Biobanking animal genetic resources: critical infrastructure and growth opportunities.

National animal gene banks have acquired substantial quantities of germplasm that protect and preserve a wide range of livestock breeds. New challenges and growth opportunities are emerging. A key challenge will be increased gene bank use, but this requires increased characterization of phenotypes and genotypes for populations and collections.

Assessment of FecGE genotypes on reproductive traits in Brazilian Morada Nova and Santa Inês sheep.

The aim of this study was to evaluate the effect of the polymorphic FecGE allele on reproductive traits in Santa Inês and Morada Nova ewes. The traits evaluated were as follows: total progeny weights at birth (PWB) and weaning (PWW) and progeny survival rates at birth (PSRB) and weaning (PSRW). A total of 389 animals, belonging to two Santa Inês herds and one Morada Nova herd, were genotyped. There was a difference between the averages for all the traits studied regarding type of parturition, herd/breed, genotype/herd, and genotype/type of parturition. For each additional progeny, if the female was FecGE/E, the PWB decreased by 1.02 kg and the PWW by 3.16 kg, also with a 0.04% reduction in PSRB and no change in PSRW. If the female was FecGE/+, the reduction in PWB was 0.24 kg, with an increase in PSRW by 0.11%, but no change in PWW and PSRB. In general, these results demonstrate that FecG+/+ females have a better ability to increase their number of progenies without reducing PWB and PWW (also similar to FecGE/+). Thus, it is suggested that further studies on the association between the traits of interest and candidate genes in sheep should be carried out so that the regions which have the greatest effect on the expression of these traits are actually identified. It was not possible to verify the effect of the FecGE allele on the PWB, PWW, PSRB, and PSRW in these Morada Nova and Santa Inês herds.

Landscape Genetics for Brazilian Equines.

Optimization of DNA collection for National gene bank and conservation programs requires information on spatial and genetic distribution of animals countrywide. The relationship between genetic and geographic distances were examined in 8 Brazilian horse breeds (Baixadeiro, Crioulo, Campeiro, Lavradeiro, Marajoara, Mangalarga Marchador, Pantaneiro and Puruca) using Single Nucleotide Polymorphism markers and collection point locations. Mantel correlations, Genetic Landscape Shape Interpolation, Allelic Aggregation Index Analyses and Spatial autocorrelation tests indicated a nonrandom distribution of horses throughout the country. Minimum collection distances for the national Gene Bank should be 530km, with clear divisions seen in genetic structure of horse populations in both North/South and East/West directions. Comparing Pantaneiro and North/Northeastern breeds, physical distance is not necessarily the defining factor for genetic differentiation. This should be considered when sampling these local breeds. These data can help optimise GenBank collection routines and conservation strategies for these breeds.

Use of logistic models to evaluate the response of superovulation treatment and embryo production in Santa Inês ewes.

The study aimed to verify the influence of the FecGE mutation in superovulated ewes and to evaluate the probability of logistic models to determine the response capacity of these ewes to superovulatory treatment. Santa Inês ewes (n = 29) were genotyped for the FecGE mutation and separated for their genotype group in carriers of the mutant E allele (FecGE/E, FecG+/E) and non-carrier (FecG+/+) alleles. The ewes underwent hormonal treatment for superovulation. Aside from the genotypes, variables included in the statistical model were reproductive status (empty, early lactation, or late lactation), age (> or < 6 years), and number of births (nulliparous, primiparous, multiparous). The carriers of the mutation could be discriminated from the non-carriers based on the number of corpora lutea, rate of frozen embryos, and fecundity. Recovery rate was significantly higher (P < 0.05) in FecGE/E (94.31%) compared to FecG+/E (63.15%) and FecG+/+ (61.90%) (P < 0.05), whereas fecundity rate of FecG+/+ ewes (50.76%) was significantly higher than FecG+/E (18.96%) and FecGE/E (32.53%) (P < 0.05). We determined in this study that the response to superovulation and embryo production can be discriminated between FecGE/E and FecG+/E ewes in relation to the FecG+/+ genotype. Logistic models that included reproductive status and mutation, or reproductive status and age, or reproductive status and number of births were effective in predicting the response to superovulatory treatment.

New Insight into the Genome-Wide Diversity and Admixture of Six Colombian Sheep Populations.

