Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus

Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xu, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B Cahoon, Chunyu Zhang

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed ‘iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and to control developmental timing of transgene expression. Evaluation of a subset of the resulting ~6000 Arabidopsis transformants revealed a high percentage of lines with full-length B. napus transgene insertions. Upon induction, numerous iFOX lines with visible phenotypes were identified, including one that displayed early leaf senescence. Phenotypic analysis of this line (rsl-1327) after methoxyfenozide induction indicated high degree of leaf chlorosis. The integrated B. napuscDNA was identified as a homolog of an Arabidopsis acyl-CoA binding protein (ACBP) gene designated BnACBP1-like. The early senescence phenotype conferred by BnACBP1-like was confirmed by constitutive expression of this gene in Arabidopsis and B. napus. Use of the inducible promoter in the iFOX line coupled with RNA-Seq analyses allowed mechanistic clues and a working model for the phenotype associated with BnACBP1-like expression. Our results demonstrate the utility of iFOX-Hunting as a tool for gene discovery and functional characterization of Brassica napus genome.

Original languageEnglish (US)
Pages (from-to)591-602
Number of pages12
JournalPlant Biotechnology Journal
Volume16
Issue number2
DOIs
StatePublished - Feb 1 2018

Fingerprint

Brassica napus
Polyploidy
Arabidopsis
polyploidy
genomics
Transgenes
methoxyfenozide
transgenes
Complementary DNA
Genes
promoter regions
Phenotype
genes
phenotype
Seeds
Diazepam Binding Inhibitor
Hypochromic Anemia
Gene Expression
Plant Genes
gene expression

Keywords

  • Arabidopsis thaliana
  • BnACBP1-like
  • Brassica napus
  • acyl-CoA binding protein
  • early leaf senescence
  • functional genomic platform
  • iFOX-Hunting system

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science

Cite this

Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus. / Ling, Juan; Li, Renjie; Nwafor, Chinedu Charles; Cheng, Junluo; Li, Maoteng; Xu, Qing; Wu, Jian; Gan, Lu; Yang, Qingyong; Liu, Chao; Chen, Ming; Zhou, Yongming; Cahoon, Edgar B; Zhang, Chunyu.

In: Plant Biotechnology Journal, Vol. 16, No. 2, 01.02.2018, p. 591-602.

Research output: Contribution to journalArticle

Ling, Juan ; Li, Renjie ; Nwafor, Chinedu Charles ; Cheng, Junluo ; Li, Maoteng ; Xu, Qing ; Wu, Jian ; Gan, Lu ; Yang, Qingyong ; Liu, Chao ; Chen, Ming ; Zhou, Yongming ; Cahoon, Edgar B ; Zhang, Chunyu. / Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus. In: Plant Biotechnology Journal. 2018 ; Vol. 16, No. 2. pp. 591-602.
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AU - Xu, Qing

AU - Wu, Jian

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AU - Liu, Chao

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