The interaction of genes controlling root traits is required for the developmental acquisition of deep and thick root traits and improving root architecture in response to low water or nitrogen content in rice (Oryza sativa L.) cultivars.

Most of the hot spots about rice research are related to roots; increasing rice yield is mainly associated with improving root traits. Understanding phenotype-gene regulation relationship in different rice cultivars can contribute to the genetic improvement of root system. The expression pattern of root genes in moroberekan (deep and thick roots and high root/shoot ratio "R/S") was compared to that in Giza178 and PM12 (numerous but shallow roots) and IR64 (fewer but deeper roots than the latter ones). In contrast to the other genotypes, moroberekan did not cease developing deep and thick roots even after 60 days from sowing, perhaps because of not only the consistent upregulation but also the interaction of root genes. Xylem sap flow was significantly higher even under drought (low water content) in moroberekan. Auxin signaling-related ARF12 and PIN1 genes could play key roles in improving root traits in response to low water or nitrogen content. Their concurrent upregulation was coincided with developing 1) deeper roots in moroberekan under drought, 2) thicker and deeper roots in PM12 under low nitrogen content (LN) and 3) new roots with thicker and deeper characteristics in the four genotypes after root trimming. The upregulation of PIN1 or ARF12 in Giza178 at LN, PM12 at drought or in IR64 under drought or LN did not greatly change the root traits. Hierarchical analysis showed that ARF12 and PIN1 were distantly related, but overlapped with other genes controlling root traits. Overexpression of ARF12 and PIN1 could improve root traits in rice cultivars.