Genetic Mapping of Anaerobic Germination-Associated QTLs Controlling Coleoptile Elongation in Rice

BACKGROUND: Increasing numbers of rice farmers are adopting direct-seeding methods to save on costs associated with labor and transplanting. Successful seedling establishment in flooded conditions requires rapid coleoptile growth to ensure access to oxygen near the water surface. It is important that the natural variations in coleoptile growth of submerged rice plants are identified. RESULTS: Coleoptile responses of submerged plants at the germination stage were analyzed in diverse rice accessions and recombinant inbred lines. Several genomic regions identified from a genome-wide association analysis were significantly associated with anaerobic germination, with many that corresponded to published quantitative trait locus (QTL) intervals. In the recombinant inbred line population derived from a cross between japonica and indica varieties, only one unique and strong signal explaining about 27 % of the phenotypic variation was detected. Distinct haplotypes associated with variations in coleoptile length were identified in diverse germplasm. CONCLUSIONS: We demonstrated the value of combining genome-wide association analysis and biparental QTL mapping approaches to identify chromosomal regions regulating coleoptile elongation in submerged rice plants. The significant genomic regions detected in this study are potential candidates for incorporation into elite cultivars to improve seedling survival during anaerobic germination. Future studies that map the QTLs and investigate the effects and functions of candidate genes may lead to new rice varieties that can be used in direct-seeding systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12284-015-0072-3) contains supplementary material, which is available to authorized users.