Evaluation of genetic diversity and selection signatures in native Turkish cattle breeds via high-density SNP data

Genetic diversity is essential for livestock populations to survive and develop adaptation against diverse environmental conditions, whereas long-term natural and artificial selection may extend homozygosity across the genome leaving genomic patterns called selection signatures. This study is the first attempt to assess genetic diversity, population structure, and selection signatures in native Turkish cattle breeds known as Anatolian Black (YK), East Anatolian Red (DAK), South Anatolian Red (GAK), South Anatolian Yellow (YGS), Turkish Grey Steppe (BI), and Zavot (ZAV) by high-density genomic data. In order to obtain deeper information about the genetic origin and selection pressure on native Turkish cattle breeds, two cosmopolitan cattle breeds namely Holstein Friesian (SA) and Brown Swiss (İE) were also involved in this study. Being 20 sample from each breeds, a total of 160 individuals were sampled from different regions of the country in which only YGS breed was sampled from the herds under national conservation program. ddRADseq method was utilised to prepare two genomic DNA libraries which were further sequenced via the Illumina HiSeq X Ten platform containing paired-end sequencing with 150x2 option . While a total of 1.786.253 SNPs were observed across eight cattle breeds, 211.119 SNPs were passed quality control processes. Compared to cosmopolitan cattle breeds, a higher genetic variation was observed in native Turkish cattle with an average of 0.380 Observed Heterozygosity (HO). Genetic distances were comparatively low between native cattle breeds, whereas the highest genetic distance (0.064) was detected between YGS and İE. The highest genetic diversity parameters such as Minor Allele Frequency (MAF) (0.381), (HO) (0.400), and Expected Heterozygosity (HE) (0.456) were observed in YGS breed. 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 YK, BI, GAK, and YGS, whereas DAK and ZAV were distinct from the other native and cosmopolitan cattle breeds. Two different approaches known as Runs of Homozygosity (ROH) and fixation index (FST) were utilised to detect selection signatures within and between studies cattle breeds, respectively. FST approach yielded 114 SNPs under selection pressure distributed on 23 autosomes. Of these SNPs, 78 overlapped with 190 protein-coding genes. ROH approach revealed 108 genomic regions overlapped with a total of 309 protein-coding genes under selection pressure. A higher number of genes under selection pressure was observed in cosmopolitan cattle breeds compared to the native ones. Indeed, selection signatures on 104 and 125 protein-coding genes were detected in İE and SA, respectively, while the number of the genes under selection pressure ranged from 6 in YK and YGS to 55 in DAK among native breeds. Several genes under selection pressure in native Turkish cattle breeds were related to fertility (CAMK4), growth (GDF11 and GHR), environmental adaptation such as heat tolerance (XCL1, PEX14, and CORT), resistance to bovine leukaemia (AP4B1, BCL2L15, and PHTF1), parasitic diseases (DDX59 and CAMSAP2), mycobacterial infections (HEBP1 and ST32B), dermatitis digitalis (RORA), bleeding disorders (P2RY12) as well as biological processes such as carbon dioxide transformation in several cells (CA10). In this study, the highest genetic diversity and lowest selection pressure were observed in YGS breed which is sampled from the herds under national conservation program. Results of this study confirm that selection pressure over the genome could be facilitated via suitable conservation programs by which heterozygosity and genetic diversity could be increased in native cattle breeds.