Comparative transcriptomic analysis reveals a series of single nucleotide polymorphism between red- and white-fleshed loquats (Eriobotrya japonica)

Loquat (Eriobotrya japonica) is an economically important crop and red-fleshed cultivars have a much higher carotenoid content than white-fleshed cultivars. We used Illumina RNA-seq technology to gain a global overview of the loquat transcriptome from a mixture of fruit samples at different developmental stages for both red-fleshed and white-fleshed loquat. A total of 94.98 million paired-end short reads were obtained and 61 586 unigenes were generated from de novo assembly with an average length of 817 bp. Among these unigenes, 44 710 unigenes were annotated by blast against Nr, Swissprot, GO, COG and KEGG databases. For these annotated unigenes, 123 biosynthesis pathways were predicted by mapping these unigenes to the reference canonical pathways and 41 unigenes were predicted to be involved in carotenoid biosynthesis. RT-qPCR analysis showed that the expression level of the LCYB gene was higher in red-fleshed loquat and the CRTRB gene had a higher expression level in white-fleshed loquat. Comparative analysis of the two transcriptomes revealed 2396 single nucleotide polymorphisms (SNPs) between red- and white-fleshed loquats. The majority of SNPs identified between the two loquat cultivars were nonsense mutations and one out of eleven SNPs in candidate genes involved in carotenoid biosynthesis was a sense mutation. This suggests that the analysis based on transcriptomes can reveal key genes related to the carotenoid biosynthesis and more carotene in red-fleshed loquat cultivars may result from both more carotene produced by the higher expression of LCYB genes and less carotene converted because of the low expression of the CRTRB gene. All these results from the transcriptome analysis will be useful for the elucidation of genetic differences between red- and white-fleshed loquat fruits and further functional analysis for genes responsible for carotenoid accumulation.