Influence of organic farming on the potato transcriptome

Abstract

Organic agriculture sparks a lively debate on its potential health and environmental benefits. Comparative studies often investigate the response of crops to organic farming through targeted approaches and within a limited experimental work. To clarify this issue, the transcriptomic profile of a cultivar of the potato grown for two years under organic and conventional farming was compared with the profile of an experimental clone grown in the same location of Southern Italy for one year. Transcriptomic raw data were obtained through Potato Oligo Chip Initiative (POCI) microarrays and were processed using unsupervised coupling multivariate statistical analysis and bioinformatics (MapMan software). One-hundred-forty-four genes showed the same expression in both years, and 113 showed the same expression in both genotypes. Their functional characterization revealed the strong involvement of the farming system in metabolism associated with the nutritional aspects of organic tubers (e.g., phenylpropanoid, flavonoid, glycoalcaloid, asparagine, ascorbic acid). Moreover, further investigation showed that eight of 42,034 features exhibited the same trend of expression irrespective of the year and genotype, making them possible candidates as markers of traceability. This paper raises the issue regarding the choice of genotype in organic management and the relevance of assessing seasonal conditions effects when studying the effects of organic cultivation on tuber metabolism.