Mapping Salinity Tolerance QTLs at Early Seedling Stage in Rice Using F\(_2\) Mapping Population

Abstract

Salinity stress is one of the most widespread soil problem next to drought, in rice growing areas around the globe. Genetically improving salt tolerance in rice is a highly important in rice breeding programs. In this investigation, QTL analysis of seven physiological traits related to salt tolerance at seedling stage was carried out using F2 population derived from a cross between a salt-tolerant variety, MTU 1061 (Indra), and a salt-sensitive variety, MTU 1121 (Sri Druthi). 234 F2:3 lines were evaluated for salt tolerance at seedling stage in a hydroponics experiment. Genotyping was carried out using 234 chosen F2 plants with 104 polymorphic SSR markers, yielding a genetic linkage map extending 2956.12 cM of whole rice genome. Applying the Inclusive Composite Interval Mapping (ICIM), a total of 51 QTLs were detected as follows; two QTLs for SIS score, four QTLs for shoot Na+ concentration, two QTLs for shoot K+ concentration, 16 QTLs for NaK ratio, 17 QTLs for shoot length, six QTLs for root length and four QTLs for shoot dry weight. Out of the 51 QTLs, one of the QTL qNaK-1-1 position was corresponding to Saltol locus on chromosome 1. The phenotypic variation explained by these QTLs ranged from 0.1 to 11% of the total variation. Overall, this research adds to our understanding of the genetic basis of salt tolerance mechanism in rice and identifies potential QTLs for future breeding efforts utilizing MAS.