QTL mapping for nitrogen-use efficiency and nitrogen-deficiency tolerance traits in rice

The improvement of nitrogen-deficiency tolerance (NDT) and nitrogen-use efficiency (NUE) traits is an important objective of many rice breeding programs. A better understanding of their relationship is required for more efficient breeding. The objectives of this study were to map quantitative trait loci (QTLs) for NDT and NUE traits, and to gain a better understanding about the genetic basis of the relationships between NUE and NDT traits. 127 recombinant inbred lines (RILs) deriving from the cross of Zhenshan97/Minghui63 were tested in field conditions with low nitrogen (LN, 0 kg/ha) and normal nitrogen conditions (NN, 135 kg/ha in 2006 and 130 kg/ha in 2007). NDT traits were the ratio of a trait value under LN to NN, including grain yield, biomass yield, grain nitrogen and biomass nitrogen. NUE traits were nitrogen response, grain yield response and physiological nitrogen-use efficiency (PE). For NDT traits, seven and eight QTLs were identified in 2006 and 2007, respectively. These QTLs were on chromosomes 1, 2, 3, 4, 7, 9, 10 and 11. For NUE traits, five and six QTLs were detected on chromosomes 1, 2, 3, 4, 6, 7, 9, 10 and 11 in 2006 and 2007, respectively. Four genomic regions, including G393-C922 on chromosome 1, RM232-C63 on chromosome 3, G235-G102 on chromosome 4 and RG678-R1440 on chromosome 7, were found to contain QTLs for NDT and NUE traits. NUE traits significantly negatively correlated with NDT traits in the two testing years, except for the correlations between physiological nitrogen-use efficiency and relative biomass nitrogen. The four QTL clusters harboring QTLs for both NDT and NUE traits, provides partial explanation and genetic mechanism for the observed correlations between NDT and NUE traits, and could be used as targets for improving NDT and NUE traits in future breeding.