The identification issue of livestock can be resolved by using molecular
identification tools that are acceptable to preserve and maintain pure breeds
worldwide. The application of a molecular identification methodology is more
important for developing nations, e.g., Pakistan, where uncontrolled
crossbreeding has become a common practice and the import of exotic animals and
germplasm is ever increasing. This presents a risk to local breeds as also stated by the FAO. Therefore, the current study was designed to
develop standard molecular markers for Cholistani cattle to ascertain their
purity for breeding purpose. In this study 50 and 48 unrelated males were
sampled for Cholistani and each crossbred cattle, respectively. Candidate
molecular markers present in Cholistani but absent in crossbred cattle and vice
versa were detected using the amplified fragment length polymorphism (AFLP)
method. Eleven markers were developed and were converted to single nucleotide
polymorphism (SNP) markers for genotyping. The allele frequencies in both
breeds were determined for discrimination ability using polymerase-chain-reaction–restriction-fragment-polymorphism (PCR-AFLP). The probability of
identifying the Cholistani breed was 0.905 and the probability of misjudgment
was 0.073 using a panel of markers. The identified markers can ascertain the
breed purity and are likely to extend the facility for breed purity testing
before entering into a genetic improvement program in the country.</p
