Genetic characterization of Latin-American Creole cattle using microsatellite markers

Genetic diversity in and relationships among 26 Creole cattle breeds from 10 American countries were assessed using 19 microsatellites. Heterozygosities, F-statistics estimates, genetic distances, multivariate analyses and assignment tests were performed. The levels of within-breed diversity detected in Creole cattle were considerable and higher than those previously reported for European breeds, but similar to those found in other Latin American breeds. Differences among breeds accounted for 8.4% of the total genetic variability. Most breeds clustered separately when the number of pre-defined populations was 21 (the most probable K value), with the exception of some closely related breeds that shared the same cluster and others that were admixed. Despite the high genetic diversity detected, significant inbreeding was also observed within some breeds, and heterozygote excess was detected in others. These results indicate that Creoles represent important reservoirs of cattle genetic diversity and that appropriate conservation measures should be implemented for these native breeds in order to minimize inbreeding and uncontrolled crossbreeding.     

Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

Background

Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions.

Methods

A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity.

Results

Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds.

Conclusions

Conservation priorities differed significantly according to the weight given to within- and between-breed genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their products should be taken into consideration to ensure their long-term survival.     

Genetic diversity and patterns of population structure in Creole goats from the Americas

Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in‐depth analysis of the within‐ and between‐breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora‐type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well‐differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P < 0.05). Our results provide a broad perspective on the extant genetic diversity of Creole goats, however further studies are needed to understand whether the observed geographical patterns of population structure may reflect the mode of goat colonization in the Americas.     

Characterization of the Russian beef cattle breed gene pools using inter simple sequence repeat DNA analysis (ISSR analysis)

The gene pools of beef cattle breeds bred in Russia were characterized on the basis of inter simple sequence repeat DNA analysis (ISSR analysis). Samples of Aberdeen Angus, Kalmyk, and Kazakh Whitehead breeds from Russia, as well as of Hereford breed, hybrids of Kazakh Whitehead and Hereford breeds, and Kazakh Whitehead breed from the Republic of Kazakhstan, were examined. In the examined breeds, 27 AG-ISSR fragments were identified, 25 of which were polymorphic. The examined breeds were different both in the fragment profiles (the presence/absence of individual ISSR fragments) and in their frequencies. It was demonstrated that the hybrid animals lacked some ISSR fragments that were present with high frequencies in parental forms, suggesting considerable genome rearrangement in the hybrid animals (at the regions of microsatellite localization) in crossings of the individuals from different breeds. The level of genetic diversity in Russian beef breeds was consistent with the values typical of farmed populations (breeds). The genetic diversity parameters assessed by applying Nei’s gene diversity index and the Shannon index varied from 0.0218 to 0.0605 and from 0.0225 to 0.0819, respectively. The highest Shannon index value was detected in the Kalmyk breed (0.0837) and Kazakh Whitehead breed from Russia (0.0819), and the highest level of Nei’s gene diversity index was found in the Kalmyk breed (0.0562) and in both populations of the Kazakh Whitehead breed (0.0509 and 0.0605). The high level of genetic similarity (according to Nei) was revealed between Russian beef cattle breeds and Hereford cattle: 0.839 (for the Kazakh Whitehead breed from Russia) and 0.769 (for the Kalmyk breed).     

Genetic characterization of Argentine and Bolivian Creole cattle breeds assessed through microsatellites

In the present report, the polymorphisms from 9 microsatellites were used to assess genetic diversity and relationships in 4 Creole cattle breeds from Argentina and Bolivia, 4 European taurine breeds, and 2 American zebu populations. The Creole populations display a relatively high level of genetic variation as estimated by allelic diversity and heterozygosity, whereas the British breeds displayed reduced levels of genetic diversity. The analysis of molecular variance indicated that 7.8% of variance can be explained by differences among taurine and zebu breeds. Consistent with these results, the first principal component (PC), which comprised the 40% of the total variance, clearly distinguishes these 2 groups. In addition, all constructed phylogenetic trees cluster together Nelore and Brahman breeds with robust bootstrap values. Only 1% of variance was due to difference between American Creole and European taurine cattle. Although this secondary split was supported by the classical genetic distance and the second PC (15%), the topology of trees is not particularly robust. The presence of zebu-specific alleles in Creole cattle allowed estimating a moderate degree of zebu admixture. When these data were compared with mitochondrial and Y chromosomal studies, a clear pattern of male-mediated introgression was revealed. The results presented here contribute to the understanding of origin and history of the American Creole cattle.     

