer, Schnable and Barbazuk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. William B. Barbazuk, University of Florida, Department of Biology, Gainesville, 32611, Florida, USA, bbarbazuk@ufl.edu