Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development

Huanan Zhang, Feng Cheng, Yuguo Xiao, Xiaojun Kang, Xiaowu Wang, Rui Kuang, Min Ni

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Seed development in dicots includes early endosperm proliferation followed by growth of the embryo to replace the endosperm. Endosperm proliferation in dicots not only provides nutrient supplies for subsequent embryo development but also enforces a space limitation, influencing final seed size. Overexpression of Arabidopsis SHORT HYPOCOTYL UNDER BLUE1::uidA (SHB1:uidA) in canola produces large seeds. We performed global analysis of the canola genes that were expressed and influenced by SHB1 during early endosperm proliferation at 8 days after pollination (DAP) and late embryo development at 13 DAP. Overexpression of SHB1 altered the expression of 973 genes at 8 DAP and 1035 genes at 13 DAP. We also surveyed the global SHB1 association sites, and merging of these sites with the RNA sequencing data identified a set of canola genes targeted by SHB1. The 8-DAP list includes positive and negative genes that influence endosperm proliferation and are homologous to Arabidopsis MINI3, IKU2, SHB1, AGL62, FIE and AP2. We revealed a major role for SHB1 in canola endosperm development based on the dynamics of SHB1-altered gene expression, the magnitude of SHB1 chromatin immunoprecipitation enrichment and the over-representation of eight regulatory genes for endosperm development. Our studies focus on an important agronomic trait in a major crop for global agriculture. The datasets on stage-specific and SHB1-induced gene expression and genes targeted by SHB1 also provide a useful resource in the field of endosperm development and seed size engineering. Our practices in an allotetraploid species will impact similar studies in other crop species.

Original languageEnglish (US)
Pages (from-to)158-171
Number of pages14
JournalPlant Journal
Volume91
Issue number1
DOIs
StatePublished - Jul 2017

Bibliographical note

Funding Information:
We thank the Genomics Center at the University of Minnesota (http://www.health.umn.edu/research/resources-researchers/genomics-center) for high-throughput sequencing. Canola transgenic lines were generated in the Ralph M. Parsons Foundation Plant Transformation Facility at the University of California at Davis (http://ucdptf.ucdavis.edu/). This work was supported by grant no. 2011-67013-30150 from the USDA National Institution of Food and Agriculture to MN and RK, grant no. IIS 1149697 from the National Science Foundation to RK and grant no. 2012CB113900 from the Ministry of Science and Technology of China to XW and FC. This work was also supported by the science and technology innovation program of the Chinese Academy of Agricultural Sciences to XW and FC, and the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, the Ministry of Agriculture of P. R. China to XW and FC. The authors have no conflict of interest to declare.

Publisher Copyright:
© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd

Keywords

  • Brassica napus
  • ChIP-seq
  • RNA-seq
  • SHB1
  • canola
  • embryo development
  • endosperm proliferation

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