An assessment of population structure in eight breeds of cattle using a whole genome SNP panel

The use of SNP markers for cattle breed identification

A potential application of single nucleotide polymorphisms (SNPs) in animal husbandry and production is identification of the animal breed. In this study, using chosen marker selection methods and genotypic data obtained with the use of Illumina Bovine SNP50 BeadChip for individuals belonging to ten cattle breeds, the reduced panels containing the most informative SNP markers were developed. The suitability of selected SNP panels for the effective and reliable assignment of the studied individuals to the breed of origin was checked by three allocation algorithms implemented in GeneClass 2. The studied breeds set included both Polish-native breeds under the genetic resources conservation programs and highly productive breeds with a global range. For all of the tested marker selection methods ("delta" and two FST-based variants), two separate methodological approaches of marker assortment were used and three marker panels were created with 96, 192, and 288 SNPs respectively, to determine the minimum number of markers required for effective differentiation of the studied breeds. Moreover, the usefulness of the most effective panels of markers to assess the population structure and genetic diversity of the analyzed breeds was examined. The conducted analyses showed the possibility of using SNP subsets from medium-density genotypic microarrays to distinguish breeds of cattle kept in Poland and to analyze their genetic structure.

Global and Local Ancestry and its Importance: A Review

The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing the phenomenon of complementarity and heterosis in several traits and genetic diversity, respectively. The traditional method of admixture analysis by pedigree records has now been replaced greatly by genome-wide marker data that enables more precise estimations. Among these markers, SNPs have been the popular choice since they are cost-effective, not so laborious, and automation of genotyping is easy. Certain markers can suggest the possibility of a population's origin from a sample of DNA where the source individual is unknown or unwilling to disclose their lineage, which are called Ancestry-Informative Markers (AIMs). Revealing admixture level at the locus-specific level is termed as local ancestry and can be exploited to identify signs of recent selective response and can account for genetic drift. Considering the importance of genetic admixture and local ancestry, in this mini-review, both concepts are illustrated, encompassing basics, their estimation/identification methods, tools/software used and their applications.

Single nucleotide polymorphisms for parentage testing of horse breeds in Korea

OBJECTIVE

In this study, we aimed to evaluate the usability single nucleotide polymorphisms (SNPs) for parentage testing of horse breeds in Korea.

METHODS

The genotypes of 93 horse samples (38 Thoroughbred horses, 17 Jeju horses, 20 Quarter horses, and 18 American miniature horses) were determined using 15 microsatellite (Ms) markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20) and 101 SNP markers.

RESULTS

Paternity tests were performed using 15 Ms markers and 101 SNP markers in Thoroughbred horses and Quarter horses. AHT5, ASB2, ASB17, ASB23, CA425, HMS7, HTG10, and LEX3 did not follow Mendelian inheritance in Thoroughbred horses, whereas in Quarter horses, only AHT4, ASB2, and HMS2 showed Mendelian inheritance, consequently, paternity was not established. Meanwhile, 31 markers, including MNEc_2_2_ 2_98568918_BIEC2_502451, in Thoroughbred horses, and 30 markers, including MNEc_ 2_30_7430735_BIEC2_816793, in Quarter horses did not conform with Mendelian inheritance and therefore, could not be used for establishing parentage.

CONCLUSION

The possibility of replacing Ms markers with SNP markers for paternity testing in horses was confirmed. However, further research using more samples is necessary.

Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.

Detecting SNP markers discriminating horse breeds by deep learning

The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead chip were used in the current study and principal component analysis (PCA), log-likelihood ratios (LLR) and Neighbor-Joining (NJ) were applied to assess the performance of different assignment methods. The results revealed that the DNN, Garson, and Olden methods are able to assign individuals to true populations with 4270, 4937, and 7999 SNP markers, respectively. The PCA was used to determine how the animals allocated to the groups using all genotyped markers available on 50k Bead chip and the subset of SNP markers identified with different methods. The results indicated that all SNP panels are able to assign individuals into their true breeds. The success percentage of genetic assignment for different methods assessed by different levels of LLR showed that the success rate of 70% in the analysis was obtained by three methods with the number of markers of 110, 208, and 178 tags for DNN, Garson, and Olden methods, respectively. Also the results showed that DNN performed better than other two approaches by achieving 93% accuracy at the most stringent threshold. Finally, the identified SNPs were successfully used in independent out-group breeds consisting 120 individuals from eight breeds and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. Furthermore, the NJ tree of allele-sharing distances on the validation dataset showed that the DNN has a high potential for feature selection. In general, the results of this study indicated that the DNN technique represents an efficient strategy for selecting a reduced pool of highly discriminant markers for assigning individuals to the true population of origin.

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.

