Drought is a major environmental stress threatening wheat (Triticum aestivum L.) productivity worldwide. Although drought impedes wheat performance at all growth stages, it is more critical during the flowering and grain-filling phases and results in substantial yield losses. In this context, stem water-soluble carbohydrates (SWSC) were dissected at flowering and grain filling stages under drought stress (DS) and well-watered (WW) conditions using a population consisted of 116 wheat accessions in this research. The main goal was to dissect the genetic basis of water-soluble carbohydrates and the agronomic traits using association mapping approach and identify linked molecular markers. The results showed significant and positive correlations for stem water-soluble carbohydrates at grain filling (SWSCG) with accumulating efficiency of stem water-soluble carbohydrates (AESWSC) and grain filling efficiency at the late stage (GFEL). The accumulating and grain filling efficiency at grain filling stage could play an important role for SWSC especially under DS condition. Four favorable alleles for plant height (PH) and grain yield (GY) were identified in two water environments. Xbarc78-4A 163 and Xbarc78-4A 155 were variant alleles for PH which were identified in both water regimes. Whereas Xwmc25-2D positively linked with GY in WW. Although Xwmc420-4A 121 and Xwmc112-2D 215 were alleles for stem water-soluble carbohydrates at flowering (SWSCF) and SWSCG in DS but the frequency were < 5% so they were considered as rare alleles. These SSR markers which explained significant level of phenotypic variability for chosen traits could be used for selection of genotypes in wheat breeding programs through marker-assisted selection.
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