Transcription of lncRNA is essential to -splicing between and that causes yellow fruit in tomato.

Phytoene synthase (PSY) has been considered as an important regulatory enzyme in carotenoids biosynthesis pathway. Previous study finds that the yellow fruit in var. accession PI 114490 is caused by loss-of-function of SlPSY1 due to -splicing between and an unknown gene transcribed from neighbour opposite strand DNA of . The genomic DNA sequences of between red and yellow-fruited tomato lines have one single-nucleotide polymorphism (SNP) in the fourth intron and one SSR in the intergenic region. In the current study, the cause of -splicing event was further investigated. The data showed that the previously defined unknown gene was a putative long non-coding RNA with three variants in many yellow-fruited tomato lines. The intronic SNP and intergenic SSR were tightly associated with -splicing event . However, transgenic tomato lines carrying the genomic DNA of from PI 114490 did not generate transcripts of and suggesting that only the intronic SNP could not cause the -splicing event. Over-expression of in red-fruited tomato line M82 did not have any phenotype change while over-expression of wild type resulted in altered leaf colour. Sub-cellular localization analysis showed that SlPSY1-ACoS-AS1 could not enter plastids where SlPSY1 has its enzyme activity. Mutation of in PI 114490 generated by CRISPR/Cas9 techniques resulted in red fruits implying that was essential to -splicing event . The results obtained here will extend knowledge to understand the mechanism of -splicing event and provide additional information for the regulation of carotenoids biosynthesis.