New Insights on Nucleotide Sequence Variants and mRNA Levels of Candidate Genes Assessing Resistance/Susceptibility to Mastitis in Holstein and Montbéliarde Dairy Cows

A major factor in the propagation of an infectious disease is host genetics. In this study, 180 dairy cows (90 of each breed: Holstein and Montbéliarde) were used. Each breed's tested dairy cows were divided into two groups of comparable size (45 cows each), mastitis-free and mastitis-affected groups. Each cow's jugular vein was punctured to obtain blood samples for DNA and RNA extraction. In the examined Holstein and Montbéliarde dairy cows, single nucleotide polymorphisms (SNPs) related with mastitis resistance/susceptibility were found in the RASGRP1, NFkB, CHL1, MARCH3, PDGFD, MAST3, EPS15L1, C1QTNF3, CD46, COX18, NEURL1, PPIE, and PTX3 genes. Chi-square analysis of identified SNPs revealed a significant difference in gene frequency between mastitic and healthy cows. Except for CHL1, mastitic dairy cows of two breeds had considerably higher mRNA levels of the examined genes than did healthy ones. Marker-assisted selection and monitoring of dairy cows' susceptibility to mastitis may be accomplished through the use of discovered SNPs and changes in the gene expression profile of the studied genes. These findings also point to a possible method for reducing mastitis in dairy cows through selective breeding of animals using genetic markers linked to an animal's ability to resist infection.

Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario

Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) F. gigantica, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the F. gigantica origin in east-southern Africa around the mid-Miocene, the F. hepatica origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of F. hepatica into the Americas and Oceania and of F. gigantica into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them "peridomestic endoparasites." The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.

Linkage Disequilibrium, Haplotype Block Structures, Effective Population Size and Genome-Wide Signatures of Selection of Two Conservation Herds of the South African Nguni Cattle

The Nguni cattle of South Africa are a Sanga breed, characterized by many eco-types and research populations that have been established in an effort to conserve the diversity within the breed. The aim of this study was to investigate the overall genetic diversity as well as similarities and differences within and between two conservation herds of the South African Nguni Cattle. Mean LD (r2) estimates were 0.413 ± 0.219 for Bartlow Combine and 0.402 ± 0.209 for Kokstad. Genome-wide average LD (r2) decreased with increasing genetic marker distance for both populations from an average of 0.76 ± 0.28 and 0.77 ± 0.27 at 0–1 kb bin to 0.31 ± 0.13 and 0.32 ± 0.13 at 900–1000 kb bin in Bartlow Combine and Kokstad populations, respectively. Variation in LD levels across autosomes was observed in both populations. The results showed higher levels of LD than previously reported in Nguni field populations and other South African breeds, especially at shorter marker distances of less than 20 kb. A total number of 77,305 and 66,237 haplotype blocks covering a total of 1570.09 Mb (61.99% genome coverage) and 1367.42 Mb (53.96% genome coverage) were detected in Bartlow Combine and Kokstad populations, respectively. A total of 18,449 haploblocks were shared between the two populations while 58,856 and 47,788 haploblocks were unique to Bartlow Combine and Kokstad populations, respectively. Effective population size (Ne) results demonstrated a rapid decrease in Ne across generations for both Bartlow Combine and Kokstad conservation herds. Two complementary methods, integrated haplotype score (iHS) and Extend Haplotype Homozygosity Test (XP-EHH), were implemented in this study to detect the selection signatures in the two herds. A total of 553 and 166 selected regions were identified in Bartlow Combine and Kokstad populations, respectively. DAVID and GO terms analysis of the regions under selection reported genes/QTLs associated with fertility, carcass weight, coat colour, immune response, and eye area pigmentation. Some genes, such as HCAR1, GNAI1, PIK3R3, WNT3, RAB5A, BOLA-N (Class IB MHC Antigen QA-2-Related), BOLA (Class IB MHC Antigen QA-2-Related), and Rab-8B, etc., were found in regions under selection in this study. Overall, the study implied reduced genetic diversity in the two herds calling for corrective measures to maintain the diversity of the South African Nguni cattle. This study presented a comprehensive analysis of the genomic architecture of South African Nguni cattle populations, providing essential genetic information of utility in the management of conservation flocks.

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.

