Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management

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.

Genetic differentiation and diversity of the Bolivian endemic titi monkeys, Plecturocebus modestus and Plecturocebus olallae

The genetic variability of New World primates is still poorly documented. We present the first genetic study on two threatened endemic titi monkey species in northern Bolivia (Plecturocebus modestus and Plecturocebus olallae) using six microsatellite markers to investigate genetic structure and variability of 54 individuals from two wild populations. A low level of genetic diversity was found (34 alleles in the total sampled population). Locus 1118 presented the greatest number of alleles. The mean number of alleles per locus in the total population was 5.6 and the average heterozygosity was 0.38 (range 0.12-0.88). The F_IS value for the total population using all microsatellite loci shows a statistically significant heterozygote deficit. The inbreeding coefficients (F_IS) were positive and significantly different from zero (0.064 for P. olallae and 0.213 for P. modestus). The genetic differentiation between populations (F_ST) was moderate with a pair-wise F_ST estimate of 0.14. Population structure analyses assigned the two populations to two differentiated clusters (K = 2). These results suggest that these two species with very close distributional ranges arose from a single population, and that they remain in a process of genetic differentiation and speciation. This study further underlines the urgent need for conservation actions for both endemic primate species.

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

BACKGROUND

Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.

RESULTS

We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow.

CONCLUSIONS

Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.

Systematic Profiling of Short Tandem Repeats in the Cattle Genome

Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

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.

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.

What can livestock breeders learn from conservation genetics and vice versa?

The management of livestock breeds and threatened natural population share common challenges, including small effective population sizes, high risk of inbreeding, and the potential benefits and costs associated with mixing disparate gene pools. Here, we consider what has been learnt about these issues, the ways in which the knowledge gained from one area might be applied to the other, and the potential of genomics to provide new insights. Although there are key differences stemming from the importance of artificial versus natural selection and the decreased level of environmental heterogeneity experienced by many livestock populations, we suspect that information from genetic rescue in natural populations could be usefully applied to livestock. This includes an increased emphasis on maintaining substantial population sizes at the expense of genetic uniqueness in ensuring future adaptability, and on emphasizing the way that environmental changes can influence the relative fitness of deleterious alleles and genotypes in small populations. We also suspect that information gained from cross-breeding and the maintenance of unique breeds will be increasingly important for the preservation of genetic variation in small natural populations. In particular, selected genes identified in domestic populations provide genetic markers for exploring adaptive evolution in threatened natural populations. Genomic technologies in the two disciplines will be important in the future in realizing genetic gains in livestock and maximizing adaptive capacity in wildlife, and particularly in understanding how parts of the genome may respond differently when exposed to population processes and selection.

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well-documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario.

A Genomic Approach for Distinguishing between Recent and Ancient Admixture as Applied to Cattle

Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), which uses the nonrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient types of admixture, and applied it to the reconstruction of admixture in cattle. Cattle are descendants of 2 independently domesticated lineages, taurine and indicine, which diverged more than 200 000 years ago. Several breeds have hybrid ancestry between these divergent lineages. Using 47 506 single-nucleotide polymorphisms, we analyzed the genomic architecture of the ancestry of 1369 individuals. We focused on 4 groups with admixed ancestry, including 2 anciently admixed African breeds (n = 58; n = 43), New World cattle of Spanish origin (n = 51), and known recent hybrids (n = 46). We estimated the ancestry of chromosomal regions for each individual and used the SBS metric to differentiate the timing of admixture among groups and among individuals within groups. By comparing SBS values of test individuals with standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed cattle. We also estimated ancestry at the chromosomal scale. The X chromosome exhibits reduced indicine ancestry in recent hybrid, New World, and western African cattle, with virtually no evidence of indicine ancestry in New World cattle.

