Refining the genetic structure and relationships of European cattle breeds through meta-analysis of worldwide genomic SNP data, focusing on Italian cattle

Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data

The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.

Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives

Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.

Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds

Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.Whole-genome sequences (WGS) with a mean coverage of 25X, ranging from 14 to 41X were obtained for 30 individuals of the breeds Fjällko, Fjällnära, Bohuskulla, Rödkulla, Ringamåla, and Väneko. WGS-based genotyping revealed 22,548,028 variants in total, comprising 18,876,115 single nucleotide polymorphisms (SNPs) and 3,671,913 indels. Out of these, 1,154,779 SNPs and 304,467 indels were novel. Population stratification based on roughly 19 million SNPs showed two major groups of the breeds that correspond to northern and southern breeds. Overall, a higher genetic diversity was observed in the southern breeds compared to the northern breeds. While the population stratification was consistent with previous genome-wide SNP array-based analyses, the genealogy of the individuals inferred from WGS based estimates turned out to be more complex than expected from previous SNP-array based estimates. Polymorphisms and their predicted phenotypic consequences were associated with differences in the coat color phenotypes between the northern and southern breeds. Notably, these high-consequence polymorphisms were not represented in SNP arrays, which are used routinely for genotyping of cattle breeds.This study is the first WGS-based population genetic analysis of Swedish native cattle breeds. The genetic diversity of native breeds was found to be high. High-consequence polymorphisms were linked with desirable phenotypes using whole-genome genotyping, which highlights the pressing need for intensifying WGS-based characterization of the native breeds.

Comparative genomic diversity analysis of copy number variations (CNV) in indicine and taurine cattle thriving in Europe and Indian subcontinent

Copy number variations (CNVs) include deletions, duplications, and insertions that are larger than 50 bp in size causing structural variation responsible for diversity, adaptation, and breed development. Indian cattle breeds are highly diverse from the taurine breeds. The pattern of CNVRs in 191 animals belonging to 39 cattle breeds (four Indicine and 35 Taurine) was studied based on Illumina 777K BovineHD chip data. The Indicine breeds revealed 2590 CNVs and 335 copy number variation regions (CNVRs) in autosomes. Out of the identified CNVs, 50 were found to be novel. Structure analysis revealed admixed nature of Siri. Neighbor joining tree from CNVR data showed that hot (Kankrej and Hallikar) and cold (Ladakhi and Siri) adapted cattle breeds clustered separately. CNVR of Indian and European breeds revealed that Balkan and Italian breeds of Podolian group are admixed with Indian cattle breeds corroborating indicine introgression (6.1-13.5%). CNVRs spanning the regions of olfactory receptors and immune system genes were identified. AMOVA revealed 9% variation among populations which is 2% greater than SNP based studies showing higher inclusion of variation by CNVR. Detailed analysis of CNVs/CNVRs in Indian cattle adapted to hot and cold climate, and their diversity among worldwide cattle is presented in this study.

Genetic Structure Analysis of 155 Transboundary and Local Populations of Cattle (Bos taurus, Bos indicus and Bos grunniens) Based on STR Markers

Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study. In order to determine the population genetic characteristics, and clarify the phylogenetic relationships of modern representatives of 155 cattle populations from different regions of the world, we collected a large set of STR data (10,250 individuals), including unique native cattle, 12 yak populations from Russia, Mongolia and Kyrgyzstan, as well as zebu breeds. Estimation of main population genetic parameters, phylogenetic analysis, principal component analysis and Bayesian cluster analysis allowed us to refine genetic structure and provided insights in relationships of native populations, transboundary breeds and populations of domestic yak. Our results can find practical application in conservation programs of endangered breeds, as well as become the basis for future fundamental research.

Evaluation of Single Nucleotide Polymorphisms (SNPs) Associated with Genetic Resistance to Bovine Paratuberculosis in Marchigiana Beef Cattle, an Italian Native Breed