Genomic variation and population structure detected by single nucleotide polymorphism arrays in Corriedale,Merino and Creole sheep

The aim of this study was to investigate the genetic diversity within and among three breeds of sheep: Corriedale, Merino and Creole. Sheep from the three breeds (Merino n = 110, Corriedale n = 108 and Creole n = 10) were genotyped using the Illumina Ovine SNP50 beadchip^®. Genetic diversity was evaluated by comparing the minor allele frequency (MAF) among breeds. Population structure and genetic differentiation were assessed using STRUCTURE software, principal component analysis (PCA) and fixation index (F_ST). Fixed markers (MAF = 0) that were different among breeds were identified as specific breed markers. Using a subset of 18,181 single nucleotide polymorphisms (SNPs), PCA and STUCTURE analysis were able to explain population stratification within breeds. Merino and Corriedale divergent lines showed high levels of polymorphism (89.4% and 86% of polymorphic SNPs, respectively) and moderate genetic differentiation (F_ST = 0.08) between them. In contrast, Creole had only 69% polymorphic SNPs and showed greater genetic differentiation from the other two breeds (F_ST = 0.17 for both breeds). Hence, a subset of molecular markers present in the OvineSNP50 is informative enough for breed assignment and population structure analysis of commercial and Creole breeds.     

Polledness in Argentinean Creole cattle,five centuries surviving

Polledness has been shown to have autosomal Mendelian inheritance, with the polled locus being dominant to the horned locus. This trait was mapped to the BTA1 centromeric end in several breeds. One of the distinctive attributes of Creole cattle, such as the Argentinean Creole, is the presence of long, lyre‐shaped horns. However, polled native animals were reported before the introduction of modern selected European breeds. Here, we studied the origin of the polled mutation, either independent or introgressed, in a Creole line from the Creole cattle founder group at the IIACS‐INTA Leales Experimental Station (northwest Argentina). The study sample (65 animals: 26 horned and 39 polled) was genotyped using high‐density SNP microarrays and three previously reported genetic markers (P_202ID, P_80kbID and P_G). A genome‐wide association study, selection signatures, linkage disequilibrium analysis and copy number variations were used to detect the responsible region and the segregating haplotypes/alleles. The interval mapped in the Leales herd (1.23–2.13 Mb) overlapped with the region previously reported in several European cattle breeds, suggesting that the same locus could be segregating in this population. The previously reported variants P_F and P_G were not detected, thus dismissing the Holstein‐Friesian and Nellore origins of the polled phenotype in this native breed. Conversely, the presence of the Celtic variant P_C suggests an almost complete co‐segregation. The cluster analysis rejected the hypothesis of recent introgression, which is compatible with the historical record of polled Creole cattle in northwest Argentina.     

Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for diseases and immunological traits. However, none of the highly adapted Latin American Creole breeds have been characterized for BoLA gene polymorphism by high resolution typing methods. In this work, we sequenced exon 2 of the BoLA class II DRB3 gene from 179 cattle (113 Bolivian Yacumeño cattle and 66 Colombian Hartón del Valle cattle breeds) using a polymerase chain reaction sequence-based typing (PCR-SBT) method. We identified 36 previously reported alleles and three novel alleles. Thirty-five (32 reported and three new) and 24 alleles (22 reported and two new) were detected in Yacumeño and Hartón del Valle breeds, respectively. Interestingly, Latin American Creole cattle showed a high degree of gene diversity despite their small population sizes, and 10 alleles including three new alleles were found only in these two Creole breeds. We next compared the degree of genetic variability at the population and sequence levels and the genetic distance in the two breeds with those previously reported in five other breeds: Holstein, Japanese Shorthorn, Japanese Black, Jersey, and Hanwoo. Both Creole breeds presented gene diversity higher than 0.90, a nucleotide diversity higher than 0.07, and mean number of pairwise differences higher than 19, indicating that Creole cattle had similar genetic diversity at BoLA-DRB3 to the other breeds. A neutrality test showed that the high degree of genetic variability may be maintained by balancing selection. The F_ST index and the exact G test showed significant differences across all cattle populations (F_ST = 0.0478; p < 0.001). Results from the principal components analysis and the phylogenetic tree showed that Yacumeño and Hartón del Valle breeds were closely related to each other. Collectively, our results suggest that the high level of genetic diversity could be explained by the multiple origins of the Creole germplasm (European, African and Indicus), and this diversity might be maintained by balancing selection.     

