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Background  Nitrogen (N) is a major input cost in rice production, in addition to causing severe pollution to agricultural and ecological environments. Root dry weight has been considered the most important component related to crop yields than the other root traits. Therefore, development of rice varieties/lines with low input of N fertilizer and higher root traits are essential for sustainable rice production.    Results  In this context, a main effect quantitative trait locus  qRDWN6   XB   on the long arm of chromosome 6 which positively confers tolerance to N deficiency in the  Indica  rice variety XieqingzaoB, was identified using a chromosomal segment substitution line (CSSL) population.  qRDWN6   XB   was determined to be located near marker InD90 on chromosome 6 based on association analysis of phenotype data from three N levels and 120 polymorphic molecular markers. The target chromosomal segment substitution line CSSL45, which has the higher root dry weight (RDW) than  indica  cultivar Zhonghui9308 and carry  qRDWN6   XB   ,  was selected for further study. A BC 5 F 2:3  population derived from a cross between CSSL45 and Zhonghui9308 was constructed. To fine-map  qRDWN6   XB  , we used the homozygous recombinant plants and ultimately this locus was narrowed to a 52.3-kb between markers ND-4 and RM19771, which contains nine candidate genes in this region. One of these genes,  LOC_Os06g15910  as a potassium transporter was considered a strong candidate gene for the  RDWN6   XB   locus.    Conclusions  The identification of  qRDWN6   XB   provides a new genetic resource for breeding rice varieties and a starting point to improve grain yield despite the decreased input of N fertilizers. The newly developed and tightly linked InDel marker ND-4 will be useful to improve the root system architecture under low N by marker-assisted selection (MAS) in rice breeding programs.

RDWN6XB, a major quantitative trait locus positively enhances root system architecture under nitrogen deficiency in rice