Single Nucleotide Polymorphisms, Gene Expression and Economic Evaluation of Parameters Associated with Mastitis Susceptibility in European Cattle Breeds

The objective of this study was to explore single nucleotide polymorphisms (SNPs), gene expression and economic evaluation of parameters associated with mastitis susceptibility in Holstein and Brown Swiss dairy cows. Two hundred and forty Holstein and Brown Swiss dairy cows (120 cows of each breed) were used in this study. The investigated dairy cows in each breed were allocated into two equal-sized groups (60 cows each); mastitis tolerant and affected groups. PCR-DNA sequencing of SELL, ABCG2, SLC11A1, FEZL, SOD1, CAT, GPX1, and AhpC/TSA revealed nucleotide sequence variations in the form of SNPs associated with mastitis tolerance/susceptibility in investigated Holstein and Brown Swiss dairy cows. Levels of SELL, SLC11A1 and FEZL gene expression were significantly up-regulated in mastitic Holstein and Brown Swiss dairy cows than in tolerant ones. Meanwhile, ABCG2, SOD1, CAT, GPX1, and AhpC/TSA genes were significantly downregulated. Regarding the economic parameters, significant differences were recorded for net returns and a reduction in the percentage of net profit, as the higher values of net returns were recorded for tolerant dairy cows than mastitic ones in both breeds; moreover, the net profit was reduced by 39% and 27% in mastitic Holstein and Brown Swiss dairy cows, respectively, when compared to tolerant ones. The results herein confirmed the potential significance of investigated genes as candidates for mastitis tolerance/susceptibility in Holstein and Brown Swiss dairy cows. Mastitis also has detrimental impacts on economic efficiency in dairy farms.

Genetic Differentiation among Livestock Breeds-Values for Fst

(1) Background: The Fst statistic is widely used to characterize between-breed relationships. Fst = 0.1 has frequently been taken as indicating genetic distinctiveness between breeds. This study investigates whether this is justified. (2) Methods: A database was created of 35,080 breed pairs and their corresponding Fst values, deduced from microsatellite and SNP studies covering cattle, sheep, goats, pigs, horses, and chickens. Overall, 6560 (19%) of breed pairs were between breeds located in the same country, 7395 (21%) between breeds of different countries within the same region, 20,563 (59%) between breeds located far apart, and 562 (1%) between a breed and the supposed wild ancestor of the species. (3) Results: General values for between-breed Fst were as follows, cattle: microsatellite 0.06-0.12, SNP 0.08-0.15; sheep: microsatellite 0.06-0.10, SNP 0.06-0.17; horses: microsatellite 0.04-0.11, SNP 0.08-0.12; goats: microsatellite 0.04-0.14, SNP 0.08-0.16; pigs: microsatellite 0.06-0.27, SNP 0.15-0.22; chickens: microsatellite 0.05-0.28, SNP 0.08-0.26. (4) Conclusions: (1) Large amounts of Fst data are available for a substantial proportion of the world's livestock breeds, (2) the value for between-breed Fst of 0.1 is not appropriate owing to its considerable variability, and (3) accumulated Fst data may have value for interdisciplinary research.

Effects of single nucleotide polymorphism ascertainment on population structure inferences

Single nucleotide polymorphism (SNP) data are widely used in research on natural populations. Although they are useful, SNP genotyping data are known to contain bias, normally referred to as ascertainment bias, because they are conditioned by already confirmed variants. This bias is introduced during the genotyping process, including the selection of populations for novel SNP discovery and the number of individuals involved in the discovery panel and selection of SNP markers. It is widely recognized that ascertainment bias can cause inaccurate inferences in population genetics and several methods to address these bias issues have been proposed. However, especially in natural populations, it is not always possible to apply an ideal ascertainment scheme because natural populations tend to have complex structures and histories. In addition, it was not fully assessed if ascertainment bias has the same effect on different types of population structure. Here, we examine the effects of bias produced during the selection of population for SNP discovery and consequent SNP marker selection processes under three demographic models: the island, stepping-stone, and population split models. Results show that site frequency spectra and summary statistics contain biases that depend on the joint effect of population structure and ascertainment schemes. Additionally, population structure inferences are also affected by ascertainment bias. Based on these results, it is recommended to evaluate the validity of the ascertainment strategy prior to the actual typing process because the direction and extent of ascertainment bias vary depending on several factors.

Genetic Diversity and Population Genetic Structure of a Guzerá (Bos indicus) Meta-Population

The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021-0.100; lineages = 0.021-0.100), Fis (Farms = -0.007-0.076; lineages = -0.014-0.070), and Fst (Farms = 0.0237-0.032; lineages = 0.029-0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level.

