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

Abstract

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.

Targeted mutagenesis of BnTT8 homologs controls yellow seed coat development for effective oil production in Brassica napus L.

“…c and d). Recently, Hong et al () also observed the same phenomenon by chemical staining of developmental seeds in rapeseed, indicating the 21 DAF is an essential stage for seed coat coloration in rapeseed. Consistent with this finding, the expression level of BnTT8 showed a gradual increase during the early seed developmental stage and peaked at 23 DAF or 35 DAF (Fig.…”

“…Recently, two transcriptomic studies also found that these down‐regulated DEGs in yellow‐seeded coats were enriched in phenylpropanoid and flavonoid biosynthesis in resynthesized yellow‐seeded rapeseed as research materials (Hong et al , ; Jiang et al , ). Although the causal gene underlying the yellow‐seeded trait is still not clear in their materials, the two functional copies of BnTT8 were significantly down‐regulated in yellow seed compared with black seed in both cases (Hong et al , ; Jiang et al , ). It is reasonable to postulate that BnTT8 is involved in the down‐regulation of these DEGs in phenylpropanoid and flavonoid biosynthesis pathways directly or indirectly.…”

“…Considering that only DFR, LODX, BAN, TT19 and AHA10 in the flavonoid biosynthesis pathways contain cis-regulatory motifs that can be directly targeted by TT8involved complexes (Xu et al, 2014), the broad suppression of phenylpropanoid/flavonoid biosynthesis genes may be the outcome of unknown regulatory mechanisms in rapeseed. Recently, two transcriptomic studies also found that these down-regulated DEGs in yellow-seeded coats were enriched in phenylpropanoid and flavonoid biosynthesis in resynthesized yellow-seeded rapeseed as research materials (Hong et al, 2017;Jiang et al, 2019). Although the causal gene underlying the yellow-seeded trait is still not clear in their materials, the two functional copies of BnTT8 were significantly down-regulated in yellow seed compared with black seed in both cases (Hong et al, 2017;Jiang et al, 2019).…”

“…Previous studies showed that yellow-seeded B. napus has a thinner seed coat, a reduced percentage of pigment and hull, and a greater content of oil and protein than the black-seeded type (Marles and Gruber, 2004;Meng et al, 1998;Tang et al, 1997). With these superior characteristics, yellow seed is widely accepted as a good-quality trait and is a focus of rapeseed research globally (Hong et al, 2017;Jiang et al, 2019;Lian et al, 2017;Meng et al, 1998;Qu et al, 2013Qu et al, , 2016Simbaya et al, 1995;Tang et al, 1997;Wen et al, 2012).…”

Big data from small tissues: extraction of high-quality RNA for different plant tissue types during oilseed Brassica spp. seed development for RNA-Sequencing

“…Removing these contaminants is a critical step, as RNA with high purity and integrity is critical for gene expression analyses. Although there are several methods available for seed RNA extraction (Kanai et al, 2017;Pereira et al, 2017;Mornkham et al, 2013;Suzuki et al, 2004); fewer protocols are available for the extraction of good quality RNA from specific seed tissue types, especially for the seed coat (Jiang et al, 2019;Liao et al, 2019;Hong et al, 2017;Kour et al, 2014).…”