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis (PTB), a widespread chronic enteritis of ruminants. The progression of the infection depends on the containment action of innate and cell-mediated immunity (CMI), and it is related to environmental and genetic factors. In particular, PTB susceptibility seems to be associated with specific genes coding for immune regulators involved in the cell-mediated response during the infection. The aim of this preliminary study was to verify, in Italian beef cattle, an association between MAP infectious status and the presence of single nucleotide polymorphisms (SNPs) in candidate genes. To the best of our knowledge, this is the first investigation conducted on a native beef cattle breed, known as Marchigiana, reared in Central Italy. The present research, based on a longitudinal study, aimed to identify and correlate phenotypic and genetic profiles characteristic of the subjects potentially able to contrast or contain PTB. In a MAP-infected herd, ELISA, IFN-γ tests, qPCR, and cultures were performed at a follow-up, occurring within a period ranging from three to six years, to evaluate the individual state of infection. Animals testing positive for at least one test were considered infected. DNA samples of 112 bovines, with known MAP statuses, were analyzed to verify an association with SNPs in the genes encoding gamma-interferon (BoIFNG), interleukin receptor 10 (IL10RA), interleukin receptor 12 (IL12RB2), and toll-like receptors (TLR1, TLR2, TLR4). Regarding statistical analysis, the differences among target genes and pairs of alleles in the analyzed groups of animals, were evaluated at a significance level of p < 0.05. For IL10RA and for IL12RB2 genes, relevant differences in genotypic frequencies among the considered cattle groups were observed. For all candidate genes studied in this investigation, SNP genotypes already associated with PTB resistance were found more frequently in our population, suggesting potential resistance traits in the Marchigiana breed.

Analysis of runs of homozygosity of cattle living in different climate zones

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.

Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data

Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort Fst outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% Fst approach, we detected a candidate region (22.6–23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions.

How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds

Simple Summary

In this paper, we study the inter-relationships among geography, climate, and genetics in Italian local cattle and sheep breeds. In terms of genetic diversity, geography (latitude and longitude) appears to play a larger role in sheep (26.4%) than that in cattle (13.8%). Once geography is accounted for, 10.1% of cattle genomic diversity and 13.3% of that of sheep are attributable to climatic effects. Stronger geographic effects in sheep can be related to a combination of higher predomestication genetic variability together with biological and productive specializations. The climate alone seems to have had less impact on the current genetic diversity in both species even if climate and geography are greatly confounded. Results confirm that both species are the result of complex evolutionary histories triggered by interactions between human needs and environmental conditions.

Abstract

Understanding the relationships among geography, climate, and genetics is increasingly important for animal farming and breeding. In this study, we examine these inter-relationships in the context of local cattle and sheep breeds distributed along the Italian territory. To this aim, we used redundancy analysis on genomic data from previous projects combined with geographical coordinates and corresponding climatic data. The effect of geographic factors (latitude and longitude) was more important in sheep (26.4%) than that in cattle (13.8%). Once geography had been partialled out of analysis, 10.1% of cattle genomic diversity and 13.3% of that of sheep could be ascribed to climatic effects. Stronger geographic effects in sheep can be related to a combination of higher pre-domestication genetic variability together with biological and productive specificities. Climate alone seems to have had less impact on current genetic diversity in both species, even if climate and geography are greatly confounded. Results confirm that both species are the result of complex evolutionary histories triggered by interactions between human needs and environmental conditions.

Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations

Local cattle and sheep populations are important for animal production and food security in South Africa. These genetic resources are well adapted to the diverse climatic conditions and hold potential to be utilized in production systems subjected to climate change. The local beef breeds are well integrated into commercial livestock production systems with access to performance recording and genetic evaluations, while local sheep breeds are mainly utilised in smallholder and communal systems. The GeneSeek^® Genomic Profiler™ Bovine 150 K SNP genotyping array was used to evaluate the diversity and inbreeding status of four indigenous (Boran, Drakensberger, Nguni, Tuli), two composite (Bonsmara and Beefmaster) and two exotic (SA Hereford and Charolais) beef breeds. The Illumina^® Ovine 50 K SNP BeadChip was used to investigate five indigenous (Black Head Persian, Damara, Fat tail, Namaqua Afrikaner, Pedi) and three commercial (Dorper, Dohne Merino and SA Merino) populations. Although ascertainment bias was indicated by the low MAF (the autosome-wide proportion of SNPs with MAF< 0.05 ranged from 6.18 to 9.97% for cattle, and 7.59–13.81% for sheep), moderate genomic diversity was observed (mean H_o ranged from 0.296 to 0.403 for cattle, and 0.327 to 0.367 for sheep). Slightly higher levels of ROH-based inbreeding were calculated for cattle (F_ROH range: 0.018–0.104), than for sheep populations (F_ROH range: 0.002–0.031). The abundance of short ROH fragments (mean proportion of <4 Mb fragments: 0.405 for cattle, and 0.794 for sheep) indicated ancient inbreeding in both species. The eight cattle populations were categorized into indicine, taurine or Sanga subspecies based on principal component, model-based clustering and phylogenetic analyses, with high levels of admixture observed within the Drakensberger, Nguni and Tuli breeds. Within the sheep populations, a clear distinction could be seen between the dual-purpose breeds, the meat breed and the indigenous breeds. Despite directional selection practiced in the cattle breeds, genomic diversity was moderate with low inbreeding. The non-commercialized, indigenous sheep populations are more vulnerable with small effective populations. These results emphasise the value of genomic information for effective management to exploit the potential contribution of local genetic cattle and sheep resources in a changing environment.

