QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice

Nitrogen is one of the most important nutrients for rice growth and development. Breeding of nitrogen deficiency tolerance (NDT) variety is considered to be the most economic measure to solve the constrain of low nitrogen stress on grain yield in rice. An interconnected breeding (IB) population of 497 lines developed using Huanghuazhan (HHZ) as the recurrent parent and eight elite lines as the donor parents were tested for five traits including grain yield, biomass, harvest index, thousand grain weight, and spikelet fertility under two nitrogen treatments in three growing seasons. Association analysis using 7,388 bins generated by sequencing identified a total of 14, 14, and 12 QTLs for the five traits under low nitrogen (LN), normal nitrogen (NN), and LN/NN conditions, respectively, across three seasons. Favorable alleles were dissected for the 40 QTLs at the 10 NDT regions, and OM1723 was considered as the most important parent with the highest frequency of favorable alleles contributing to NDT-related traits. Six superior lines all showed significantly higher GY in LN environments and similar GY under NN environments except for H10. Substitution mapping using near-isogenic introgression lines delimited the qTGW2-1, which was identified on chromosome 2 under LN, NN, and LN/NN conditions into two QTLs, which were located in the two regions of about 200 and 350 kb with different favorable alleles. The bins 16, 1301, 1465, 1486, 3464, and 6249 harbored the QTLs for NDT detected in this study, and the QTLs/genes previously identified for NDT or nitrogen use efficiency (NUE) could be used for enhancing NDT and NUE by marker-assisted selection (MAS).