Quantitative Trait Loci Analysis of Responses to Nitrogen and Phosphorus Deficiency in Rice Chromosomal Segment Substitution Lines

Abstract

Tolerance to low nitrogen and low phosphorus conditions is a highly desired characteristic for sustainable crop production. In this study, a set of 125 chromosome segment substitution lines (CSSL), each containing a single or few introgression segments from a japonica cv. Nipponbare with the genetic background of an indica cv. 9311, were evaluated using augmented design under the field experiment with normal, low nitrogen (N0), and low phosphorus (P0) conditions. The grain yield and panicle number per plant were measured for each CSSL, and their relative values based on N0 or P0 and normal conditions were considered as the measurement for tolerance to low soil nutrient. The results showed that both the N0 and P0 conditions had strong negative effect on yield and panicle number, and there were different responses among the CSSLs to the stresses, and the relative traits had a significant nega- tive correlation with the traits under the normal condition. 9311 showed better tolerance to low nutrient conditions than Nipponbare. A total of 38 chromosomal regions or quantitative trait loci (QTL) all with negative allelic effects from Nipponbare were detected for the measured traits under the nitrogen and the phosphorus stresses, of those 26 QTLs were for the yield and panicle number, 12 QTLs for the relative traits. Five chromosomal regions were identified in common under both the stresses, while most QTLs (81%) were specifically detected only in low nitrogen or phosphorus condition. Such different QTLs suggest that the responses to limiting nitrogen and phosphorus conditions are regulated by different sets of genes in rice. Most QTLs for the relative traits were co-localized with those for the yield and the panicle number under either nitrogen or phosphorus stresses, indicating that the tolerance QTLs may be involved in nitrogen and phosphorus uptake or assimilation pathway in rice.