Single nucleotide polymorphisms of leptin gene in five Ethiopian indigenous cattle breeds and the Korean Hanwoo breed

Considering the escalating number of scientific reports on the association between the leptin gene and diverse physiological traits and performance of cattle populations, this study was directed towards identifying SNPs in the leptin gene among five indigenous cattle breeds of Ethiopia. DNA samples were extracted from the nasal swabs of the Ethiopian indigenous cattle breeds: Arsi (n = 18), Horro (n = 20), Begait (n = 21), Boran (n = 19), and Fogera (n = 17) and the Korean Hanwoo (a representative taurine breed) (n = 20), followed by PCR amplification of exon 2 and exon 3 regions of the leptin gene and sequence analysis of the PCR products. Five SNPs, two (generating missense mutations) on exon 2 and three (generating silent mutations) on exon 3 regions, were explicated in this study. Allele frequency and genotype frequency distribution pertaining to the SNPs were recorded for the studied cattle breeds besides the minor allele frequency and deviation from the Hardy-Weinberg equilibrium. Positive F_IS index values were recorded for all the markers except SNP2, illustrative of heterozygote deficiency. MEGA X software-based evolutionary divergence analysis of the phylogenetic tree based on the SNP data revealed that the large-sized breeds, Hanwoo, Begait, Boran, and Fogera, were more closely clustered compared to the small-sized Arsi breed. Among the seven haplotypes documented from the various breeds, sequence analysis was suggestive of haplotypes 1 and 2 to be ancestral haplotypes for the leptin gene. This study is envisaged to accelerate molecular breeding programs for the genetic improvement of the Ethiopian cattle breeds.

Assessing breed integrity of Göttingen Minipigs

BACKGROUND

Göttingen Minipigs (GMP) is the smallest commercially available minipig breed under a controlled breeding scheme and is globally bred in five isolated colonies. The genetic isolation harbors the risk of stratification which might compromise the identity of the breed and its usability as an animal model for biomedical and human disease. We conducted whole genome re-sequencing of two DNA-pools per colony to assess genomic differentiation within and between colonies. We added publicly available samples from 13 various pig breeds and discovered overall about 32 M loci, ~ 16 M. thereof variable in GMPs. Individual samples were virtually pooled breed-wise. FST between virtual and DNA pools, a phylogenetic tree, principal component analysis (PCA) and evaluation of functional SNP classes were conducted. An F-test was performed to reveal significantly differentiated allele frequencies between colonies. Variation within a colony was quantified as expected heterozygosity.

RESULTS

Phylogeny and PCA showed that the GMP is easily discriminable from all other breads, but that there is also differentiation between the GMP colonies. Dependent on the contrast between GMP colonies, 4 to 8% of all loci had significantly different allele frequencies. Functional annotation revealed that functionally non-neutral loci are less prone to differentiation. Annotation of highly differentiated loci revealed a couple of deleterious mutations in genes with putative effects in the GMPs .

CONCLUSION

Differentiation and annotation results suggest that the underlying mechanisms are rather drift events than directed selection and limited to neutral genome regions. Animal exchange seems not yet necessary. The Relliehausen colony appears to be the genetically most unique GMP sub-population and could be a valuable resource if animal exchange is required to maintain uniformity of the GMP.

Copy number variation of CADM2 gene revealed its association with growth traits across Chinese Capra hircus (goat) populations

Copy number variations (CNVs) are the wide structural variations ranging from 50 bp to several Mb at genome which can affect gene expression and further impacting growth and development traits of livestock. Comparing with single nucleotide polymorphisms (SNPs), CNVs can better explain the genetic and phenotypic diversity, are increasingly important in biological research. As a member of immunoglobulin super-family, cell adhesion molecule 2 (CADM2) plays a vital role in cancer development and metabolic regulation. Here, we tested the CNV of CADM2 gene in 443 goats across five breeds (Guizhou white goat, GZW; Guizhou black goat, GZB; Africa Nubian goat, AN; Boer goat × Huai goat, BH; Boer goat, BG) and detected its association with phenotypic traits. Subsequently, we analyzed the CADM2 gene expression level in different tissues of NB goats (n = 3, Nubian × Black) and the transcriptional expression in lung is much higher than others. The results showed that the CNV of CADM2 has a significant association with withers height and body length in GZB goat (P < 0.01), in which individuals with type of deletion were superior to those with duplication or normal type in term of body hight and body length (P < 0.01). In summary, this study confirmed the association between CNV of CADM2 gene and growth traits, and our research data indicated the CADM2-CNV may considered as a prospective candidate for the molecular marker-assisted selection breeding of goat growth traits, which conducived to accelerating the genetic amelioration in Chinese goats.

Genetic structure and admixture in sheep from terminal breeds in the United States

