Transcriptomic Analysis of Seed Coats in Yellow-Seeded Brassica napus Reveals Novel Genes That Influence Proanthocyanidin Biosynthesis

Yellow seeds are a favorable trait for Brassica crops breeding due to better quality than their black-seeded counterparts. Here, we compared the Brassica napus seed coat transcriptomes between yellow- and brown-seeded near-isogenic lines (Y-NIL and B-NIL) that were developed from the resynthesized yellow-seeded line No. 2127-17. A total of 4,974 differentially expressed genes (DEG) were identified during seed development, involving 3,128 up-regulated and 1,835 down-regulated genes in yellow seed coats. Phenylpropanoid and flavonoid biosynthesis pathways were enriched in down-regulated genes, whereas the top two pathways for up-regulated genes were plant–pathogen interaction and plant hormone signal transduction. Twelve biosynthetic genes and three regulatory genes involved in the flavonoid pathway exhibited similar expression patterns in seed coats during seed development, of which the down-regulation mainly contributed to the reduction of proanthocyanidins (PAs) in yellow seed coats, indicating that these genes associated with PA biosynthesis may be regulated by an unreported common regulator, possibly corresponding to the candidate for the dominant black-seeded gene D in the NILs. Three transcription factor (TF) genes, including one bHLH gene and two MYB-related genes that are located within the previous seed coat color quantitative trait locus (QTL) region on chromosome A09, also showed similar developmental expression patterns to the key PA biosynthetic genes and they might thus potentially involved participate in flavonoid biosynthesis regulation. Our study identified novel potential TFs involved in PAs accumulation and will provide pivotal information for identifying the candidate genes for seed coat color in B. napus.

• Publication year

  2017

• Venue

  Frontiers in Plant Science

• Publication date

  2017-10-05

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.3389/fpls.2017.01674PMID 29051765PMCID 5633857
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Twelve flavonoid biosynthetic genes and three transcription factor genes showed similar developmental expression patterns, and their reduced expression was associated with lower proanthocyanidin accumulation in yellow seed coats, with the transcription factor genes located in the seed coat color QTL region on chromosome A09.

  Confidence 0.93

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• Down-regulated genes were enriched in phenylpropanoid and flavonoid biosynthesis pathways, whereas up-regulated genes were enriched in plant-pathogen interaction and plant hormone signal transduction.

  Confidence 0.96

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• Comparing yellow- and brown-seeded near-isogenic lines identified 4,974 differentially expressed genes in Brassica napus seed coat transcriptomes during seed development, with more genes up-regulated than down-regulated in yellow seed coats.

  Confidence 0.98

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review

• brassica napus seed coat transcriptomes

  dataset

  The seed coat RNA expression profiles measured from Brassica napus yellow- and brown-seeded lines across seed development stages.

  Aliases: seed coat transcriptomes

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• flavonoid biosynthetic genes

  gene family

  Genes encoding enzymes that participate in the flavonoid branch of secondary metabolism in seed coats.

  Aliases: biosynthetic genes involved in the flavonoid pathway

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• phenylpropanoid and flavonoid biosynthesis pathways

  pathway

  Metabolic pathways in seed coats that produce phenylpropanoid and flavonoid compounds, including pigmentation-related metabolites.

  Aliases: phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• plant hormone signal transduction

  pathway

  A functional pathway category covering genes that mediate hormone signal perception and downstream responses.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• plant-pathogen interaction

  pathway

  A functional pathway category representing genes involved in host responses to pathogen-related signals.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• proanthocyanidins

  compound

  Flavonoid-derived compounds in seed coats that contribute to brown pigmentation and are measured as PA content.

  Aliases: PAs

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• seed coat color qtl region on chromosome a09

  genomic region

  A previously mapped quantitative trait locus region on chromosome A09 associated with Brassica napus seed coat color variation.

  Aliases: previous seed coat color QTL region on chromosome A09, QTL region on chromosome A09

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• transcription factor genes

  gene family

  Genes encoding regulatory proteins that control expression of downstream seed coat pigmentation genes.

  Aliases: TF genes

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review
• yellow- and brown-seeded near-isogenic lines

  organismal material

  A pair of Brassica napus near-isogenic lines that differ mainly in seed coat color and were used for transcriptome comparison.

  Aliases: Y-NIL and B-NIL, Y-NIL, B-NIL

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewAnonymous (12632b8b5f) review

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