Evolutionary process of Bos taurus cattle in favourable versus unfavourable environments and its implications for genetic selection

More than Three Decades of Bm86: What We Know and Where to Go

Tick and tick-borne disease control have been a serious research focus for many decades. In a global climate of increasing acaricide resistance, host immunity against tick infestation has become a much-needed complementary strategy to common chemical control. From the earliest acquired resistance studies in small animal models to proof of concept in large production animals, it was the isolation, characterization, and final recombinant protein production of the midgut antigen Bm86 from the Australian cattle tick strain of Rhipicephalus (Boophilus) microplus (later reinstated as R. (B.) australis) that established tick subunit vaccines as a viable alternative in tick and tick-borne disease control. In the past 37 years, this antigen has spawned numerous tick subunit vaccines (either Bm86-based or novel), and though we are still describing its molecular structure and function, this antigen remains the gold standard for all tick vaccines. In this paper, advances in tick vaccine development over the past three decades are discussed alongside the development of biotechnology, where existing gaps and future directives in the field are highlighted.

ExAgBov: A public database of annotated variations from hundreds of bovine whole-exome sequencing samples

Large reference datasets of annotated genetic variations from genome-scale sequencing are essential for interpreting identified variants, their functional impact, and their possible contribution to diseases and traits. However, to date, no such database of annotated variation from broad cattle populations is publicly available. To overcome this gap and advance bovine NGS-driven variant discovery and interpretation, we obtained and analyzed raw data deposited in the SRA public repository. Short reads from 262 whole-exome sequencing samples of Bos Taurus were mapped to the Bos Taurus ARS-UCD1.2 reference genome. The GATK best practice workflow was applied for variant calling. Comprehensive annotation of all recorded variants was done using the Ensembl Variant Effect Predictor (VEP). An in-depth analysis of the population structure revealed the breeds comprising the database. The Exomes Aggregate of Bovine- ExAgBov is a comprehensively annotated dataset of more than 20 million short variants, of which ~2% are located within open reading frames, splice regions, and UTRs, and more than 60,000 variants are predicted to be deleterious.

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup "I", were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

Introgression, admixture, and selection facilitate genetic adaptation to high-altitude environments in cattle

Domestication and subsequent selection of cattle to form breeds and biological types that can adapt to different environments partitioned ancestral genetic diversity into distinct modern lineages. Genome-wide selection particularly for adaptation to extreme environments left detectable signatures genome-wide. We used high-density genotype data for 42 cattle breeds and identified the influence of Bos grunniens and Bos javanicus on the formation of Chinese indicine breeds that led to their divergence from India-origin zebu. We also found evidence for introgression, admixture, and migration in most of the Chinese breeds. Selection signature analyses between high-altitude (≥1800 m) and low-altitude adapted breeds (<1500 m) revealed candidate genes (ACSS2, ALDOC, EPAS1, EGLN1, NUCB2) and pathways that are putatively involved in hypoxia adaptation. Immunohistochemical, real-time PCR and CRISPR/cas9 ACSS2-knockout analyses suggest that the up-regulation of ACSS2 expression in the liver promotes the metabolic adaptation of cells to hypoxia via the hypoxia-inducible factor pathway. High altitude adaptation involved the introgression of alleles from high-altitude adapted yaks into Chinese Bos taurus taurus prior to their formation into recognized breeds and followed by selection. In addition to selection, adaptation to high altitude environments has been facilitated by admixture and introgression with locally adapted cattle populations.

Strategies to improve the efficiency of beef cattle production

Globally, there are approximately one billion beef cattle, and compared with poultry and swine, beef cattle have the poorest conversion efficiency of feed to meat. However, these metrics fail to consider that beef cattle produce high-quality protein from feeds that are unsuitable for other livestock species. Strategies to improve the efficiency of beef cattle are focusing on operational and breeding management, host genetics, functional efficiency of rumen and respiratory microbiomes, and the structure and composition of feed. These strategies must also consider the health and immunity of the herd as well as the need for beef cattle to thrive in a changing environment. Genotyping can identify hybrid vigor with positive consequences for animal health, productivity, and environmental adaptability. The role of microbiome–host interactions is key in efficient nutrient digestion and host health. Microbial markers and gene expression patterns within the rumen microbiome are being used to identify hosts that are efficient at fibre digestion. Plant breeding and processing are optimizing the feed value of both forages and concentrates. Strategies to improve the efficiency of cattle production are a prerequisite for the sustainable intensification needed to satisfy the future demand for beef.

