Environmental response and genomic regions correlated with rice root growth and yield under drought in the OryzaSNP panel across multiple study systems

The rapid progress in genotyping of rice must be matched by advances in phenotyping. A better understanding of the genetic variation in rice for drought response and root traits as well as practical methods for studying them are needed. In this study, the OryzaSNP set (a set of 20 diverse genotypes that have been mapped for SNP markers) was phenotyped in a range of field and container studies to better characterize the diversity of rice root responses to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. Based on the SNP data, we identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7 - 40.7 Mb) and on chromosome 8 (20.3-21.9 Mb). Rice root and drought-yield QTL have been previously identified in these regions. Across experiments, the particular soil type or growth medium used likely had just as strong of an effect on plant growth as the type of setup and/or container dimensions. The correlation and co-location of root traits from a range of study syste ms points to the potential utility of container root study systems to represent responses in field studies, but the best correlations between field and container studies were observed when the two setups had some similar properties. Due to the co- location of the identified genomic regions with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought