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Two lines of Alexandria chicken (selected L1 and control L2) were characterized for their genetic diversity and identified population priorities for egg traits. Eight microsatellite markers linked to QTLs associated with the studied egg traits were used. Eight microsatellite markers linked to QTLs associated with the studied egg traits were used as well as scanning electron microscopy was used to assess the effect of selection on eggshell ultra-structure. The ultra-structure of eggshell measurements and associated genetic markers may be useful in selection to improve eggshell quality.