Polymorphism identification of carotenoid binding protein gene transcription in the silkworm, Bombyx mori

Carotenoids play important and diverse roles in insects and their uptake and transport rely on carotenoid binding protein (CBP). The study excavated a cluster of CBP-like transcripts, including full CBP from all of the six yellow cocoon Bombyx strains investigated. Sequencing of 54 cDNA clones revealed 17 different types of transcripts which derived from alternative splicing of CBP gene locus. Five of the novel transcripts were similar with spatial and temporal distribution patterns to CBP, but their expression levels were relatively lower. The author disclosed two more novel alternative spliced transcripts with different transcription start sites from CBP in the 5’ UTRs as well as 11 SNP sites neighboring intron 1 after amplification and sequencing. qRT-PCR analysis gave evidence that relatively more mRNA was transcribed from A-type CBP gene than that from B-type in tissues like silk gland and midgut. Sequences of A- and B-type CBP genes were different in length of domains neighboring the 5’ UTR, thus their mRNA varied both in quantity and transcript types. The SNPs surrounding intron 1 can serve as stable markers to distinguish transcripts from the two isoforms, and they can be used for molecular marker assisted selection.