Updating the application of Metarhizium anisopliae to control cattle tick Rhipicephalus microplus (Acari: Ixodidae)

The bovine tick, Rhipicephalus microplus, is the main ectoparasite of cattle and causes loss of billions of dollars worldwide in lost meat, milk, and leather production, as well as control expenses. In addition to systemically impacting the host during the parasitic act, this parasite is also an important disease vector. Traditionally, the main commercial control of the tick is achieved through application of chemical acaricides, which can leave residues in the meat and milk. Moreover, ticks can become resistant to these chemicals due to their massive and incorrect use. Many alternative methods have been tested including vaccines and natural products from plant origin. However, the efficacy of these treatments is variable and limited, especially when used alone. Arthropod-pathogenic fungi, such as Metarhizium anisopliae, are among the natural microbial agents with promising potential to be used alone or in association with other products, for example with chemical acaricides. This article discusses several aspects of bovine tick control related to the use of M. anisopliae, which is one of the most studied and viable alternative tools for effective tick control.

Four Novel SNPs of MYO1A Gene Associated with Heat-Tolerance in Chinese Cattle

Based on the previous GWAS research related to bovine heat tolerance trait, this study aimed to explore the effect of myosin-1a (MYO1A) gene on bovine heat tolerance trait, and find the molecular markers related to the heat tolerance of Chinese cattle. In our study, four novel candidate SNPs highly conserved in B. indicus breeds but barely existed in B. taurus were identified in MYO1A gene according to Bovine Genome Variation Database and Selective Signatures (BGVD). PCR and DNA sequencing were used to genotype 1072 individuals including 34 Chinese indigenous cattle breeds as well as Angus and Indian zebu. Two synonymous mutations (rs208210464 and rs110123931), one missense mutation (rs209999142; Phe172Ser), and one intron mutation (rs135771836) were detected. The frequencies of mutant alleles of the four SNPs gradually increased from northern groups to southern groups of Chinese cattle, which was consistent with the distribution of various climatic conditions of China. Additionally, four SNPs were significantly associated with four climatic conditions including annual mean temperature (T), relative humidity (H), temperature-humidity index (THI), and average annual sunshine hours (100-cloudiness) (SR). Among these, rs209999142 and Hap 1/1 had better performance than others. Our results suggested that rs209999142 was associated with heat-tolerance trait and rs208210464, rs110123931, and rs135771836 showed high phenotypic effect on heat-tolerance trait because of the strong linkage with rs209999142. These SNPs could be used as candidates for marker-assisted selection (MAS) in cattle breeding.

A Novel SNP in EIF2AK4 Gene Is Associated with Thermal Tolerance Traits in Chinese Cattle

Simple Summary

China harbors two lineages of cattle (Bos taurus and Bos indicus) that display pronounced geographical distribution differences. Northern Chinese cattle predominantly belong to B. taurus and southern Chinese cattle belong to B. indicus. Both B. taurus and B. indicus contribute to the admixture of cattle in central China. Thermal stress induces oxidative stress and DNA damage in mammals. In general, B. indicus are more resistant to thermal stress than B. taurus. Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4), which pertains to the family of serine–threonine kinase, is a candidate gene for thermal stress. However, the effects of the bovine EIF2AK4 gene on the thermal tolerance traits of Chinese cattle breeds remain unknown. Our results suggest that a variant of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.

