Expression Analysis and eQTL Mapping of BnTT3 Gene in Brassica napus L.

Abstract

In flavonoid biosynthesis pathway, the key enzyme dihydroflavonol 4-reductase (DFR) involved in the proanthocya- nidin and anthocyanin biosynthesis pathway is encoded by TRANSPARENT TESTA 3 (TT3) gene. The objective of this research was to identify the upstream regulatory networks of BnTT3 using the composite interval mapping method (CIM). Hence, we per- formed an eQTL analysis for the transcript-level variation of BnTT3 gene in seeds at 40 days after flower (DAF) in 94 recombi- nant inbred lines (RILs) derived from a cross between the yellow-seeded female parent GH06 and black-seeded male parent ZY821. Five eQTLs for expression levels of BnTT3 were detected on four different chromosomes (A03, A08, A09, and C01) in B. napus, accounting for 5.22% to 24.05% of phenotypic variation. Two major eQTLs were found and located among the markers KS10260-KBrB019I24.15 and B055B21-5-KS30880 of chromosome A09, with explained 24.05% and 16.55% of phenotypic variation, respectively. Three minor eQTLs were also detected to be located on chromosomes A03, A08, and C01. The flanking sequences with 200 kb of two major eQTLs on chromosome A09 of B. napus showed well synteny to those of A. thaliana, Bras- sica rapa, Brassica oleracea and other Brassiceae relatives. Furthermore, the annotation results showed that they belong to the trans-QTL, containing 78 genes in the two trans-QTL regions. Some transcription factors (MYB51, MYB52, and bZIP5) might be upstream regulatory factors associated with transcriptional regulation of BnTT3. Therefore, further study about these genes func- tion will be helpful to elucidate the molecular mechanism of the seed coat colour formation, as well as lay the foundation for se- lecting candidate genes of seed coat colour in B. napus.