Genome-wide genetic variation and population structure of native and cosmopolitan cattle breeds reared in Türkiye

Abstract

This is the first comprehensive study to reveal genetic variation and population structure at genome level in six Anatolian (Anatolian Black, East Anatolian Red, South Anatolian Red, South Anatolian Yellow, Turkish Grey Steppe, and Zavot) and two cosmopolitan (Brown Swiss and Holstein Friesian) cattle breeds reared in Türkiye. Being 20 samples from each population, a total of 160 blood samples retrieved from representative herds were utilized to generate genomic libraries by ddRADseq method. Genomic libraries sequenced by Illumina HiSeq X Ten instrument revealed a total of 211,119 bi-allelic SNPs with high call rate. Compared to cosmopolitan cattle breeds, a higher genetic variation was observed in native Turkish cattle with an average of 0.380 observed heterozygosity. Genetic distances were comparatively low between native cattle breeds, whereas the highest genetic distance (0.064) was detected between South Anatolian Yellow and Brown Swiss. Population structure analyses showed that the native Turkish and cosmopolitan cattle breeds were clearly different from each other according to their phylogenetic origin. Besides, a high level of genetic admixture was detected among Anatolian Black, Turkish Grey Steppe, South Anatolian Red, and South Anatolian Yellow, whereas East Anatolian Red and Zavot were distinct from the other native and cosmopolitan cattle breeds. TreeMix algorithm under the assumption of one and two migration events revealed a migration route from Anatolian clade to Anatolian Black, while a second migration edge was drawn from Brown Swiss to East Anatolian Red. This study demonstrates the importance of national conservation studies in the native breeds whose population size has dramatically decreased. In addition, SNP arrays and next-generation sequencing platforms are recommended for future studies to reveal the genetic variation of other local Turkish livestock species to arrange effective conservation programs.

Keywords:

• Anatolian cattle
• animal genetic resources
• ddRADseq
• genomic variation
• NGS

Acknowledgment

The authors thank to ‘General Directorate of Agricultural Research and Policies’, ‘Eastern Mediterranean Agricultural Research Institute’ and all staff working on the In-situ Conservation Subproject of South Anatolian Yellow for proving blood samples of South Anatolian Yellow. The numerical calculations reported in this paper were fully/partially performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (TRUBA resources).

Authors’ contributions

ED: Data collection, Methodology, Data curation, Funding acquisition, Draft writing; NM: Data analysis, Methodology; SK: Data collection, Methodology; RK: Data analysis, Methodology; HD: Resources, Methodology; ÜB: Resources, Methodology; MSB: Supervision, Project administration, Funding acquisition; TK: Supervision, Project administration, Data collection, Funding acquisition.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This study was financially supported ‘The Scientific Research Projects Coordination Unit of Akdeniz University (project no: FDK-2022-5876)’ and ‘The Scientific and Technological Research Council of Türkiye (project no: 221O553)’. ‘The Scientific and Technological Research Council of Türkiye’ also supported the 12-month stay of Eymen Demir at the Slovak University of Agriculture in Nitra, Slovak Republic (project no. 1059B142100368)’.