Molecular Marker Development for Tip-Burn Resistant Cabbage By RNA-Seq

The cabbage, Brassica oleracea var. capitata L., is one of very important economic crops, but to perform research at molecular level is difficult due to the lack of information of its genomic data. Although the sequences of genes of cabbage have been reported by high-throughput sequencing and de novo transcriptome assembly recently, it is still difficult to development of molecular marker for study the interesting trait. To develop molecular marker for tip-burn resistance of cabbage, we integrated results of gene expression and SNP calling. We extracted 116 differentially expressed genes in comparison of subspecies, tip-burn sensitive and resistant varieties, and 138 differentially expressed genes in comparison of normal and calcium-deficient conditions from RNA-seq analysis. Besides we called 135,745 homotype SNPs between two varieties. Through literature review, we checked out related in genes involved in calcium transport or anti-porter pathway like CAX1, ACA4, ACA11. From integrating these data, we derived a few of candidates of marker related in disorder for calcium deficiency in cabbage. Candidates of marker will be tested in F2 mapping population of two varieties and also be applied to other plants. The candidate sequence from this study provides valuable markers for research to develop cabbage breeds which have tip-burn resistant variety.