Genetic analysis of germinating ability under alkaline and neutral salt stress by a high-density bin genetic map in rice

The knowledge about the genetic basis of alkaline salt stress and neutral salt stress in rice is limited. Here, we located quantitative trait loci (QTL) for seed germination rate (GR) under alkaline salt stress (NaHCO 3 ) and neutral salt stress (NaCl) using backcross inbred lines population, which was derived from a cross between indica cv. Changhui 891 (CH891) and japonica cv. 02428 with 3057 bins markers. A total of ten QTL for five salt stress-related traits were detected. The QTL detected for control condition, NaCl stress, and NaHCO 3 stress were quite different, which suggested that the genes controlling the transport of the Na + , in the form of NaCl and the NaHCO 3 , may be different or induced incoordinately by salt stress. Furthermore, on the basis of the high-density genetic map, the ten QTL were mapped on 40–980 kb chromosomal regions on Nipponbare genome, and 16 candidate genes related to stress or metal transport were found. These results contribute to the fine mapping and use of these GR-related QTL.