Genetics of yield component traits under salt stress at flowering stage and selection of salt tolerant pre-breeding lines for rice improvement

Rice is highly vulnerable to salt stress at both seedling and flowering stage. While research efforts largely focused on seedling stage salinity tolerance, flowering stage salt tolerance studies are limited. Development of rice cultivars with salt tolerance at both stages will enhance rice productivity in salt affected farmlands. In the present study, two introgression line (IL) populations of a salt-tolerant landrace ‘Nona Bokra (N)’ were developed in the genetic backgrounds of two U.S. cultivars ‘Cheniere (C)’ and ‘Jupiter (J)’ and were evaluated for elucidation of the genetic basis of agronomically important traits at flowering stage and development of salt tolerant pre-breeding lines. Evaluation of both sets of ILs (JN-ILs and CN-ILs) under saline (EC = 8 dSm −1 ) environment led to identification of a total of 33 QTLs for seven different yield and yield component traits impacted by salt stress. Majority of large-effect QTLs for traits such as panicle length ( qPL1.1 JN ), spikelet sterility ( qSS1.1 JN ), thousand-grain weight ( qTGW1.1 JN ), days to flowering ( qDFF1.1 CN ), and plant height ( qPH1.1 CN ) were located on chromosome 1. Some candidate genes present within the major effect QTL regions include potassium channel OsKAT1, NAC domain-containing protein, potassium transporters, and photosensitive leaf rolling 1. Comparison of the results with earlier reports on seedling stage suggested a different set of genes controlling salt tolerance at both stages. In addition, pre-breeding lines with improved flowering stage salinity tolerance were identified. These pre-breeding rice lines will accelerate fine mapping, map-based cloning, and pyramiding of desirable alleles for both flowering and seedling stage salt tolerance through marker assisted selection.