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

Yi Yuan,Shuang Zhu,Yue Wang,You-Ping Wang,Jacqueline Batley,Jinjin Jiang,Lei Zeng

doi:10.1186/s12870-019-1821-z

Yi Yuan, Shuang Zhu + Show 5 more

Open Access

https://doi.org/10.1186/s12870-019-1821-z

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Abstract

BackgroundBrassica 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.ResultsA 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.ConclusionThis 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.

Highlights

Brassica napus is of substantial economic value for vegetable oil, biofuel, and animal fodder production
Transcriptome sequencing and read mapping of yellowand black-seeded B. napus RNA-Seq was performed at three weeks after flowering (3 Weeks after flowering (WAF)), 4 WAF, 5 WAF, 6 WAF, and mature stage of yellow- and black-seeded B. napus to investigate the transcriptome difference that might be related to the quality variation between two rapeseeds
Differentially expressed gene (DEG) associated with fatty acid biosynthesis and metabolism We found that genes involved in FA biosynthesis, metabolism, and degradation were changed (Fig. 5)

Summary

Introduction

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. Yellow-seeded B. napus was improved with better seed oil and meal quality due to fewer pigments and polyphenols; breeding yellow rapeseed has been preferred for decades, and studies on the molecular mechanism of this phenotype have been reported as well [3]. As reported in Arabidopsis thaliana, mutations in transparent testa (TT) genes are responsible for seed coat color variations, including early (EBGs) and late (LBGs) biosynthesis genes [9]. Yu (2013) reviewed the molecular mechanism of manupulating seed coat color in Brassica species, including the homologous TTs cloned in Brassicas [20]. Functional analysis of BnTT10 and BnTT1 revealed that they are involved in PA metabolism, lignin synthesis, seed coat pigmentation, and fatty acid (FA) biosynthesis [18, 19]

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