Effective methods for practical application of gene expression analysis in field-grown rice roots

Autor: Junko Ishikawa-Sakurai, Maya Matsunami, Yoshiaki Nagamura, Tsuneo Kuwagata, Yoko Tominaga, Mari Murai-Hatano, Hidehiro Hayashi
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Zdroj: SC30201905100019
NARO成果DBd
ISSN: 1573-5036
DOI: 10.1007/s11104-018-3834-z
Popis: Gene expression analysis under field conditions improves our understanding of crop responses to fluctuating environmental conditions. We evaluated RNA extraction methods and reference genes for a quantitative real-time PCR study of rice roots grown under field conditions. Roots were collected from paddy (Andosol) at different growth stages, from tillering to ripening. RNA was extracted by three methods using commercially available RNA-extraction kits, and RNA yield and quality were compared. Our RNA extraction method enabled us to obtain adequate concentration and yield of RNA from the roots during a broad period of growth. Adequate RNA concentration was successfully extracted from the field-grown rice roots using large quantities of tissue samples and by purifying the samples prior to the extraction. Among the seven candidate reference genes, TATA-binding protein coding gene (TBP2) was observed to be highly stable across all the root samples and growth stages, in real-time PCR assays. Root gene expression analysis of water channel- and nitrogen uptake-related proteins clearly indicated dynamic changes (with respect to diurnal and growth stages) in their expression levels and their associations with meteorological factors. Some aquaporin genes such as OsPIP1;3, OsPIP2;4, and OsPIP2;5, showed clear diurnal changes. Among them, the expression pattern of OsPIP2;5 paralleled the potential evaporation (Ep) and leaf stomatal conductance on a sunny day. The gene expression analysis clearly showed diverse expression patterns; the gene expression levels of many aquaporins decreased after panicle formation stage, whereas the abundance of some genes such as OsNIP2;1 and OsAMT1;3 increased at the later growth stage. Our method will be useful for evaluating the variations of gene expression in the roots of field-grown rice under fluctuating environmental condition.
Databáze: OpenAIRE
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