Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed

Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color inB. napus, we compared 31 RNA-seq libraries of yellow- and black-seededB. napusat five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such asTT8(BnaC09g24870D),TT5(BnaA09g34840DandBnaC08g26020D),TT12(BnaC06g17050DandBnaA07g18120D),AHA10(BnaA08g23220DandBnaC08g17280D),CHI(BnaC09g50050D),BAN(BnaA03g60670D) andDFR(BnaC09g17150D). GeneBnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seededB. napus. This study provides insight into the formation of seed coat color inB. napus.