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In Egypt, around 60% of cultivated lands of Northern Delta region are considered soil salinity areas. A two-year three field experiments were carried out to evaluate six Egyptian Barley genotypes under different soil salinity levels (4 , 8 and 12 dSm-1) during two consecutive seasons 2019/2020 and 2020/2021 using agro-morphological, germination percentage, seedling vigor, grain quality, stress indices, multivariable analysis and inter simple sequence repeats (ISSRs) marker. Increasing salinity level from (4 to 12 dSm-1) diminished the performance of all measured traits; however increasing protein content reached to 15.39% and heading data was quickens by 5.44% with strong and negative relationship with grain yield. Six salt stress indices were calculated based on grain yield; results showed that mean productivity (MP), harmonic Mean (HM) and stress tolerance index (STI) were more effective indices for detecting the high yielding genotypes. Ten ISSR primers were used to assess the genetic diversity among all genotypes; all primers showed high average percentage of polymorphic loci was 81.6%. The ISSR (UBC 835) primer generate the highest band number, polymorphism, polymorphism information content (PIC), effective multiplex ratio (EMR), diversity index (DI),), resolving power (RP), and marker index MI values were (8,100%, 0.50, 0.43, 5.80 3.20 and 0.88) respectively. Furthermore, ISSR (UBC 835) primer had amplified specific allele with molecular size 800 bp found in the tolerance cultivars (Line 4 and Giza 137) indicating that this primer is highly informative as a positive marker for salt tolerance. The heatmap cluster constructed using Euclidean distance and average linkage based on 12 phenotypic traits, seven salt tolerance indices and 10 ISSR primers showing that the six Barley genotypes were clustered into two main clusters, each cluster include the most closed genotypes together based on their response to salinity stress which could be used future in salinity breeding programs for high yield production under salinity soil areas in Egypt.
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