Impact of genetic drift on access and benefit sharing under the Nagoya Protocol: the case of the Meishan pig

Genetic drift (GD) randomly impacts small breeds and imported populations. Therefore, it can impact policies that affect conservation of animal genetic resources. This paper evaluates GD for a population of Meishan pigs imported into the United States and explores the ramifications of GD on access and benefit sharing of genetic resources under the Nagoya Protocol (NP) of the United Nations' Convention on Biological Diversity. The NP was motivated by concerns about fair and equitable benefit sharing of genetic resources across life forms. In this experiment, 35 microsatellite markers were used to quantify the level of GD that occurred between Meishan pigs (Meishan-China; n = 22) imported into the United States in the late 1980s and contemporary Meishan (Meishan-US; n = 42), which have been randomly bred since importation. The Meishan-US consisted of 2 subpopulations (Meishan-MARC and Meishan-ISU). Five other breeds were also included in the analysis to serve as reference populations: Fengjing and Minzhu, which were imported with Meishan-China, and Duroc, Berkshire, and Yorkshire from the United States. Mean shift in allele frequency was 0.11 (SE = 0.019) due to GD for Meishan-US vs. Meishan-China with some loci having changed allele frequencies by greater than 0.20. Principle coordinate analysis confirmed divergence among the Meishan populations. Model-based clustering tended to place the U.S. and Chinese breeds into 2 distinct clusters, likely due to differences in allele frequencies between U.S. and Chinese breeds. Contemporary Meishan-US has become differentiated from the original imported animals due to GD. Attributing future performance of Meishan-US to Meishan-China, as set forth by NP, is problematic due to GD. As an imported breed becomes established there will be an increasing number of breeders who may have different selection goals and private treaty contracts will govern the exchange of stock between them. Therefore, considering biological phenomena and social dynamics simultaneously draws into question whether a rigorous access and benefit sharing protocol as envisioned in the NP will be operational.

Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection

Genetic variation in Gir cattle (Bos indicus) has so far not been well characterized. In this study, we used whole genome sequencing of three Gir bulls and a pooled sample from another 11 bulls to identify polymorphisms and loci under selection. A total of 9 990 733 single nucleotide polymorphisms (SNPs) and 604 308 insertion/deletions (indels) were discovered in Gir samples, of which 62.34% and 83.62%, respectively, are previously unknown. Moreover, we detected 79 putative selective sweeps using the sequence data of the pooled sample. One of the most striking sweeps harbours several genes belonging to the cathelicidin gene family, such as CAMP, CATHL1, CATHL2, and CATHL3, which are related to pathogen- and parasite-resistance. Another interesting region harbours genes encoding mitogen-activated protein kinases, which are involved in directing cellular responses to a variety of stimuli, such as osmotic stress and heat shock. These findings are particularly interesting because Gir is resistant to hot temperatures and tropical diseases. This initial selective sweep analysis of Gir cattle has revealed a number of loci that could be important for their adaptation to tropical climates.

Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Background

Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed.

Methods

46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity.

Results

Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, R_t = 5.7 ± 1.4, H_o = 0.63 ± 0.19 and H_e = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (F_is = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (F_st = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity.

Conclusions

Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.

Genetic diversity in farm animals--a review

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.

Precision animal breeding

We accept that we are responsible for the quality of life of animals in our care. We accept that the activities of man affect all the living things with which we share this planet. But we are slow to realize that as a result we have a duty of care for all living things. That duty extends to the breeding of animals for which we are responsible. When animals are bred by man for a purpose, the aim should be to meet certain goals: to improve the precision with which breeding outcomes can be predicted; to avoid the introduction and advance of characteristics deleterious to well-being; and to manage genetic resources and diversity between and within populations as set out in the Convention on Biological Diversity. These goals are summed up in the phrase precision animal breeding. They should apply whether animals are bred as sources of usable products or services for medical or scientific research, for aesthetic or cultural considerations, or as pets. Modern molecular and quantitative genetics and advances in reproductive physiology provide the tools with which these goals can be met.