Abstract
Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.
Highlights
Brassica napus L. (2n = 38, AACC) is an economically important oilseed crop that is widely cultivated as a source of vegetable oil, biodiesel, and protein-rich meal for animal feed (Kimber and Mcgregor, 1995)
We assayed the expression levels of 18 flavonoid biosynthesis genes (Supplementary Figure S3), including 12 structural genes (i.e., BnTT3, BnTT4, BnTT5, BnTT6, BnTT7, BnTT10, BnTT12, BnTT15, BnTT18, BnTT19, BnAHA10, and BnBAN) and six regulatory genes (BnTT1, BnTT2, BnTT8, BnTT16, BnTTG1, and BnTTG2) (Qu et al, 2013) in B. napus recombinant inbred lines (RILs) derived from a cross between the male parent Zhongyou 821 and female parent GH06 by qRT-PCR, and normalized the gene expression levels according to the expression values of the male parent
In an analysis of orthologous regions of expression quantitative trait locus (eQTL), we identified 243 copies of 18 genes involved in flavonoid biosynthesis from A. thaliana (37), B. rapa (55), B. oleracea (52), and B. napus (99) (Supplementary Table S4; Figure 3) (Krzywinski et al, 2009), respectively
Summary
Some homologs of genes involved in flavonoid biosynthesis have been cloned and characterized in B. napus (Wei et al, 2007; Xu et al, 2007; Ni et al, 2008; Akhov et al, 2009; Auger et al, 2009; Chai et al, 2009; Lu et al, 2009; Chen et al, 2013) These results provide a foundation for further studies of the molecular and regulatory mechanisms underlying seed coat color formation in B. napus. The molecular mechanism underlying yellow seed coat formation in Brassica is poorly understood
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