Selection for performance in diverse production settings has resulted in variation across sheep breeds worldwide. Although sheep are an important species to the United States, the current genetic relationship among many terminal sire breeds is not well characterized. Suffolk, Hampshire, Shropshire and Oxford (terminal) and Rambouillet (dual purpose) sheep (n = 248) sampled from different flocks were genotyped using the Applied Biosystems Axiom Ovine Genotyping Array (50K), and additional Shropshire sheep (n = 26) using the Illumina Ovine SNP50 BeadChip. Relationships were investigated by calculating observed heterozygosity, inbreeding coefficients, eigenvalues, pairwise Wright’s F_ST estimates and an identity by state matrix. The mean observed heterozygosity for each breed ranged from 0.30 to 0.35 and was consistent with data reported in other US and Australian sheep. Suffolk from two different regions of the United States (Midwest and West) clustered separately in eigenvalue plots and the rectangular cladogram. Further, divergence was detected between Suffolk from different regions with Wright’s F_ST estimate. Shropshire animals showed the greatest divergence from other terminal breeds in this study. Admixture between breeds was examined using admixture, and based on cross‐validation estimates, the best fit number of populations (clusters) was K = 6. The greatest admixture was observed within Hampshire, Suffolk, and Shropshire breeds. When plotting eigenvalues, US terminal breeds clustered separately in comparison with sheep from other locations of the world. Understanding the genetic relationships between terminal sire breeds in sheep will inform us about the potential applicability of markers derived in one breed to other breeds based on relatedness.

Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle

Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position-unassigned SNPs, or "buried SNPs" include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.

Whole genome studies of origin, selection and adaptation of the Russian cattle breeds

Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.

Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B. indicus breeds (average 20.3%-29.3% on the 777k chip, 35.5%-45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much lower, 4% (2.8%-7%) in B. indicus breeds, while it was 33.5% in Holstein. With on average 164,357 heterozygous loci in B. indicus breeds, the 777k SNP chip has sufficient heterozygous loci to design a chip customized for B. indicus breeds. Principal component analysis clearly differentiated B. indicus from B. taurus breeds. Differentiation among B. indicus breeds was only achieved by plotting the third and fifth principal components using 777k genotype data. Admixture analysis showed that many B. indicus animals, previously believed to be of pure origin, are in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively higher effective population sizes in four B. indicus breeds compared to two B. taurus breeds. The results of admixture analyses show that it is important to assess the genomic composition of a bull before using it in a breeding programme.

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.

Novel methods for genotype imputation to whole-genome sequence and a simple linear model to predict imputation accuracy

Background

Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal reference population for imputation to Next Generation Sequencing data in cattle.

Methods

Methods for clustering of animals for imputation were explored, using 1000 Bull Genomes Project sequence data on 1146 animals from a variety of beef and dairy breeds. Imputation from 50 K to 777 K was first carried out to choose an ideal clustering method, using ADMIXTURE or PLINK clustering algorithms with either genotypes or reconstructed haplotypes.

Results

Due to efficiency, accuracy and ease of use, clustering with PLINK using haplotypes as quasi-genotypes was chosen as the most advantageous grouping method. It was found that using a clustered population slightly decreased computing time, while maintaining accuracy across the population. Although overall accuracy remained the same, a slight increase in accuracy was observed for groups of animals in some breeds (primarily purebred beef cattle from breeds with fewer sequenced animals) and for other groups, primarily crossbreed animals, a slight decrease in accuracy was observed. However, it was noted that some animals in each breed were poorly imputed across all methods. When imputed sequences were included in the reference population to aid imputation of poorly imputed animals, a small increase in overall accuracy was observed for nearly every individual in the population. Two models were created to predict imputation accuracy, a complete model using all information available including Euclidean distances from genotypes and haplotypes, pedigree information, and clustering groups and a simple model using only breed and an Euclidean distance matrix as predictors. Both models were successful in predicting imputation accuracy, with correlations between predicted and true imputation accuracy as measured by concordance rate of 0.87 and 0.83, respectively.

Conclusions

A clustering methodology can be very useful to subgroup cattle for efficient genotype imputation. In addition, accuracy of genotype imputation from medium to high-density Single Nucleotide Polymorphisms (SNP) chip panels to whole-genome sequence can be predicted well using a simple linear model defined in this study.

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

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.

Insight into the genetic composition of South African Sanga cattle using SNP data from cattle breeds worldwide

Background

Understanding the history of cattle breeds is important because it provides the basis for developing appropriate selection and breed improvement programs. In this study, patterns of ancestry and admixture in Afrikaner, Nguni, Drakensberger and Bonsmara cattle of South Africa were investigated. We used 50 K single nucleotide polymorphism genotypes that were previously generated for the Afrikaner (n = 36), Nguni (n = 50), Drakensberger (n = 47) and Bonsmara (n = 44) breeds, and for 394 reference animals representing European taurine, African taurine, African zebu and Bos indicus.

Results and discussion

Our findings support previous conclusions that Sanga cattle breeds are composites between African taurine and Bos indicus. Among these breeds, the Afrikaner breed has significantly diverged from its ancestral forebears, probably due to genetic drift and selection to meet breeding objectives of the breed society that enable registration. The Nguni, Drakensberger and Bonsmara breeds are admixed, perhaps unintentionally in the case of Nguni and Drakensberger, but certainly by design in the case of Bonsmara, which was developed through crossbreeding between the Afrikaner, Hereford and Shorthorn breeds.

