Genome-wide insights into population structure and genetic history of Tunisian local cattle using the illumina bovinesnp50 beadchip

Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.

Assessment of Genetic and Health Management of Tunisian Holstein Dairy Herds with a Focus on Longevity

In Tunisia, the recognition of the possibility of including longevity and disease resistance in dairy cattle selection objectives has been hypothesized as a useful strategy by both researchers and producers. However, in this paper, the state of the art, with a focus on health and longevity, is reviewed. Along the same lines, the heritability for the milk traits, fertility traits, and longevity of Tunisian Holstein dairy cows complies with the literature. Therefore, the influence of genetics on some diseases of the dairy cow was investigated. In addition, a decreasing efficiency in cow fertility has been observed over the last few years. The results showed that the risk of culling increased with common diseases. When analyzed with the Weibull model, functional lifespan was strongly influenced by milk yield; therefore, the risk increased with a reduced milk yield. In her first three lactations, the relative risk of selection increased gradually with lactation. Thus, the risk of thinning is highest at the beginning and end of the first feeding and the end of her second feeding. In conclusion, the risk of culling was reduced in parity. The factors that influence the life of the herd, such as health, husbandry, environmental conditions, and management, are often ignored when evaluating longevity.

Discovering of Genomic Variations Associated to Growth Traits by GWAS in Braunvieh Cattle

A genome-wide association study (GWAS) was performed to elucidate genetic architecture of growth traits in Braunvieh cattle. Methods: The study included 300 genotyped animals by the GeneSeek^® Genomic Profiler Bovine LDv.4 panel; after quality control, 22,734 SNP and 276 animals were maintained in the analysis. The examined phenotypic data considered birth (BW), weaning (WW), and yearling weights. The association analysis was performed using the principal components method via the egscore function of the GenABEL version 1.8-0 package in the R environment. The marker rs133262280 located in BTA 22 was associated with BW, and two SNPs were associated with WW, rs43668789 (BTA 11) and rs136155567 (BTA 27). New QTL associated with these liveweight traits and four positional and functional candidate genes potentially involved in variations of the analyzed traits were identified. The most important genes in these genomic regions were MCM2 (minichromosome maintenance complex component 2), TPRA1 (transmembrane protein adipocyte associated 1), GALM (galactose mutarotase), and NRG1 (neuregulin 1), related to embryonic cleavage, bone and tissue growth, cell adhesion, and organic development. This study is the first to present a GWAS conducted in Braunvieh cattle in Mexico providing evidence for genetic architecture of assessed growth traits. Further specific analysis of found associated genes and regions will clarify its contribution to the genetic basis of growth-related traits.

Genomic characterization of the nucleus for conservation of the Chino Santandereano breed using SNP markers

The Chino Santandereano (CHS) creole cattle breed has undergone an adaptation process of more than 500 years to the Colombian mountainous tropics. Despite its advantages, the breed has been replaced by specialized cattle that put it at risk of extinction. The aim of this work was to estimate the genomic diversity and population structure of the nucleus of conservation of the CHS breed. Thirty-seven CHS and 20 Brahman animals were genotyped due to the possible introgression of genes with the GGP Bovine LD v3 chip. Quality control was performed, and linkage disequilibrium (LD), effective population size (Ne), ROH segments, homozygosity, and genomic inbreeding in the breed were estimated. Subsequently, 50 K genomic information of the Holstein (n = 30) and Romosinuano (n = 8) breeds were included to estimate the minor allele frequency (MAF) with common markers and constructing the graphs of the principal component analysis (PCA). Pairwise FSTs were estimated and a neighbor-joining tree was constructed using the IBS matrix. Admixture was used with k = 2 to 10 for the racial composition. LD (r²) was found up to a distance of 0.13 Mb, r² > 0.3 at a distance of 340.3 kb, and Ne of 32 ± 1. ROH inbreeding was 5.36 ± 0.86%, with a higher contribution from recent inbreeding (4.55%). The PCA showed that the creole breeds were closer together, and the Brahman was more distant. The admixture analysis suggested k = 5 possible ancestral groups and shows that within the CHS breed, there seem to be two different groups with little Holstein and Brahman introgression. The genetic diversity parameters obtained in this work show minimal diversity in this breed and reinforce the need to protect this resource and the conservation banks.

Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle

Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistics and 92 outlier markers based on Bayescan test. The 13 outlier windows detected by at least two approaches, harboured genes (e.g. GH1, ACE, ASIC3, HSPH1, MVD, BCL2, HIGD2A, CBFA2T3) that may be involved in physiological adaptations required to cope with environmental stressors that are typical of the North African area such as infectious diseases, extended drought periods, scarce food supply, oxygen scarcity in the mountainous areas and high-intensity solar radiation. Our data also point to candidate genes involved in transcriptional regulation suggesting that regulatory elements had also a prominent role in North African cattle response to environmental constraints. Our study yields novel insights into the unique adaptive capacity in these endangered populations emphasizing the need for the use of whole genome sequence data to gain a better understanding of the underlying molecular mechanisms.

Evolution and domestication of the Bovini species

Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

The genetic heritage of Alpine local cattle breeds using genomic SNP data

BACKGROUND

Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds.

RESULTS

After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location.

CONCLUSIONS

This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.

Evaluation of two bovine SNP genotyping arrays for breed clustering and stratification analysis in well-known taurine and indicine breeds

The present study aimed to evaluate the efficiency of two Bovine SNP genotyping arrays (i.e., 50 K and HD) for breed clustering and stratification related studies in taurine and indicine breeds. The whole-genome SNP data at two densities were assembled into three datasets (A, B and C). Dataset A (N = 213) included 50 K genotypic data for five taurine (Holstein-Friesian, Guernsey, Brown Swiss, Angus and Jersey) and two indicine (Gir and Nellore) breeds. Dataset B (N = 241) included the same breeds with HD density data. Dataset C (N = 299) included 50 K SNP genotypic data for six taurine (Holstein-Friesian, Jersey, Guernsey, Brown Swiss, Angus and Hereford) and six indicine (Hariana, Kankrej, Brahman, Nellore, Sahiwal and Gir) breeds. The analysis was done using ADMIXTURE program (bioinformatics-based) and cross-validation errors and Principal Component Analysis (statistical analysis). The proportion of polymorphic markers and minor allele frequencies were assessed for each breed. The proportion of markers polymorphic was consistently higher in taurine breeds when compared with breeds from indicine group. Minor allele frequency estimates and ADMIXTURE results showed differential patterns for both the lineages. However, no significant increase in the accuracy of genomic clustering was found on moving from 50 K to HD density data.

Linkage disequilibrium and past effective population size in native Tunisian cattle

To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D', decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance. This is consistent with the absence of strong selective pressure within the Tunisian population and suggests that, in order to be effective, any potential genome-wide association mapping studies will need to use chips with higher marker density. An analysis of effective population size (Ne) based on LD data showed a decline in past Ne, with a sudden drop starting about eight generations ago. This finding, combined with the high levels of recent inbreeding revealed by runs of homozygosity (ROH) analysis, indicate that this population is endangered and may be in urgent need of a conservation plan that includes a well-designed genetic management program.

Genetic diversity and population structure of domestic and wild reindeer (Rangifer tarandus L. 1758): A novel approach using BovineHD BeadChip

Reindeer (Rangifer tarandus L. 1758) are an essential element of the Russian Far North, providing a significant source of nutrition for the representatives of 18 ethnicities. The species has wild and domestic forms, which are in constant interaction. The aim of our study was to characterize the genetic structure of domestic and wild reindeer populations, using a genome-wide bovine genotyping array (BovineHD BeadChip). The wild reindeer samples were obtained from the western Taymyr Peninsula population and from the taiga and tundra populations in the Sakha Republic (Yakutia). The domestic populations included the Evenk, Even, and Chukotka-Khargin breeds of Yakutia and the Nenets breed from the Nenets Autonomous district and Murmansk region. The level of genetic diversity was higher for the wild population. Analyzing Neighbor-Net tree, multidimensional scaling, and Structure results, we observed strong genetic population structure and clear differentiation between domestic and wild populations. All regional populations of domestic reindeer were clearly separated, while wild reindeer showed similar genetic backgrounds. Nevertheless, we found contrasting patterns in the genetic structure of the tundra and taiga reindeer, in accordance with their morphological and ecological differences. Thus, our study revealed a clear genetic differentiation between domestic and wild reindeer populations. It provides novel insights into the genetic diversity and structure of reindeer populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species.

Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information

Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.

Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip

Objective

In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array.

Methods

Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip.

Results

Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average r² value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, inter-population, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving.

Conclusion

Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.

High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

The current study aimed at genomic characterization and improved understanding of genetic diversity of two Indian mithun populations (both farm, 48 animals and field, 24 animals) using genome wide genotype data generated with Illumina BovineHD BeadChip. Eight additional populations of taurine cattle (Holstein and NDama), indicine cattle (Gir) and other evolutionarily closely related species (Bali cattle, Yak, Bison, Gaur and wild buffalo) were also included in this analysis (N = 137) for comparative purposes. Our results show that the genetic background of mithun populations was uniform with few possible signs of indicine admixture. In general, observed and expected heterozygosities were quite similar in these two populations. We also observed increased frequencies of small-sized runs of homozygosity (ROH) in the farm population compared to field mithuns. On the other hand, longer ROH were more frequent in field mithuns, which suggests recent founder effects and subsequent genetic drift due to close breeding in farmer herds. This represents the first study providing genetic evidence about the population structure and genomic diversity of Indian mithun. The information generated will be utilized for devising suitable breeding and conservation programme for mithun, an endangered bovine species in India.

Conservation status and historical relatedness of Italian cattle breeds

Background

In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array.

Results

After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding.

Conclusions

This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0406-x) contains supplementary material, which is available to authorized users.

Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed

Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (N_e) revealed a demographic trend of diminishing N_e over time and that recent estimated N_e values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (F_ROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.

Population Structure Analysis of Bull Genomes of European and Western Ancestry

Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models for individual-specific allele frequencies that directly capture a wide range of complex structure from genome-wide genotypes. As measured by magnitude of differentiation, selection pressure on SNPs within genes is substantially greater than that on intergenic regions. Additionally, broad regions of chromosome 6 harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull genomes can support genetic management strategies that capture structural complexity and promote sustainable genetic breadth.

Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which r² value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average r² between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on r² varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds

Background

The native cattle breeds are an important genetic resource for meat and milk production throughout Asia. In Asia cattle were domesticated around 10,000 years ago and in Korea cattle are being raised since 2000 B.C. There are three native breeds of cattle in Korea viz. Brown Hanwoo, Brindle Hanwoo and Jeju Black. While one of these breeds, Brown Hanwoo, is a part of a Food and Agricultural Organization and national genetic evaluation plans, others get little attention. This study is an effort to understand and provide a detailed insight into the population structure and genetic variability of the Korean cattle breeds along with other Asian breeds using various methods. In this study we report the genetic variation and structure of the Korean cattle breeds and their comparison with five other Asian cattle breeds along with a panel of animals from European taurine, African taurine and indicine cattle breeds.

Results

Asian cattle were found to be least differentiated which reflects their recent history. Amongst the Asian breeds Hainan, which is an indicine breed, had the lowest gene diversity while Yanbian had the highest followed by Mongolian and Korean cattle. Amongst the Korean breeds Brown Hanwoo had the highest diversity followed by Brindle Hanwoo and Jeju Black. The genetic diversity in Asian cattle breeds was found comparable to the European taurines and more than the African taurines and Zebu cattle. Korean cattle breed, Brown Hanwoo was consistently found to be closer to Yanbian, a Chinese cattle breed. We found low divergence and moderate levels of genetic diversity among the native Korean breeds. Indicine introgression from Hainan was seen in other Asian breeds. From Europe, Limousin, Holstein and Hereford introgression was found in Asian breeds.

Conclusions

In this study we provide a genome-wide insight into the genetic history of the native cattle breeds of Korea. The outcomes of this study will help in prioritization and designing of the conservation plans.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0444-8) contains supplementary material, which is available to authorized users.

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

BACKGROUND

Two 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.

RESULTS

Genome-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).

CONCLUSION

The 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.