Abstract

Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4, also known as GCN2), which pertains to the family of serine–threonine kinase, is involved in oxidative stress and DNA damage repair. A missense single-nucleotide polymorphism (SNP) (NC_037337.1 g.35615224 T > G) in exon 6 of the EIF2AK4 gene which encodes a p.Ile205Ser substitution was observed in the Bovine Genome Variation Database and Selective Signatures (BGVD). The purpose of the current study is to determine the allelic frequency distribution of the locus and analyze its association with thermal tolerance in Chinese indigenous cattle. In our study, the allelic frequency distribution of the missense mutation (NC_037337.1 g.35615224 T > G) in Chinese cattle was analyzed by sequencing 1105 individuals of 37 breeds including 35 Chinese indigenous cattle breeds and two exotic breeds. In particular, association analysis was carried out between the genotypes and three environmental parameters including annual mean temperature (T), relative humidity (RH), and temperature–humidity index (THI). The frequency of the mutant allele G (NC_037337.1 g.35615224 T > G) gradually decreased from the southern cattle groups to the northern cattle groups, whereas the frequency of the wild-type allele T showed an opposite pattern, consistent with the distribution of indicine and taurine cattle in China. In accordance with the association analysis, genotypes were significantly associated with T (P < 0.01), RH (P < 0.01), and THI (P < 0.01), suggesting that the cattle with genotype GG were found in regions with higher T, RH, and THI. Thus, our results suggest that the mutation (NC_037337.1 g.35615224 T > G) of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.

Genomic analyses suggest adaptive differentiation of northern European native cattle breeds

Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle (Bos taurus) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.

Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices

Background

The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment. Industrial microbes such as Saccharomyces cerevisiae are also faced with a large range of fermentation conditions that affect their technological properties. Finding the molecular determinism of such variations is a critical task for better understanding the genetic bases of phenotypic plasticity and can also be helpful in order to improve breeding methods.

Results

In this study we implemented a QTL mapping program using two independent cross (~ 100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to whole genome sequencing approaches, both crosses were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the environmental conditions. Molecular dissection of a major QTL demonstrated that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits.

Conclusions

The detection of QTLs and their interactions with environment emphasizes the complexity of yeast industrial traits. The validation of the interaction of SSU1 allelic variants with the nature of the fermented juice increases knowledge about the impact of the sulfite pump during fermentation. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5145-4) contains supplementary material, which is available to authorized users.

Biobanking Genetic Material for Agricultural Animal Species

Biobanking animal germplasm and tissues is a major component of conserving genetic resources. Effectively constructing such gene banks requires an understanding and evaluation of genetic resources, the ability to conserve various tissues through cryopreservation, and a robust information technology infrastructure to allow managers and potential users to fully understand and make use of the collection. Progress has been made internationally in developing national genetic resource collections. As these collections have been developed, it has become apparent that gene banks can serve a multitude of roles, thereby serving short- and long-term needs of research communities and industry. This article documents the development of gene banks and provides examples of how they have been used to date and the extent to which they have captured genetic diversity for future use.

A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)

Ecoregional differences contribute to genetic environmental interactions and impact animal performance. These differences may become more important under climate change scenarios. Utilizing genetic diversity within a species to address such problems has not been fully explored. In this study Hereford cattle were genotyped with 50K Bead Chip or 770K Bovine Bead Chip to test the existence of genetic structure in five U.S. ecoregions characterized by precipitation, temperature and humidity and designated: cool arid (CA), cool humid (CH), transition zone (TZ), warm arid (WA), and warm humid (WH). SNP data were analyzed in three sequential analyses. Broad genetic structure was evaluated with STRUCTURE, and ADMIXTURE software using 14,312 SNPs after passing quality control variables. The second analysis was performed using principal coordinate analysis with 66 Tag SNPs associated in the literature with various aspects of environmental stressors (e.g., heat tolerance) or production (e.g., milk production). In the third analysis TreeSelect was used with the 66 SNPs to evaluate if ecoregional allelic frequencies deviated from a central frequency and by so doing are indicative of directional selection. The three analyses suggested subpopulation structures associated with ecoregions from where animals were derived. ADMIXTURE and PCA results illustrated the importance of temperature and humidity and confirm subpopulation assignments. Comparisons of allele frequencies with TreeSelect showed ecoregion differences, in particular the divergence between arid and humid regions. Patterns of genetic variability obtained by medium and high density SNP chips can be used to acclimatize a temperately derived breed to various ecoregions. As climate change becomes an important factor in cattle production, this study should be used as a proof of concept to review future breeding and conservation schemes aimed at adaptation to climatic events.