Conclusions

We established patterns of admixture and ancestry for South African Sanga cattle breeds, which provide a basis for developing appropriate strategies for their genetic improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0266-1) 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.

Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (HO=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (HO=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.

Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle

Background

Copy number variation (CNV) is an important source of genetic variability associated with phenotypic variation and disease susceptibility. Comprehensive genome-wide CNV maps provide valuable information for genetic and functional studies. To identify CNV in Japanese Black cattle, we performed a genome-wide autosomal screen using genomic data from 1,481 animals analyzed with the Illumina Bovine High-Density (HD) BeadChip Array (735,293 single-nucleotide polymorphisms (SNPs) with an average marker interval of 3.4 kb on the autosomes).

Results

We identified a total of 861 CNV regions (CNVRs) across all autosomes, which covered 43.65 Mb of the UMD3.1 genome assembly and corresponded to 1.74 % of the 29 bovine autosomes. Overall, 35 % of the CNVRs were present at a frequency of > 1 % in 1,481 animals. The estimated lengths of CNVRs ranged from 1.1 kb to 1.4 Mb, with an average of 50.7 kb. The average number of CNVR events per animal was 35. Comparisons with previously reported cattle CNV showed that 72 % of the CNVR calls detected in this study were within or overlapped with known CNVRs. Experimentally, three CNVRs were validated using quantitative PCR, and one CNVR was validated using PCR with flanking primers for the deleted region. Out of the 861 CNVRs, 390 contained 717 Ensembl-annotated genes significantly enriched for stimulus response, cellular defense response, and immune response in the Gene Ontology (GO) database. To associate genes contained in CNVRs with phenotypes, we converted 560 bovine Ensembl gene IDs to their 438 orthologous associated mouse gene IDs, and 195 of these mouse orthologous genes were categorized into 1,627 phenotypes in the Mouse Genome Informatics (MGI) database.

Conclusions

We identified 861 CNVRs in 1,481 Japanese Black cattle using the Illumina BovineHD BeadChip Array. The genes contained in CNVRs were characterized using GO analysis and the mouse orthologous genes were characterized using the MGI database. The comprehensive genome-wide CNVRs map will facilitate identification of genetic variation and disease-susceptibility alleles in Japanese Black cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0335-z) contains supplementary material, which is available to authorized users.

Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds

Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r²≥ 0.20 would require about 30,000–50,000 SNPs. However, r²≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

Genome-wide scan for selection signatures in six cattle breeds in South Africa

BACKGROUND

The detection of selection signatures in breeds of livestock species can contribute to the identification of regions of the genome that are, or have been, functionally important and, as a consequence, have been targeted by selection.

METHODS

This study used two approaches to detect signatures of selection within and between six cattle breeds in South Africa, including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31) and Holstein (n = 29). The first approach was based on the detection of genomic regions in which haplotypes have been driven towards complete fixation within breeds. The second approach identified regions of the genome that had very different allele frequencies between populations (F ST).

RESULTS AND DISCUSSION

Forty-seven candidate genomic regions were identified as harbouring putative signatures of selection using both methods. Twelve of these candidate selected regions were shared among the breeds and ten were validated by previous studies. Thirty-three of these regions were successfully annotated and candidate genes were identified. Among these genes the keratin genes (KRT222, KRT24, KRT25, KRT26, and KRT27) and one heat shock protein gene (HSPB9) on chromosome 19 between 42,896,570 and 42,897,840 bp were detected for the Nguni breed. These genes were previously associated with adaptation to tropical environments in Zebu cattle. In addition, a number of candidate genes associated with the nervous system (WNT5B, FMOD, PRELP, and ATP2B), immune response (CYM, CDC6, and CDK10), production (MTPN, IGFBP4, TGFB1, and AJAP1) and reproductive performance (ADIPOR2, OVOS2, and RBBP8) were also detected as being under selection.

CONCLUSIONS

The results presented here provide a foundation for detecting mutations that underlie genetic variation of traits that have economic importance for cattle breeds in South Africa.

Genetic variants in the upstream region of activin receptor IIA are associated with female fertility in Japanese Black cattle

Background

Female fertility, a fundamental trait required for animal reproduction, has gradually declined in the last 2 decades in Japanese Black cattle. To identify associated genetic variants in Japanese Black cattle, we evaluated female fertility as a metric to describe the average inverse of the number of artificial inseminations required for conception from the first through the fourth parity (ANAI₄) and conducted a genome-wide association study (GWAS) using 430 animals with extreme ANAI₄ values from 10,399 animals.

