Quantitative trait loci for stay‐greenness and agronomic traits provide new insights into chlorophyll homeostasis and nitrogen use in rice

Functional stay‐green (FSG) is characterized by delayed senescence during the reproductive stage in rice. A recombinant inbred line (RIL) population derived from ‘Pusa 677’/‘PSG16’ was used to study the genetics of FSG in a rice mutant, ‘PSG16’. The RILs exhibited significant variation under two N regimes for agro‐morphological traits, leaf chlorophyll content, flowering time, yield components and nitrogen (N) use. Using a genome wide linkage map spanning 1910.8 cM with 104 polymorphic markers, we have mapped six major quantitative trait loci (QTLs). One robust QTL on chromosome 1 was associated consistently across different N regimes with chlorophyll content and flowering time. The QTL on chromosome 7 was associated with grain number, whereas the QTL on chromosome 6 was found related to N harvest index and spikelet fertility. Although ‘PSG16’ showed a clear advantage in grain yield as well as having better N assimilation, we could not establish a direct genetic relationship SG trait and N use. Based on the QTL information, FSG trait of ‘PSG16’ could be useful in deciphering multiple stress responses in rice.