Genomic prediction for tick resistance in Braford and Hereford cattle

One of the main animal health problems in tropical and subtropical cattle production is the bovine tick, which causes decreased performance, hide devaluation, increased production costs with acaricide treatments, and transmission of infectious diseases. This study investigated the utility of genomic prediction as a tool to select Braford (BO) and Hereford (HH) cattle resistant to ticks. The accuracy and bias of different methods for direct and blended genomic prediction was assessed using 10,673 tick counts obtained from 3,435 BO and 928 HH cattle belonging to the Delta G Connection breeding program. A subset of 2,803 BO and 652 HH samples were genotyped and 41,045 markers remained after quality control. Log transformed records were adjusted by a pedigree repeatability model to estimate variance components, genetic parameters, and breeding values (EBV) and subsequently used to obtain deregressed EBV. Estimated heritability and repeatability for tick counts were 0.19 ± 0.03 and 0.29 ± 0.01, respectively. Data were split into 5 subsets using k-means and random clustering for cross-validation of genomic predictions. Depending on the method, direct genomic value (DGV) prediction accuracies ranged from 0.35 with Bayes least absolute shrinkage and selection operator (LASSO) to 0.39 with BayesB for k-means clustering and between 0.42 with BayesLASSO and 0.45 with BayesC for random clustering. All genomic methods were superior to pedigree BLUP (PBLUP) accuracies of 0.26 for k-means and 0.29 for random groups, with highest accuracy gains obtained with BayesB (39%) for k-means and BayesC (55%) for random groups. Blending of historical phenotypic and pedigree information by different methods further increased DGV accuracies by values between 0.03 and 0.05 for direct prediction methods. However, highest accuracy was observed with single-step genomic BLUP with values of 0.48 for -means and 0.56, which represent, respectively, 84 and 93% improvement over PBLUP. Observed random clustering cross-validation breed-specific accuracies ranged between 0.29 and 0.36 for HH and between 0.55 and 0.61 for BO, depending on the blending method. These moderately high values for BO demonstrate that genomic predictions could be used as a practical tool to improve genetic resistance to ticks and in the development of resistant lines of this breed. For HH, accuracies are still in the low to moderate side and this breed training population needs to be increased before genomic selection could be reliably applied to improve tick resistance.

Genomic adaptation of admixed dairy cattle in East Africa

Dairy cattle in East Africa imported from the U.S. and Europe have been adapted to new environments. In small local farms, cattle have generally been maintained by crossbreeding that could increase survivability under a severe environment. Eventually, genomic ancestry of a specific breed will be nearly fixed in genomic regions of local breeds or crossbreds when it is advantageous for survival or production in harsh environments. To examine this situation, 25 Friesians and 162 local cattle produced by crossbreeding of dairy breeds in Kenya were sampled and genotyped using 50K SNPs. Using principal component analysis (PCA), the admixed local cattle were found to consist of several imported breeds, including Guernsey, Norwegian Red, and Holstein. To infer the influence of parental breeds on genomic regions, local ancestry mapping was performed based on the similarity of haplotypes. As a consequence, it appears that no genomic region has been under the complete influence of a specific parental breed. Nonetheless, the ancestry of Holstein-Friesians was substantial in most genomic regions (>80%). Furthermore, we examined the frequency of the most common haplotypes from parental breeds that have changed substantially in Kenyan crossbreds during admixture. The frequency of these haplotypes from parental breeds, which were likely to be selected in temperate regions, has deviated considerably from expected frequency in 11 genomic regions. Additionally, extended haplotype homozygosity (EHH) based methods were applied to identify the regions responding to recent selection in crossbreds, called candidate regions, resulting in seven regions that appeared to be affected by Holstein-Friesians. However, some signatures of selection were less dependent on Holsteins-Friesians, suggesting evidence of adaptation in East Africa. The analysis of local ancestry is a useful approach to understand the detailed genomic structure and may reveal regions of the genome required for specialized adaptation when combined with methods for searching for the recent changes of haplotype frequency in an admixed population.