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

Background

During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach.

Results

Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools.

Conclusions

This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00639-w.

Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.

The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

Background

Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds.

Methods

Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations.

Results

The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r² and r²_adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs.

Conclusion

African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07270-x.

Genome-wide assessment of diversity and differentiation between original and modern Brown cattle populations

Identifying genomic regions involved in the differences between breeds can provide information on genes that are under the influence of both artificial and natural selection. The aim of this study was to assess the genetic diversity and differentiation among four different Brown cattle populations (two original vs. two modern populations) and to characterize the distribution of runs of homozygosity (ROH) islands using the Illumina Bovine SNP50 BeadChip genotyping data. After quality control, 34 735 SNPs and 106 animals were retained for the analyses. Larger heterogeneity was highlighted for the original populations. Patterns of genetic differentiation, multidimensional scaling, and the neighboring joining tree distinguished the modern from the original populations. The F_ST -outlier identified several genes putatively involved in the genetic differentiation between the two groups, such as stature and growth, behavior, and adaptability to local environments. The ROH islands within both the original and the modern populations overlapped with QTL associated with relevant traits. In modern Brown (Brown Swiss and Italian Brown), ROH islands harbored candidate genes associated with milk production traits, in evident agreement with the artificial selection conducted to improve this trait in these populations. In original Brown (Original Braunvieh and Braunvieh), we identified candidate genes related with fat deposition, confirming that breeding strategies for the original Brown populations aimed to produce dual-purpose animals. Our study highlighted the presence of several genomic regions that vary between Brown populations, in line with their different breeding histories.

Eusebi P, Rivero CJ, Justo JR, Fernández M, Cañón J, Cortés Ó. Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas

Simple Summary

Genetic characterization of breeds at risk of extinction is crucial in order to develop efficient conservation plans. In this study, for the first time to our knowledge, a set of bovine breeds summarized as Morenas Gallegas (Cachena, Caldelá, Frieiresa, Limiá, and Vianesa), located in the Northwest of Spain, were studied by using genomics tools. Our aim was to analyze their genetic diversity and their genetic relationships with a set of local and cosmopolitan European bovine breeds. The results evidence the specific genetic signature of the Morenas Gallegas bovine breeds. Cachena was the only breed located in the same cluster as the Spanish bovine breeds analyzed, while Caldelá, Frieiresa, Limiá, and Vianesa were clearly separated. The genetic diversity of the set of Morenas Gallegas breeds is intermediate or high, but Frieiresa breed showed the higher value of inbreeding coefficient and requires special attention in the next years. Vianesa shows two different lineages, with an evident Frieiresa component and without it. Our results are the proof of the valuable genetic reservoir that Morenas Gallegas bovine breeds is due to their uniqueness in comparison with other Spanish bovine breeds.

Abstract

A set of five local bovine breeds in danger of extinction named Cachena, Caldelá, Limiá, Frieiresa, and Vianesa and included in the group of Morenas Gallegas are located in the Autonomous Community of Galicia at the Northwest of Spain. Local authorities launched a conservation plan at the end of the 21th century in order to preserve this important genetic reservoir. However, Morenas Gallegas bovine breeds never have been analyzed with genomic tools and this information may be crucial to develop conservation plans. The aim of the study was to analyze their genetic diversity and genetic relationships with a set of local and cosmopolitan European bovine breeds using single nucleotide polymorphisms. Our results show own genetic signatures for the Morenas Gallegas breeds which form a separate cluster when compared to the Spanish breeds analyzed, with the exception of the Cachena breed. The genetic diversity levels of the Morenas Gallegas were intermediate or high, and low inbreeding coefficients can be found except for the Frieiresa breed (11%). Vianesa breed evidenced two lineages depending on the Frieiresa component influence. The Morenas Gallegas bovine breeds group represent an important Spanish bovine genetic reservoir and despite their classification within a single generic group, the five breeds show their own genetic uniqueness.