Molecular Mapping and QTL for Seed Pigmentations and 19 Genes of Flavonoid Pathway in Brassica napus L

This research focused on QTL identification responsible for four seed pigmentations and nineteen genes in flavonoid pathway to systematically elucidate the characteristics of flavonoid pathway, and provide the necessary information for seeking the key genes or regulation nodes controlled the yellow seed trait formation in B. napus.

We employed a sample of 94 recombinant inbred lines (RILs) from a population derived from a cross between black-seeded male parent cultivar Zhongyou 821 and yellow-seeded female parent line GH06. Major QTLs controlling four kinds of seed pigmentations were identified by genetic map construction. Then, transcript-level variation analysis was carried out on RNA from seeds of 30 days after flower (DAF) by qRT-PCR. Regarding as quantitative traits, the transcript levels of the flavonoid biosynthesis genes families were examined by QTL mapping method for eQTL detection. To confirm the candidate genes, sequences of association makers were used for BLASTN search in the BRAD and our local B. napus genome sequence database.

A total of 57 QTLs for seed pigmentations and 75 eQTLs for nineteen genes were detected and distributed among 15 different linkage groups. Interestingly, 4 hotspot regions including 19 QTLs and 30 eQTLs were identified and distributed on the chromosome A03, A09 and C08, respectively. Besides, the most interesting hotspot in our study was the lower hotspot on chromosome A09, showed well synteny to genome sequences of A. thaliana, A. lyrata and Brassica relatives. A total of 8 transcription factors were identified in this region, three of them belongs to the flavonoid biosynthesis related MYB transcription factor family. Additionally, In trans-eQTL hotspot on chromosome A03, C08 and the upper A09, we identified 5, 1 and 10 transcription factors, respectively. Among these transcription factors, bZIP25, MYC1 and other function unclear transcription factors could be regarded as candidate genes in the trans-eQTL hotspots for further verification.

Molecular markers closely linked with these QTLs could be applied in marker-assisted selection of improving of feeding value of rapeseed. The functions of these candidate genes will provide insight into the molecular and biochemical mechanism of seed coat development in Brassicaceae, and elucidate the regulatory network underlying seed coat colour formation in B. napus.