Evaluation and GWAS of radicle gravitropic response in a core rice germplasm population

Aims Since gravitropism is one of the primary determinants of root development, facilitating root penetration into soil and subsequent absorption of water and nutrients, we studied this response in rice. Methods The gravitropism of 226 Chinese rice micro-core accessions and drought-resistant core accessions were assessed through the modified gravity-bending experiment and genome-wide association analysis (GWAS) was used to map the associated QTLs. Results The average value of gravitropic response speed of seminal roots was 41.05°/h, ranging from 16.77°/h to 62.83°/h. The gravity response speed of Indica (42.49°/h) was significantly (P < 0.002) higher than Japonica (39.71°/h) subspecies. The gravitational response speed of seminal roots was significantly positively correlated with the number of deep roots (r = 0.16), the growth speed of seminal roots (r = 0.21) and the drought resistance coefficient (r = 0.14). Conclusions In total, 3 QTLs (quantitative traits) associated with gravitropic response speed were identified on chromosome 4, 11 and 12. There are some known QTLs relating to roots traits and drought resistance located nearby the QTLs identified here, which confirms the close relationship between radicle gravitropism and the drought resistance. From within these intervals, 5 candidate genes were screened and verified by qPCR in a few rice varieties with extreme phenotypic values, demonstrating that gene LOC_Os12g29350 may regulate gravitropism negatively. This may be a promising candidate to be confirmed in further studies.