Local and global patterns of admixture and population structure in Iranian native cattle

Abstract

BackgroundTwo separate domestication events gave rise to humped zebu cattle in India and humpless taurine cattle in the Fertile Crescent of the Near and Middle East. Iran covers the Eastern side of the Fertile Crescent and exhibits a variety of native cattle breeds, however, only little is known about the admixture patterns of Iranian cattle and their contribution to the formation of modern cattle breeds.ResultsGenome-wide data (700 k chip) of eight Iranian cattle breeds (Sarabi N = 19, Kurdi N = 7, Taleshi N = 7, Mazandarani N = 10, Najdi N = 7, Pars N = 7, Kermani N = 9, and Sistani N = 9) were collected from across Iran. For a local assessment, taurine (Holstein and Jersey) and indicine (Brahman) outgroup samples were used. For the global perspective, 134 world-wide cattle breeds were included. Between breed variation amongst Iranian cattle explained 60 % (p < 0.001) of the total molecular variation and 82.88 % (p < 0.001) when outgroups were included. Several migration edges were observed within the Iranian cattle breeds. The highest indicine proportion was found in Sistani. All Iranian breeds with higher indicine ancestry were more admixed with a complex migration pattern. Nineteen founder populations most accurately explained the admixture of 44 selected representative cattle breeds (standard error 0.4617). Low levels of African ancestry were identified in Iranian cattle breeds (on average 7.5 %); however, the signal did not persist through all analyses. Admixture and migration analyses revealed minimal introgression from Iranian cattle into other taurine cattle (Holstein, Hanwoo, Anatolian breeds).ConclusionThe eight Iranian cattle breeds feature a discrete genetic composition which should be considered in conservation programs aimed at preserving unique species and genetic diversity. Despite a complex admixture pattern among Iranian cattle breeds, there was no strong introgression from other world-wide cattle breeds into Iranian cattle and vice versa. Considering Iran’s central location of cattle domestication, Iranian cattle might represent a local domestication event that remained contained and did not contribute to the formation of modern breeds, or genetics of the ancestral population that gave rise to modern cattle is too diluted to be linked directly to any current cattle breeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0416-z) contains supplementary material, which is available to authorized users.

Domestication of cattle: Two or three events?

“…Furthermore, the central block of the neighbour‐net depicts multiple complex connections among breeds, suggesting relatively recent divergence across many populations (Felius, ). Despite being classified as B. taurus , Middle Eastern breeds occupy central positions both in the neighbour‐net and MDS analyses, suggesting an admixed genetic background with an indicus component, as has been observed for several breeds from the Middle East and Fertile Crescent (Decker et al., ; Karimi et al., ; Loftus et al., ). Consistent with the hypothesis of admixture of European taurine populations with local aurochs prior to their extinction approximately 400 YA (Achilli et al., ; Park et al., ; Upadhyay et al., ), the B. p. primigenius sample in this study is placed close to Eurasian taurine groups in the MDS analysis.…”

Population Structure Analysis of Bull Genomes of European and Western Ancestry

“…However, these methods may be sensitive to early divergence events or unable to capture hierarchical relationships7. Analysis of regional breeds often needs to include other published cattle genomes in order to estimate introgression or admixture589. This poses a significant challenge in population genomics.…”

“…The 1000 Bull Genomes Consortium has successfully collaborated with institutions from more than 20 countries to collect 1577 whole genome sequences (as of version 5). Although the structural complexity of cattle has previously been studied based on array-based genome profiles or selected genetic markers, focusing on regions and breeds456789, a population genomic study involving whole genome sequences related to European and Western ancestry has not been performed.…”

Cattle selectivity by leopards suggests ways to mitigate human–leopard conflict

“…Cattle are the dominant livestock in forested areas bred for milk, dairy products, beef, and breeding (Babrgir, Farhadinia, & Moqanaki, ; Noack et al., ). Mazandarani is the main local cattle breed of low introgression and better genetic quality than other native breeds (Karimi, Koshkoiyeh, Fozi, Porto‐Neto, & Gondro, ; Karimi, Strucken et al., ). Stud cattle and cows with juveniles are kept in village corrals, and a majority of cattle graze in forest, usually unattended by shepherds and dogs (this study; Babrgir et al., ; Ghoddousi et al., ; Khorozyan et al., ; Khorozyan et al., ).…”

“…Cattle are the dominant livestock in forested areas bred for milk, dairy products, beef, and breeding (Babrgir, Farhadinia, & Moqanaki, 2017;Noack et al, 2010). Mazandarani is the main local cattle breed of low introgression and better genetic quality than other native breeds (Karimi, Koshkoiyeh, Fozi, Porto-Neto, & Gondro, 2016;Karimi, Strucken et al, 2016). Stud Khorozyan et al, 2015;Khorozyan et al, 2017).…”