title: Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.
abstract: Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880.
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Thatcher
authors.affiliation: DuPont Pioneer, Johnston, Iowa 50131.
authors.forename: Wengang
authors.initials: W
authors.lastname: Zhou
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880.
authors.forename: April
authors.initials: A
authors.lastname: Leonard
authors.affiliation: DuPont Pioneer, Johnston, Iowa 50131 Huazhi Rice Biotech Company, Changsha, Hunan 410125, China.
authors.forename: Bing-Bing
authors.initials: BB
authors.lastname: Wang
authors.affiliation: DuPont Pioneer, Johnston, Iowa 50131.
authors.forename: Mary
authors.initials: M
authors.lastname: Beatty
authors.affiliation: DuPont Pioneer, Johnston, Iowa 50131.
authors.forename: Gina
authors.initials: G
authors.lastname: Zastrow-Hayes
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 Shandong Agricultural University, Shandong 271000, China.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Zhao
authors.affiliation: DuPont Pioneer, Johnston, Iowa 50131.
authors.forename: Andy
authors.initials: A
authors.lastname: Baumgarten
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 bailin.li@cgr.dupont.com.
authors.forename: Bailin
authors.initials: B
authors.lastname: Li
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D009928:Organ Specificity / Q000235:genetics; D010940:Plant Proteins / Q000378:metabolism; D016133:Polymerase Chain Reaction; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000378:metabolism; D040641:Quantitative Trait Loci / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D003313:Zea mays / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D020033:Protein Isoforms; D020543:Proteome; D012333:RNA, Messenger