Identification and mapping of quantitative trait loci associated with salinity tolerance in rice (Oryza Sativa) using SSR markers

Document Type: Research Paper


1 Department of Agricultural Biotechnology, International University of Imam Khomeini, P. O. Box 34149-16818, Qazvin, I.R. Iran.

2 Department of Plant Breeding, University of Shahed, P.O. Box 3319118651, Tehran, I.R. Iran.


Salinity stress is one of the most widespread soil problems next to drought, in rice growing areas. Reducing
Sodium (Na+), while maintaining Potassium (K+) uptake in rice are traits that would aid in salinity tolerance.
Therefore, the identification of quantitative trait loci (QTLs) associated with those for Na+ and K+
uptake, will enable breeders to use marker-assisted selection to transfer QTLs into elite lines in rice
improvement programs. In view of this, 62 advanced backcross-inbred lines (BILs), at the BC2F5 generation,
derived from the cross of Tarome-Molaei (salt tolerant) and Tiqing (Salt sensitive), were used to identify
the QTLs involved in salinity stress tolerance, using SSR markers. Advanced backcross inbred lines along
with their parents were evaluated for six parameters viz. Sodium (Na+) and Potassium (K+) in roots and
shoots and the Na+/K+ ratio, using the modified Yoshida’s nutrient solution at an electrical conductivity
of 6 and 12 dS/m. A total of 114, out of 235 simple sequence repeats (SSRs) markers that showed polymorphism in the parents, were used to genotype the BILs. A linkage map was constructed with an average
interval of 15.3 centiMorgan (cM) between the markers, spanning 1747.3 cM across all 12 rice chromosomes.
Using the composite interval mapping (CIM) and a minimum logarithm of the odds (LOD) threshold
of 3.0, a total of 14 QTLs were detected as follows; on chromosome 1 (5 QTLs), 3 (1QTL), 4 (3 QTLs), 5 (2
QTLs), 6 (1 QTL), and 8 (2 QTLs) for all six traits except, Sodium (Na+) in the shoot. The phenotypic
variation explained by these QTLs ranged from 9 to 30% of the total variation. A QTL (QKr1.2) for K+ content
in the root was identified with the highest LOD score (7.8), on chromosome 1. This QTL explicated 30% of the total variation and was identified as a major QTL conferring salt tolerance in rice.