Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development.
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.
Department of Computer Science and Engineering, University of Minnesota at Twin Cities, Minneapolis, MN, 55455, USA.
Huanan
H
Zhang
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Feng
F
Cheng
Department of Plant Biology, University of Minnesota at Twin Cities, Saint Paul, MN, 55108, USA.
Yuguo
Y
Xiao
Department of Plant Biology, University of Minnesota at Twin Cities, Saint Paul, MN, 55108, USA.
Xiaojun
X
Kang
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
Xiaowu
X
Wang
Department of Computer Science and Engineering, University of Minnesota at Twin Cities, Minneapolis, MN, 55455, USA.
Rui
R
Kuang
Department of Plant Biology, University of Minnesota at Twin Cities, Saint Paul, MN, 55108, USA.
Min
M
Ni
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D029688:Brassica napus / Q000235:genetics / Q000378:metabolism*; D056625:Endosperm / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D012639:Seeds / Q000235:genetics / Q000378:metabolism*
D029681:Arabidopsis Proteins; D010940:Plant Proteins; C511745:SHB1 protein, Arabidopsis

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