Using UHF proximity loggers to quantify male-female interactions: a scoping study of estrous activity in cattle

Reproductive efficiency is an important determinant of profitable cattle breeding systems and the success of assisted reproductive techniques (ART) in wildlife conservation programs. Methods of estrous detection used in intensive beef and dairy cattle systems lack accuracy and remain the single biggest issue for improvement of reproductive rates and such methods are not practical for either large-scale extensive beef cattle enterprises or free-living mammalian species. Recent developments in UHF (ultra high frequency) proximity logger telemetry devices have been used to provide a continuous pair-wise measure of associations between individual animals for both livestock and wildlife. The objective of this study was to explore the potential of using UHF telemetry to identify the reproductive cycle phenotype in terms of intensity and duration of estrus. The study was conducted using Belmont Red (interbred Africander Brahman Hereford-Shorthorn) cattle grazing irrigated pasture on Belmont Research Station, northeastern Australia. The cow-bull associations from three groups of cows each with one bull were recorded over a 7-week breeding season and the stage of estrus was identified using ultrasonography. Telemetry data from bull and cows, collected over 4 8-day logger deployments, were log transformed and analyzed by ANOVA. Both the number and duration of bull-cow affiliations were significantly (P<0.001) greater in estrous cows compared to anestrus cows. These results support the development of the UHF technology as a hands-off and noninvasive means of gathering socio-sexual information on both wildlife and livestock for reproductive management.

Tick infestation patterns in free ranging African buffalo (Syncercus caffer): Effects of host innate immunity and niche segregation among tick species

Ticks are of vast importance to livestock health, and contribute to conflicts between wildlife conservation and agricultural interests; but factors driving tick infestation patterns on wild hosts are not well understood. We studied tick infestation patterns on free-ranging African buffalo (Syncercus caffer), asking (i) is there evidence for niche segregation among tick species?; and (ii) how do host characteristics affect variation in tick abundance among hosts? We identified ticks and estimated tick burdens on 134 adult female buffalo from two herds at Kruger National Park, South Africa. To assess niche segregation, we evaluated attachment site preferences and tested for correlations between abundances of different tick species. To investigate which host factors may drive variability in tick abundance, we measured age, body condition, reproductive and immune status in all hosts, and examined their effects on tick burdens.

Two tick species were abundant on buffalo, Amblyomma hebraeum and Rhipicephalus evertsi evertsi. A. hebraeum were found primarily in the inguinal and axillary regions; R. e. evertsi attached exclusively in the perianal area. Abundances of A. hebraeum and R. e. evertsi on the host were unrelated. These results suggest spatial niche segregation between A. hebraeum and R. e. evertsi on the buffalo. Buffalo with stronger innate immunity, and younger buffalo, had fewer ticks. Buffalo with low body condition scores, and pregnant buffalo, had higher tick burdens, but these effects varied between the two herds we sampled.

This study is one of the first to link ectoparasite abundance patterns and immunity in a free-ranging mammalian host population. Based on independent abundances of A. hebraeum and R. e. evertsi on individual buffalo, we would expect no association between the diseases these ticks transmit. Longitudinal studies linking environmental variability with host immunity are needed to understand tick infestation patterns and the dynamics of tick-borne diseases in wildlife.

Genetic parameters of infectious bovine keratoconjunctivitis and its relationship with weight and parasite infestations in Australian tropical Bos taurus cattle

Background

Infectious bovine keratoconjunctivitis (IBK) or ‘pinkeye’ is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phenotypic correlations with cattle tick counts, number of helminth (unspecified species) eggs per gram of faeces and growth traits in Australian tropically adapted Bos taurus cattle were estimated.

Methods

Animals were clinically examined for the presence of IBK infection before and after weaning when the calves were 3 to 6 months and 15 to 18 months old, respectively and were also recorded for tick counts, helminth eggs counts as an indicator of intestinal parasites and live weights at several ages including 18 months.

