Transcriptome Sequencing to Investigate Genes Involved in Fruits Color in the Three MAGIC Populations of Cultivated Strawberry

Fruits color is an important trait for consumer preference and marketability in crops. Ripened fruits of cultivated strawberry, Fragaria × ananassa (2n = 8x = 56) show white to dark red color variation which are mainly affected by concentrations and compositions of anthocyanins. Their gene regulation networks under multiple combinations of genes are unclear and it makes difficult to control fruit color in strawberry breeding. In order to find gene regulation networks involved in fruits color, we investigated relationships between anthocyanin concentrations and gene-expression patterns in three MAGIC (multi-parent advanced generation inter-cross) populations developed in the three breeding stations (Tochigi, Fukuoka and Chiba prefectures) in Japan. Surface tissues of receptacles in a total of 545 individuals (181 from Tochigi-, 184 from Fukuoka- and 180 from Chiba-populations) in the 2nd inter crossed generation of the MAGIC populations were used for anthocyanin quantification and transcriptome profiling. Anthocyanins were extracted into 1% formic acid/methanol solution and analyzed with HPLC. cDNA libraries constructed with QuantSeq (Lexogen) were sequenced by HiSeq 2000 (Illumina). Trimmed reads were mapped on the reference genome of strawberry (FANhybrid_r1.2) with Bowtie 2 and counted transcripts with HT-seq software. So far, 669 genes showed significant correlation (p<0.001) between expression patterns and anthocyanin concentration in the three populations. Eleven of 669 genes commonly showed significant correlation in two of three populations. A few mutual eQTL were identified in the three populations. More high throughput transcriptomics would be necessary to verify significant eQTL from labile genetic regulations of the cultivated strawberry.