Soybean leaves transcriptomic data dissects the phenylpropanoid pathway genes as a defence response against Phakopsora pachyrhizi

Md. Zakir Hossain, Yasuhiro Ishiga, Naoki Yamanaka, Eri Ogiso-Tanaka, Yuichi Yamaoka

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is responsible for severe yield losses of up to 90% in all soybean producing countries. Till today, eight resistance to Phakopsora pachyrhizi (Rpp) loci have been mapped in soybean. Their resistance mechanism is race specific but largely unknown. The transcriptomes of susceptible BRS184 and Rpp3 with ASR isolates T1-2 at 24 h after inoculation (hai) and without ASR inoculation (mock) were annotated by similarity searching with different databases. A total of 4518 differentially expressed genes were identified. We found 70.89%, 56.61%, 32.13%, and 56.04% genes in the protein family databases (PFAM), Gene Ontology (GO), Eukaryotic clusters of Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG), respectively. KEGG disclosed that 52% of the phenylpropanoid pathway related genes were up-regulated. The relative gene expression study for selected genes of that pathway was conducted by RT-qPCR using Rpp1-Rpp4 carrying lines with T1-2 infection. The RT-qPCR results revealed that the Rpp lines utilized these genes in a rate limiting manner as a defence response. With the exception of glycinol 4-dimethylallyltransferase (G4DT) and chalcone reductase (CHR), all the genes showed the greatest expression at 12 hai, but the gene expressions which occur between 24 and 96 hai make these Rpp lines unique to their respective ASR isolates. Moreover, functional coordination of arogenate dehydratase 6 (ADT6) and 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (ispG), chalcone synthase (CHS) and CHR, and G4DT and phytyltransferase 3 (PT3) may have a great impact on soybean resistance against ASR.

Original languageEnglish
Pages (from-to)424-433
Number of pages10
JournalPlant Physiology and Biochemistry
Volume132
DOIs
Publication statusPublished - Nov 1 2018

Fingerprint

Phakopsora pachyrhizi
phenylpropanoids
transcriptomics
Soybeans
soybean rust
soybeans
Genes
leaves
genes
Dimethylallyltranstransferase
Encyclopedias
Genome
gene expression
naringenin-chalcone synthase
genome
Gene Expression
Protein Databases
Gene Ontology
Diphosphates
resistance mechanisms

Keywords

  • Asian soybean rust
  • Phakopsora pachyrhizi
  • Phenylpropanoid pathway
  • Soybean

ASJC Scopus subject areas

  • Physiology
  • Genetics
  • Plant Science

Cite this

Soybean leaves transcriptomic data dissects the phenylpropanoid pathway genes as a defence response against Phakopsora pachyrhizi. / Hossain, Md. Zakir; Ishiga, Yasuhiro; Yamanaka, Naoki; Ogiso-Tanaka, Eri; Yamaoka, Yuichi.

In: Plant Physiology and Biochemistry, Vol. 132, 01.11.2018, p. 424-433.

Research output: Contribution to journalArticle

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abstract = "Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is responsible for severe yield losses of up to 90{\%} in all soybean producing countries. Till today, eight resistance to Phakopsora pachyrhizi (Rpp) loci have been mapped in soybean. Their resistance mechanism is race specific but largely unknown. The transcriptomes of susceptible BRS184 and Rpp3 with ASR isolates T1-2 at 24 h after inoculation (hai) and without ASR inoculation (mock) were annotated by similarity searching with different databases. A total of 4518 differentially expressed genes were identified. We found 70.89{\%}, 56.61{\%}, 32.13{\%}, and 56.04{\%} genes in the protein family databases (PFAM), Gene Ontology (GO), Eukaryotic clusters of Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG), respectively. KEGG disclosed that 52{\%} of the phenylpropanoid pathway related genes were up-regulated. The relative gene expression study for selected genes of that pathway was conducted by RT-qPCR using Rpp1-Rpp4 carrying lines with T1-2 infection. The RT-qPCR results revealed that the Rpp lines utilized these genes in a rate limiting manner as a defence response. With the exception of glycinol 4-dimethylallyltransferase (G4DT) and chalcone reductase (CHR), all the genes showed the greatest expression at 12 hai, but the gene expressions which occur between 24 and 96 hai make these Rpp lines unique to their respective ASR isolates. Moreover, functional coordination of arogenate dehydratase 6 (ADT6) and 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (ispG), chalcone synthase (CHS) and CHR, and G4DT and phytyltransferase 3 (PT3) may have a great impact on soybean resistance against ASR.",
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AU - Yamaoka, Yuichi

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