Genetic diversity among Angus, American Brahman, Senepol and Romosinuano cattle breeds

The objective of this study was to quantify the genetic diversity among breeds under evaluation for tropical adaptability traits that affect the performance of beef cattle at the USDA/ARS SubTropical Agricultural Research Station (STARS) near Brooksville, FL, USA. Twenty-six microsatellite loci were used to estimate parameters of genetic diversity among the breeds American Brahman, Angus, Senepol and Romosinuano; the latter was comprised of two distinct bloodlines (Costa Rican and Venezuelan). Genotypes of 47 animals from each of these STARS herds were analysed for genetic diversity and genetic distance. Using two methods, the greatest genetic distance was detected between the Costa Rican line of Romosinuano and the Senepol. Gene diversity ranged between 0.64 (Costa Rican line of Romosinuano) and 0.75 (American Brahman). The breed relationship inferences, which are based on genetic distance, provide additional tools for consideration in future crossbreeding studies and for testing the relationship between quantified breed diversity and observed heterosis.     

Indigenous domestic breeds as reservoirs of genetic diversity: the Argentinean Creole cattle

Contrary to highly selected commercial breeds, indigenous domestic breeds are composed of semi-wild or feral populations subjected to reduced levels of artificial selection. As a consequence, many of these breeds have become locally adapted to a wide range of environments, showing high levels of phenotypic variability and increased fitness under natural conditions. Genetic analyses of three loci associated with milk production (alpha(S1)-casein, kappa-casein and prolactin) and the locus BoLA-DRB3 of the major histocompatibility complex indicated that the Argentinean Creole cattle (ACC), an indigenous breed from South America, maintains high levels of genetic diversity and population structure. In contrast to the commercial Holstein breed, the ACC showed considerable variation in heterozygosity (H(e)) and allelic diversity (A) across populations. As expected, bi-allelic markers showed extensive variation in He whereas the highly polymorphic BoLA-DRB3 showed substantial variation in A, with individual populations having 39-74% of the total number of alleles characterized for the breed. An analysis of molecular variance (AMOVA) of nine populations throughout the distribution range of the ACC revealed that 91.9-94.7% of the total observed variance was explained by differences within populations whereas 5.3-8.1% was the result of differences among populations. In addition, the ACC breed consistently showed higher levels of genetic differentiation among populations than Holstein. Results from this study emphasize the importance of population genetic structure within domestic breeds as an essential component of genetic diversity and suggest that indigenous breeds may be considered important reservoirs of genetic diversity for commercial domestic species.     

Restriction Fragment Length Polymorphism (RFLP) in Exon 2 of the BoLA-DRB3 Gene in South American Cattle

The Bola-DRB3 gene participates in the development of the immune response and is highly polymorphic. For these reasons, it has been a candidate gene in studies of the genetic basis of disease resistance and in population genetic analysis. South American native cattle breeds have been widely replaced by improved exotic breeds leading to a loss of genetic resources. In particular, South American native breeds have high levels of fertility and disease resistance. This work describes genetic variability in the BoLA-DRB3 gene in native (Caracu, Pantaneiro, Argentinean Creole) and exotic (Holstein, Jersey, Nelore, Gir) cattle breeds in Brazil and Argentina. PCR-RFLP alleles were identified by combining the restriction patterns for the BoLA-DRB3.2 locus obtained with RsaI, BstY and HaeIII restriction enzymes. Allelic frequencies and deviations from the Hardy-Weinberg equilibrium were also calculated. Analysis of the 24 BoLA-DRB3 PCR-RFLP alleles identified showed differences in the allele distributions among breeds.     

SNP芯片数据估计动物个体基因组品种构成的方法及应用

自然和人工选择、地理隔离和遗传漂移等原因使动物基因组中许多位点的等位基因频率在群体间会产生差异。源于不同品种(祖先)杂交(交配)的动物个体,其基因组与这些品种(祖先)的基因频率(基因型)会存在一定的相关性。因此采用合适的统计模型和分析方法,可以估计出每个品种(祖先)对于个体基因组的遗传贡献比例,又称为个体的基因组品种构成(genomic breed composition, GBC)。本文介绍了利用SNP芯片数据估计动物个体GBC的原理、方法及步骤,并且通过对198头待鉴定的日本红毛和牛GBC的评估,演示了用回归模型和混合分布模型估计动物个体GBC的具体步骤,其中包括SNP子集的筛选、参考群体中动物个体选择以及待测定动物GBC的计算。参考动物群体选自日本红毛和牛(Akaushi)、安格斯牛(Angus)、海福特牛(Hereford)、荷斯坦牛(Holstein)和娟珊牛(Jersey) 5个品种共36 574头,每个个体有40K或50K芯片数据。本文在现有商用 SNP芯片基础上筛选用于品种鉴定和估计动物个体GBC的SNP子集,是对现有SNP芯片功能的拓展和深入开发利用。此外,在基因组选择中如何利用SNP基因型估计动物个体GBC的结果,提高纯种和杂种动物的预测准确度,也是值得深入研究的领域。     

Assessing priorities for conservation in Tuscan cattle breeds using microsatellites

Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (D_m) matrices showed that the pair Calvana–Chianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (C_T = 1.8%). The Calvana breed made null or negative within-breed contributions (f¯_W = 0.0%; C_W = −0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (f¯_T = −0.7%; C_T = −1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (f¯_T = 2.1%; C_T = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (f¯_T = 0.47%; C_T = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock.     

