Mapping of QTLs controlling seedling establishment using a direct seeding method in rice

Low-temperature is one of the most common environmental stresses that affect plant growth and development and places a major limit on plant productivity. Tolerance to low-temperature is an important objective of rice breeding programs in temperate areas and at high altitudes in tropical and sub-tropical areas. Vigorous rice growth during the seedling stage at low-temperature is an important characteristic for stable seedling establishment (SES) in direct seeding methods, in which rice is sown directly into a flooded field. The aim of this study was to identify QTLs controlling SES using 3 mapping populations of backcrossed inbred lines (BILs) with Arroz Da Terra and Italica Livorno as the donor parents. SES was evaluated by a field evaluation system in this study, which is used in current rice breeding programs because of the complexity of environmental conditions in SES in rice cultivation in a paddy field. A total of 9 chromosomal regions for SES were identified, which explained 10.9% to 25.6% of total phenotypic variation. For all of QTLs except for qSES5-2, alleles from the donor parents increased phenotypic values. These QTLs should be useful for the improvement of SES in rice breeding programs in low-temperature regions.