Genomic scan for selection signatures in native (Sarabi, Najdi and Taleshi) and ‎Holstein cattle breeds using hapFLK method

Document Type : Research Paper


1 M.Sc. Student,, Department of Animal Science, College of Agriculture & Natural Resources, ‎University of Tehran, Karaj, Iran

2 Professor, Department of Animal Science, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

3 Assistant Professor, Department of Animal Science, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

4 Assistant Professor, Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran


In order to identify the signatures of selection in three Iranian native cattle and Holstein breeds, genomic information of 153 native cattle (including 63 Sarabi, 44 Najdi and 46 Taleshi) and 60 Holstein cattle and 46 Brahma cattle (as an outgroup breed) were used. In order to determine the genotype of the samples, Illumina Bead Chip 40K (for native breeds) and Illumina Bead Chip 770K (for Holstein and Brahman breeds) were used. The genomic information of foreign breeds was extracted from the WIDDE database. After the quality control of the data, hapFLK statistical method with hapFLK v1.4 software was used to identify selection signatures. Considering the high hapFLK value of 0.1%, selection signatures were identified using the Ensmble Biomart tool, which included 57 genes on chromosome 25. Then, using the PANTHER database, the general biological function of the genes was checked, and the QTLs in the selected region were extracted using the Animalgenome database, and the genes were compared with other researches.The results showed that these genes were associated with different biological pathways such as ATP-dependent activity, binding, catalytic activity, molecular adapter activity, molecular function regulator, molecular transducer activity, transcription regulator activity and transporter activity.The QTLs reported in these areas were also related to the traits of stature and withers hight, milk yield and contents, muscle iron content, body weight and calving ease traits.


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