Results

Negative genetic correlations were estimated between IBK incidence and weight traits for animals in pre-weaning and post-weaning datasets. Genetic correlations among weight measurements were positive, with moderate to high values. Genetic correlations of IBK incidence with tick counts were positive for the pre-weaning and negative for the post-weaning datasets but negative with helminth eggs counts for the pre-weaning dataset and slightly positive for the post-weaning dataset. Genetic correlations between tick and helminth eggs counts were moderate and positive for both datasets. Phenotypic correlations of IBK incidence with helminth eggs per gram of faeces were moderate and positive for both datasets, but were close to zero for both datasets with tick counts.

Conclusions

Our results suggest that genetic selection against IBK incidence in tropical cattle is feasible and that calves genetically prone to acquire IBK infection could also be genetically prone to have a slower growth. The positive genetic correlations among weight traits and between tick and helminth eggs counts suggest that they are controlled by common genes (with pleiotropic effects). Genetic correlations between IBK incidence and tick and helminth egg counts were moderate and opposite between pre-weaning and post-weaning datasets, suggesting that the environmental and (or) maternal effects differ between these two growth phases. This preliminary study provides estimated genetic parameters for IBK incidence, which could be used to design selection and breeding programs for tropical adaptation in beef cattle.

Evolution in biocontrol strains: insight from the harlequin ladybird Harmonia axyridis

After being used as a biocontrol agent against aphids for decades without harmful consequences, the Asian harlequin ladybird Harmonia axyridis has suddenly become an invasive pest on a worldwide scale. We investigate the impact of captive breeding on several traits of this ladybird such as genetic diversity, fecundity, survival and pathogen resistance. We conducted an experiment in the laboratory to compare the fecundity and the susceptibility to the entomopathogenic fungus Beauveria bassiana of wild and biocontrol adults of H. axyridis. We compiled these new findings with already published data. Altogether, our findings suggest that mass rearing of biological control agents may strongly impact genetic diversity and life-history traits. We discuss how such changes may subsequently affect the fitness of biological control strains in natural environments.

Conservation priorities of genetic diversity in domesticated metapopulations: a study in taurine cattle breeds

We estimated neutral diversity of 21 European cattle breeds with 105 microsatellites. Nine of them resembled unselected Balkan Buša strains with diffuse breeding barriers and the 12 others were strongly differentiated, isolated breeds. Because of the impact of neutral genetic diversity on long-term population adaptive capacity, we discuss the long-term outcome of different conservation priorities in a subdivided metapopulation of the investigated cattle breeds. The optimal contribution to a pool of total genetic diversity allocated more than 95% of long-term relevant neutral diversity to virtually unselected strains of the Balkan Buša, while the maximization of total variance preferred inbred breeds. Current artificial selection methods, such as genomic selection sped up and a recovery of underestimated traits becomes quickly impossible. We emphasize that currently neutral and even deleterious alleles might be required for future genotypes in sustainable and efficient livestock breeding and production systems of a 21st century. We provide cumulative evidences that long-term survival relies on genetic complexity and complexity relies on allelic diversity. Our results suggest that virtually unselected, nonuniform strains harbor a crucial proportion of neutral diversity and should be conserved with high global priority. As one example, we suggest a cooperative maintenance of the nondifferentiated, highly fragmented, and fast vanishing metapopulation of Balkan Buša.

Molecular genetic approaches for identifying the basis of variation in resistance to tick infestation in cattle

In recent years there has been renewed interest in the adaptation of cattle to challenging environments, largely driven by advances in genomic methods. The current interest in tick resistance is understandable given the major production and welfare implications of tick infestation in tropical and subtropical zones where around 70% of beef cattle are located. Heritability for tick burden in cattle has been shown to range about 0.30, which is sufficient to result in the success of some programs of selection for tick resistance in cattle. Gene-expression studies strongly indicate that both immune and non-immune mechanisms are associated with tick resistance in cattle. Recent quantitative-trait mapping studies have identified chromosome segments and single nucleotide polymorphisms associated with tick burden, but no causal variant has been identified so far. Most of the genetic markers identified for tick burden explain a relatively small proportion of the variance, which is typical of markers for quantitative traits. This leads to the conclusion that panels of multiple markers for tick resistance rather than a single marker will most likely be developed, possibly involving specific panels for zebu or taurine breeds, which could be used for future selection and breeding programs in cattle.