Association analysis of closely linked markers to major QTLs Saltol and SKC1 and salt tolerance-related traits in rice varieties

So far to genetic improvement of rice varieties to salinity stress, considerable researches has been performed related to QTL mapping with identifying of major QTLs of Saltol and SKC1 on chromosome 1 as a result. These QTLs are involved in control of some important traits related to salinity stress. The present study was conducted to evaluate and validate of closely linked markers of the QTLs in landrace and improved varieties. With above aims phenotyping carried out as factorial experiment in randomized complete block design with two factor variety (45 genotypes) and salinity (three levels control, 6 and 12 dS.m-2 NaCl). Ahlami Tarom, Binam, Pokalli, Has. Atashgah, Dom Zard, Shahpasand Mazandaran, Tarom Mahali, Gharib, Ghasroldashti, Mousa Tarom were assigned to tolerant group under 12 dS.m-2 condition. The varieties were genotyped for 23 microsatellite markers that were introduced out of fine mapping programs as closely linked markers to major QTLs of Saltol and SKC1. The results revealed although varieties clustering in term of phenotypic traits were not very conformity with genotypic clustering, the association analysis results was conveys this fact that on the chromosome 1 in the landrace and improved Iranian varieties there are some informative and significant markers including RM10136, RM10655 and RM3412 with regression model explaining considerable percent of phenotyping salt tolerance related traits. The results of present study can be used in breeding programs such as marker assisted selection directly if the results are confirmed.