RNA-Seq reveals differential expression patterns of genes associated with carotenoid accumulation in loquat

Abstract

Loquat (Eriobotrya japonica Lindl.) cultivars can be classified as yellow- and white-fleshed based on fruit color. The pulps of yellow-fleshed cultivars appear yellow because of high contents of carotenoids, while the pulps of white-fleshed cultivars appear ivory white due to the lack of carotenoid accumulation. To elucidate the genes associated with the carotenoid accumulation, de novo assembly of the fruit transcriptome in three loquat cultivars having different pulp colors, including ‘Golden nugget’ (yellow pulp), ‘Jiefangzhong’ (yellow pulp), and ‘Baiyu’ (white pulp), at breaker stage, was conducted in this study. By RNA-seq, a total of 11.92 Gb clean data was obtained, and 51,934 unigenes were assembled and annotated. Based on BLAST search, 26,447 unigenes had a hit in at least one of the protein and nucleotide databases used in the present study. Swiss-Port annotation and Clusters of Orthologous Group were assigned for 16,679 and 13,986 unigenes, respectively. Moreover, Gene Ontology enrichment analysis classified 18,842 unigenes into 53 functional groups, which largely detected in biological process category, followed by cellular component category and molecular function category. We detected 3438 differentially expressed genes using Reads Per kb per Million reads method. Of these genes, six were identified as carotenoid accumulation-related genes. Our study revealed a certain relationship between carotenoid accumulation and expression patterns of carotenogenic genes.