Results

We found that 2 variants, namely a single-nucleotide polymorphisms (SNP; g.48476925C > T) and a 3-bp indel (g.48476943_48476946insGGC), in the upstream region of the activin receptor IIA gene (ACVR2A) were associated with ANAI₄. ACVR2A transcripts from Japanese Black cattle of the Q haplotype, defined by the SNP and the 3-bp indel, with increased ANAI₄ were 1.29–1.32-fold more abundant than q-derived transcripts. In agreement, reporter assay results revealed that the activity of the ACVR2A promoter was higher in reporter constructs with the Q haplotype than in those with the q haplotype by approximately 1.2 fold. Expression of exogenous ACVR2A induced dose-dependent increases of reporter activity from the follicle-stimulating hormone, beta polypeptide (FSHB) promoter in response to activin A in a pituitary gonadotrophic cell line. The findings suggested that sequence variations in the upstream region of ACVR2A with the Q haplotype increased ACVR2A transcription, which in turn induced FSHB expression. This association was replicated using a sample population size of 1,433 animals; the frequency of the Q haplotype was 0.39, and Q-to-q haplotype substitution resulted in an increase of 0.02 in terms of ANAI₄.

Conclusions

This GWAS identified variants in the upstream region of ACVR2A, which were associated with female fertility in Japanese Black cattle. The variants affected the level of ACVR2A mRNA expression, which could lead to an allelic imbalance. This association was replicated with a sample population of 1,433 animals. Thus, the results suggest that the Q haplotype could serve as a useful marker to select Japanese Black cattle with superior female fertility.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0282-0) contains supplementary material, which is available to authorized users.

Genetic structure and relationships of 16 Asian and European cattle populations using DigiTag2 assay

In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3). In addition, Japanese Holstein exhibited an admixture pattern with Asian and European cattle (K=3‐5). Mongolian (K=13‐16) and Japanese Black (K=14‐16) populations exhibited admixture patterns with different ancestries. Bos indicus populations exhibited a uniform genetic structure at K=2‐11, thereby suggesting that there are close genetic relationships among Bos indicus populations. However, the Bhutan and Bangladesh populations formed a cluster distinct from the other Bos indicus populations at K=12‐16. In conclusion, our study could sufficiently explain the genetic construction of Asian cattle populations, including: (i) the close genetic relationships among Bos indicus populations; (ii) the genetic influences of European breeds on Japanese breeds; (iii) the genetic admixture in Japanese Holstein, Mongolian and Japanese Black cattle; and (iv) the genetic subpopulations in Southeast Asia.

Molecular phylogenetic analysis of Chinese indigenous blue-shelled chickens inferred from whole genomic region of the SLCO1B3 gene

In total, 246 individuals from 8 Chinese indigenous blue- and brown-shelled chicken populations (Yimeng Blue, Wulong Blue, Lindian Blue, Dongxiang Blue, Lushi Blue, Jingmen Blue, Dongxiang Brown, and Lushi Brown) were genotyped for 21 SNP markers from the SLCO1B3 gene to evaluate phylogenetic relationships. As a representative of nonblue-shelled breeds, White Leghorn was included in the study for reference. A high proportion of SNP polymorphism was observed in Chinese chicken populations, ranging from 89% in Jingmen Blue to 100% in most populations, with a mean of 95% across all populations. The White Leghorn breed showed the lowest polymorphism, accounting for 43% of total SNPs. The mean expected heterozygosity varied from 0.11 in Dongxiang Blue to 0.46 in Yimeng Blue. Analysis of molecular variation (AMOVA) for 2 groups of Chinese chickens based on eggshell color type revealed 52% within-group and 43% between-group variations of the total genetic variation. As expected, FST and Reynolds' genetic distance were greatest between White Leghorn and Chinese chicken populations, with average values of 0.40 and 0.55, respectively. The first and second principal coordinates explained approximately 92% of the total variation and supported the clustering of the populations according to their eggshell color type and historical origins. STRUCTURE analysis showed a considerable source of variation among populations for the clustering into blue-shelled and nonblue-shelled chicken populations. The low estimation of genetic differentiation (FST) between Chinese chicken populations is possibly due to a common historical origin and high gene flow. Remarkably similar population classifications were obtained with all methods used in the study. Aligning endogenous avian retroviral (EAV)-HP insertion sequences showed no difference among the blue-shelled chickens.

Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations

Background

Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds.

Results

We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings.

Conclusions

The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0109-5) contains supplementary material, which is available to authorized users.

How do SNP ascertainment schemes and population demographics affect inferences about population history?

Background

The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using F_ST and principal components analysis (PCA).

Results

Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group polymorphism decreases estimates of F_ST between groups. Subpopulation-biased selection of SNPs changes the weighting of principal component axes and can affect inferences about proportions of admixture and population histories using PCA. PCA-based inferences of population relationships are largely congruent across types of ascertainment bias, even when ascertainment bias is strong.

