Comparative transcriptomics of boiled storage roots of sweetpotato

Firmness is a key quality trait influencing consumer preference of boiled sweetpotato roots. Identification of markers for firmness could enable breeders to effectively develop and screen for desirable clones during the initial stages of the breeding pipelines, based on consumer preferences. This could potentially enhance the adoption rates of new and improved varieties upon release. In this study, a comparative transcriptomic analysis was conducted to identify candidate genes possibly influencing the firmness of boiled sweetpotato roots. Four varieties; the hard, slow cooking NASPOT11 (cream-fleshed) and SPK004 (orange-fleshed), and the soft, fast-cooking Wagabolige (cream-fleshed) and Resisto (orange-fleshed) were used. Total RNA was isolated from three replicates of each variety and mRNA libraries were prepared and sequenced on an Illumina HiSeq2500 platform using a paired-end strategy. In all the samples, more than 80 % of the reads mapped uniquely to the I. batatas haplotype resolved genome. There were 45 855 genes with detectable levels of expression. Of these, 7 635 were differentially expressed (padj < 0.05), with 3 633 significantly upregulated and 4133 significantly downregulated in the hard, slow cooking varieties. Amongst the most significantly upregulated genes in the hard, slow-cooking varieties were cell wall related genes; g62109; a pectin acetylesterase family protein, g35627; xyloglucan endotransglucosylase/hydrolase, and g4017; a cell wall-associated kinase. This strongly suggests that cell wall composition plays an important role in the development of firmness in boiled sweetpotato roots. These findings provide a valuable resource for genetic and genomic studies aimed at understanding and developing markers for the texture of sweetpotato roots.