QTL analysis of nitrogen content of plant shoot under two nitrogen conditions in rice (Oryza sativa L.).

As an essential macronutrient, nitrogen (N) is one of the most important factors which could limit agricultural productivity and plays an important role in rice yield formation. To investigate the genetic mechanism of N absorption and utilization efficiency and to improve N utilization efficiency in rice a QTL analysis was done. The main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs) for nitrogen content (NC) of plant shoot at heading and mature stages in two N conditions were identified using a double haploid population derived from a cross between a japonica Chun Jiang06 (CJ06) and an indica Taichung Native 1 (TN1). A total of three NC QTLs were detected on chromosomes 5, 6 and 8 in two N conditions. The phenotypic variation explained by individual QTL ranged from 9.73 to 39.50%. Two pairs of digenic epistatic loci were associated with NC. The QTL qNc8-4 was detected in both high nitrogen (HN) and low nitrogen (LN) conditions, and explained phenotypic variation 18.35% and 39.5% in HN and LN conditions, respectively. The analysis revealed that the additive effect of qNc8-4 came from TN1. Then the qNc8-4 was considered as the main effect loci affecting NC of rice shoot. We suggest that QTL markers of qNc8-4, RM4085 and RM1111, expressing in LN conditions, may be used to improve the N absorption and utilization efficiency in low input rice varieties through marker assisted selection (MAS) breeding programs. It is the first time to use a genetic population like this to map the QTLs of NC of plant shoot in rice, and these results will supply references and research forecast for further study on practicable methods of N utilization, cloning the genes which affect NC and improving N utilization efficiency of varieties by MAS.