Conclusions

Analyses of ascertainment bias in genomic data have largely been conducted on human data. As genomic analyses are being applied to non-model organisms, and across taxa with deeper divergences, care must be taken to consider the potential for bias in ascertainment of variation to affect inferences. Estimates of F_ST, time of separation, and population divergence as estimated by principal components analysis can be misleading if this bias is not taken into account.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1469-5) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel

Information about genetic diversity and population structure among cattle breeds is essential for genetic improvement, understanding of environmental adaptation as well as utilization and conservation of cattle breeds. This study investigated genetic diversity and the population structure among six cattle breeds in South African (SA) including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31), and Holstein (n = 29). Genetic diversity within cattle breeds was analyzed using three measures of genetic diversity namely allelic richness (AR), expected heterozygosity (He) and inbreeding coefficient (f). Genetic distances between breed pairs were evaluated using Nei's genetic distance. Population structure was assessed using model-based clustering (ADMIXTURE). Results of this study revealed that the allelic richness ranged from 1.88 (Afrikaner) to 1.73 (Nguni). Afrikaner cattle had the lowest level of genetic diversity (He = 0.24) and the Drakensberger cattle (He = 0.30) had the highest level of genetic variation among indigenous and locally-developed cattle breeds. The level of inbreeding was lower across the studied cattle breeds. As expected the average genetic distance was the greatest between indigenous cattle breeds and Bos taurus cattle breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The results of this study provided useful insight regarding genetic structure of SA cattle breeds.

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (F_IS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (F_ST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

K. T, Ramasamy S, Ellahi MB, Mohammed F, Teneva A, Shamsuddin M, Podesta MG, Diallo A. Candidate gene approach for parasite resistance in sheep--variation in immune pathway genes and association with fecal egg count

Sheep chromosome 3 (Oar3) has the largest number of QTLs reported to be significantly associated with resistance to gastro-intestinal nematodes. This study aimed to identify single nucleotide polymorphisms (SNPs) within candidate genes located in sheep chromosome 3 as well as genes involved in major immune pathways. A total of 41 SNPs were identified across 38 candidate genes in a panel of unrelated sheep and genotyped in 713 animals belonging to 22 breeds across Asia, Europe and South America. The variations and evolution of immune pathway genes were assessed in sheep populations across these macro-environmental regions that significantly differ in the diversity and load of pathogens. The mean minor allele frequency (MAF) did not vary between Asian and European sheep reflecting the absence of ascertainment bias. Phylogenetic analysis revealed two major clusters with most of South Asian, South East Asian and South West Asian breeds clustering together while European and South American sheep breeds clustered together distinctly. Analysis of molecular variance revealed strong phylogeographic structure at loci located in immune pathway genes, unlike microsatellite and genome wide SNP markers. To understand the influence of natural selection processes, SNP loci located in chromosome 3 were utilized to reconstruct haplotypes, the diversity of which showed significant deviations from selective neutrality. Reduced Median network of reconstructed haplotypes showed balancing selection in force at these loci. Preliminary association of SNP genotypes with phenotypes recorded 42 days post challenge revealed significant differences (P<0.05) in fecal egg count, body weight change and packed cell volume at two, four and six SNP loci respectively. In conclusion, the present study reports strong phylogeographic structure and balancing selection operating at SNP loci located within immune pathway genes. Further, SNP loci identified in the study were found to have potential for future large scale association studies in naturally exposed sheep populations.

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel

In this study we used a medium density panel of SNP markers to perform population genetic analysis in five Italian cattle breeds. The BovineSNP50 BeadChip was used to genotype a total of 2,935 bulls of Piedmontese, Marchigiana, Italian Holstein, Italian Brown and Italian Pezzata Rossa breeds. To determine a genome-wide pattern of positive selection we mapped the F st values against genome location. The highest F st peaks were obtained on BTA6 and BTA13 where some candidate genes are located. We identified selection signatures peculiar of each breed which suggest selection for genes involved in milk or meat traits. The genetic structure was investigated by using a multidimensional scaling of the genetic distance matrix and a Bayesian approach implemented in the STRUCTURE software. The genotyping data showed a clear partitioning of the cattle genetic diversity into distinct breeds if a number of clusters equal to the number of populations were given. Assuming a lower number of clusters beef breeds group together. Both methods showed all five breeds separated in well defined clusters and the Bayesian approach assigned individuals to the breed of origin. The work is of interest not only because it enriches the knowledge on the process of evolution but also because the results generated could have implications for selective breeding programs.

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

BACKGROUND

Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations.A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history.

RESULTS

The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ─ including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ─, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds.

CONCLUSIONS

High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the populations used, we found a good agreement between the different analyses. Our results are also in agreement with historical reports and provide insight in the events that shaped the current genetic variation of pig populations from the Iberian Peninsula. The results exposed will aid to design and implement strategies for the future management of endangered minority pig breeds and wild populations.