Naemi, Heri, Najdi and Sawakni sheep breeds inhabiting Kingdom of Saudi Arabia were studied on both physiological and molecular bases. Native polyacrylamide gel-electrophoreses for two enzymes Malate Dehydrogenase (Mdh) and Malic Enzyme (Me) recorded 5 isoenzyme loci from which 4 were polymorphic and 1 was monomorphic. Mdh showed three fractions, the first was recorded in Sawakni and Najdi breeds, the second was monomorphic and was recorded in all breeds while the third was recorded in all except Heri. Malic enzyme showed two polymorphic fractions, the first was recorded in Heri and Naemi and the second was recorded in all breeds. Both metabolic enzymes activities were higher in Sawakni than in the native breeds. 607, 227, 498 and 595 bp nucleotides from CO1, ND4, cytb genes and d-loop, respectively, were sequenced with no base substitutions among and/or within breeds except for ND4 gene and d-loop. The molecular tree clustered the three breeds other than Naemi in one group and Naemi was basal. Isoenzymes therefore, discriminate clearly the studied breeds although they are not as accurate as molecular tools indicating their applicability with more efficiency in physiology than in genetics while the d-loop was efficient in discriminating the studied breeds phynotypically
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