Transcriptomic comparison between developing seeds of yellow- and black-seeded Brassica napus reveals that genes influence seed quality

Abstract

Background: Brassica napus is of substantial economic value for vegetable oil, biofuel, and animal fodder production. The breeding of yellow-seeded B. napus to improve seed quality with higher oil content, improved oil and meal quality with fewer antinutrients merits attention. Screening the genes related to this phenotype is valuable for future rapeseed breeding.Results: A total of 85,407 genes, including 4317 novel genes, were identified in the developing seeds of yellow-and black-seeded B. napus, and yellow rapeseed was shown to be an introgression line between black-seeded B. napus and yellow-seeded Sinapis alba. A total of 15,251 differentially expressed genes (DEGs) were identified among all the libraries, and 563 and 397 common DEGs were identified throughout black and yellow seed development, including 80 upregulated and 151 downregulated genes related to seed development and fatty acid accumulation. In addition, 11 up-DEGs and 31 down-DEGs were identified in all developmental stages of yellow rapeseed compared with black seed. Enrichment analysis revealed that many DEGs were involved in biosynthetic processes, pigment metabolism, and oxidation-reduction processes, such as flavonoid and phenylpropanoid biosynthesis, phenylalanine metabolism, flavone and flavonol biosynthesis, and fatty acid biosynthesis and metabolism. We found that more than 77 DEGs were related to flavonoid and lignin biosynthesis, including 4CL, C4H, and PAL, which participated in phenylalanine metabolism, and BAN, CHI/TT5, DFR, F3H, FLS, LDOX, PAP, CHS/TT4, TT5, bHLH/TT8, WD40, MYB, TCP, and CYP, which were involved in flavonoid biosynthesis. Most of these DEGs were downregulated in yellow rapeseed and were consistent with the decreased flavonoid and lignin contents. Both up-and down-DEGs related to fatty acid biosynthesis and metabolism were also analyzed, which could help to explain the improved oil content of yellow rapeseed.Conclusion: This research provided comprehensive transcriptome data for yellow-seeded B. napus with a unique genetic background, and all the DEGs in comparison with the black-seeded counterpart could help to explain seed quality differences, such as lower pigmentation and lignin contents, and higher oil content.

Genetic and Comparative Transcriptome Analysis Revealed DEGs Involved in the Purple Leaf Formation in Brassica juncea

“…And apart from B. oleracea, almost no difference in transcript expression level of 4CL5 was found between purple and green leaves (Mushtaq et al, 2016). The 4CL gene played an important role in the pathways of lignin biosynthesis (Jiang et al, 2019).The down-regulated 4CL in our study may decrease the lignin biosynthesis and increase anthocyanin biosynthesis. Surprisingly, the most significant typical pathways between the purple and green leaves were the plant-pathogen interaction, alpha-linolenic acid metabolism, plant hormone signal transduction, and linoleic acid metabolism.…”

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

“…Considering that only DFR , LODX , BAN , TT19 and AHA10 in the flavonoid biosynthesis pathways contain cis‐regulatory motifs that can be directly targeted by TT8‐involved complexes (Xu et al , ), 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 , ; 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 , ).…”

“…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). It is reasonable to postulate that BnTT8 is involved in the downregulation of these DEGs in phenylpropanoid and flavonoid biosynthesis pathways directly or indirectly.…”

“…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 oilseedBrassicaspp. 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).…”