Transcriptomic study of rice crowns from genotypes differing in tolerance to Zn deficiency

The transcriptome of crown tissue from several Zn-efficient and Zn-inefficient rice genotypes, exposed or not to Zn deficiency, was investigated using RNA sequencing. By grouping data from different genotypes within each efficiency group, we were able to 1) identify several well-known and novel Zn transporters involved in Zn retranslocation from the crown to the shoot and roots in response to Zn deficiency; 2) determine that Zn deficiency triggers the conversion of soluble sugars into starch; and 3) detect several candidate genes possibly conferring Zn efficiency. Overall design: The crowns of three Zn-efficient and three Zn-inefficient rice genotypes were harvested after 8 days of treatment, with or without Zn, and RNA was extracted and sequenced as paired-end for 150 bp. RNA sequencing reads were aligned against the Nipponbare reference genome and differentially expressed genes between treatments and efficiency groups were detected.

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Nanda AK, Pujol V, Wissuwa M