The aims of the current study were to investigate the effect of drought stress on phenological and morphological traits of sunflower genotypes and to determine the important traits for identifying drought-tolerant and drought-sensitive cultivars. For this purpose, a lattice square-design experiment was conducted with 64 sunflower genotypes in an 8 × 8 pattern with two replications under non-stress and moisture-stress conditions (irrigation holding at the flowering stage) during 2 years 2016 and 2017. Measured and recorded traits were included the some phenological and morphological traits seeds. Sil-96 genotype showed the highest yield under both non-stress and moisture-stress conditions. Among the morphological traits, the head and stem diameters were highly significant to determine the final yield. In comparing the genotypes, it was concluded that the number of seeds per head was the most influential component affecting the yield. Furthermore, 1000-seed weight was the most important factor affecting grain yield under moisture-stress conditions. The result of association analysis study shows that 45 of inter-simple sequence repeat markers in a general linear model are associated with yield and yield component traits and 23 of them were verified in a mixed linear model (MLM) association approach. Also, 32 markers were informative for morpho-physiological traits and 24 of them verified using the MLM. Finally, 19 informative markers were identified for phenological traits and 10 of them were verified by the MLM.

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