title: Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.
abstract: Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Shawn R
authors.initials: SR
authors.lastname: Thatcher
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Olga N
authors.identifier: http://orcid.org/0000-0002-3996-6617
authors.initials: ON
authors.lastname: Danilevskaya
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Xin
authors.initials: X
authors.lastname: Meng
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Mary
authors.initials: M
authors.lastname: Beatty
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Gina
authors.initials: G
authors.lastname: Zastrow-Hayes
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Charlotte
authors.initials: C
authors.lastname: Harris
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Brandon
authors.identifier: http://orcid.org/0000-0002-0092-6845
authors.initials: B
authors.lastname: Van Allen
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.).
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Habben
authors.affiliation: DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.) bailin.li@cgr.dupont.com.
authors.forename: Bailin
authors.initials: B
authors.lastname: Li
mesh_terms: D017398:Alternative Splicing; D055864:Droughts; D056625:Endosperm / Q000235:genetics / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D055106:Genome-Wide Association Study; D059365:Nonsense Mediated mRNA Decay; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics; D012639:Seeds / Q000235:genetics / Q000254:growth & development; D013312:Stress, Physiological / Q000235:genetics; D003313:Zea mays / Q000235:genetics / Q000254:growth & development / Q000502:physiology*
chemical_list: D010940:Plant Proteins