Pedigree analysis of eight Spanish beef cattle breeds

The genetic structure of eight Spanish autochthonous populations (breeds) of beef cattle were studied from pedigree records. The populations studied were: Alistana and Sayaguesa (minority breeds), Avileña – Negra Ibérica and Morucha ("dehesa" breeds, with a scarce incidence of artificial insemination), and mountain breeds, including Asturiana de los Valles, Asturiana de la Montaña and Pirenaica, with extensive use of AI. The Bruna dels Pirineus breed possesses characteristics which make its classification into one of the former groups difficult. There was a large variation between breeds both in the census and the number of herds. Generation intervals ranged from 3.7 to 5.5 years, tending to be longer as the population size was larger. The effective numbers of herds suggest that a small number of herds behaves as a selection nucleus for the rest of the breed. The complete generation equivalent has also been greatly variable, although in general scarce, with the exception of the Pirenaica breed, with a mean of 3.8. Inbreeding effective population sizes were actually small (21 to 127), especially in the mountain-type breeds. However, the average relatedness computed for these breeds suggests that a slight exchange of animals between herds will lead to a much more favourable evolution of inbreeding. The effective number of founders and ancestors were also variable among breeds, although in general the breeds behaved as if they were founded by a small number of animals (25 to 163).     

Analysis of the genetic variation of vascular endothelial growth factor gene in three Chinese indigenous cattle breeds

PCR–SSCP and DNA sequencing methods were employed to screen the genetic variation of vascular endothelial growth factor (VEGF) gene in 675 individuals belonging to three Chinese indigenous cattle breeds including Qinchuan (QC), Jiaxian Red (JX) and Nanyang (NY) breed. Three new single nucleotide polymorphisms (SNPs) (g.6765T > C ss130456744, g.6860A > G ss130456745, g.6893T > C ss130456746) were found. One SNP (g.6765T > C) was detected in intron II of VEGF gene in all three breeds and the other two SNPs (g.6860A > G, g.6893T > C) were in exon III of VEGF gene only in NY breed. Among them, two synonymous mutations of exon III were identified: CCA (Pro) > CCG (Pro) at position 65th amino acid (aa) and TGT (Cys) > TGC (Cys) at position 76th aa of VEGF(190aa) in NY breed. Our study revealed that NY breed exhibited the most abundant genetic diversity in VEGF gene within the three cattle breeds. Furthermore, JX cattle breed was more similar to QC breed than to NY breed. Our genetic data in the present study supported the hypothesis that the distribution pattern of Chinese indigenous cattle breeds was closely related to the geographical and climatic background again.     

Genetic variation within the Hereford breed of cattle

Genetic differentiation among Hereford populations from Britain, Ireland, Sweden, Canada and New Zealand together with six other beef breeds was assessed using blood type polymorphisms. Changes in the genetic structure of the British Hereford population over time were also examined. Loci surveyed were seven red cell antigen systems (A, B, C, F, L, S, Z), and two serum protein loci (transferrin and albumin). Within group variation was measured by the average expected heterozygosity, and between group relationships by genetic distance. There was significant genetic differentiation among Hereford populations from different countries. Differences between Hereford groups, however, were not as large as differences between breeds. There were also significance differences among British herds. The proportion of Canadian genes in the British 'hybrid' population was estimated to have increased from 0·42 (±0·34) in the 1970s to 0·98 (±0·11) in the 1990s. Canadian Hereford groups were found to be less heterozygous than other groups, and replacement of the British population with Canadian animals may lead to loss of variation. Breeding strategies that preserve original native genes in British Hereford populations should be considered by commercial breeders, in order to prevent the long-term loss of genetic variation within the breed.     

Genome‐wide variability and selection signatures in Italian island cattle breeds

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo‐Bruna and Sardo‐Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within‐breed genetic heterogeneity. The F_ST comparison revealing the largest number of significant SNPs was Sardo‐Bruna vs. Sardo‐Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo‐Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo‐Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi‐dimensional scaling and the admixture analysis the Sardo‐Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo‐Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.     

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive,non‐random SNP heterozygosity

Local breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350‐year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high‐density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62–90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r² = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.     

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 (H_O=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (H_O=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.     

Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.