Creole sheep represent a strategic genetic resource for populations living in marginal areas under financial restrictions on the American continent. Six Colombian sheep breeds (two wool (BCL-Boyacá and NCL-Nariño, 12 and 14 samples) and four hair (OPCE-Ethiopian, 54 samples; OPCS-Sudan, 74 samples; OPCP-Pelibeuy, 59 samples; OPCW-Wayúu, 24 samples) were genotyped using the Illumina Ovine SNP50 BeadChip. Data was also included from international 44 breeds from International Sheep Genomics Consortium (ISGC) and from data published in previous a previous work on the Caribbean and African breeds. Although geographically separated, wool (NCL, BCL) and hair types (OPCE, OPCS, OPCW) presented little genetic differentiation (FST 0.05) at a global level but several groups of animals separated suggesting local clustering due to geographical isolation. The OPCP underwent a recent crossing with Mexican Pelibuey, explaining its differentiation. Findings in this work such as the proximity to West African Djallonké (WAD) and Barbados Black Belly (BBB), suggest different introductions of African type animals from the Caribbean region on a pre-existing genetic basis formed by animals deriving from the first importations coming from Europe in colonial times. As expected, Colombian wool breeds showed, in particular in Admixture software results, a greater genomic component in common with European breeds and in particular with Iberian ones (Churra). This study provides a basis for future research into the genetic diversity within and between the Colombian sheep breeds analysed, and scientific data for policy decisions on Farm Animal Genetic Resources (FAnGR).

Selection signatures for heat tolerance in Brazilian horse breeds.

Since domestication, horse breeds have adapted to their environments and differentiated from one another. This paper uses two methods to detect selection signatures in 23 horse breeds, eight of which are Brazilian (610 animals), both cold-blooded and warm-blooded, from temperate and tropical regions. These animals were genotyped using the GGP Equine BeadChip and we analysed the data by Principal Component Analysis (PCA). The samples were separated into groups based on their geographical area of origin and PCA results studied. The genomic regions under selection were detected by hapFLK and PCAdapt methodologies, identifying six regions under selection with at least one Brazilian horse breed. These regions contain genes associated with heat tolerance, skin colour, body size, energy production/metabolism, genes involved in protein degradation/turnover/DNA repair, genes reducing the impact of oxidative stress/cellular repair, and transcriptional regulation. This work confirmed LCORL and NCAPG gene regions in previous studies associated with body size on Equine Chromosome Autosome 3 (ECA3). On the same ECA3, a region implicating genes linked to coat colour was identified, also previously related to heat stress. Regions with genes coding heat shock proteins were found on ECA1 and 2, and many candidate genes for oxidation-reduction which are a natural response to heat stress. However, a larger sample size and whole-genome SNPs are needed to understand better and identify new candidate regions as well as their functional relation with heat tolerance.

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci.

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3'-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Lentivirus Susceptibility in Brazilian and US Sheep with TMEM154 Mutations.

Small ruminant lentiviruses (SRLVs) affect sheep and goats worldwide. The major gene related to SRLV infections is the Transmembrane Protein Gene 154 (TMEM154). We estimated the haplotype frequencies of TMEM154 in the USA (USDA-ARS) and Brazil (Embrapa) Gene Banks by using two different SNP genotyping methodologies, FluidigmTM and KASPTM. We also genotyped the ZNF389_ss748775100 deletion variant in Brazilian flocks. A total of 1040 blood samples and 112 semen samples from 15 Brazilian breeds were genotyped with Fluidigm for the SNP ZNF389_ss748775100 and 12 TMEM154 SNPs. A total of 484 blood samples from the Santa Inês breed and 188 semen samples from 14 North American sheep breeds were genotyped with KASP for 6 TMEM154 SNPs. All the Brazilian samples had the "I/I" genotype for the ZNF389_ss748775100 mutation. There were 25 TMEM154 haplotypes distributed across the Brazilian breeds, and 4 haplotypes in the US breeds. Haplotypes associated with susceptibility were present in almost all breeds, which suggests that genetic testing can help to improve herd health and productivity by selecting non-susceptible animals as founders of the next generations. Fluidigm and KASP are reliable assays when compared with Beadchip arrays. Further studies are necessary to understand the unknown role of TMEM154 mutations, host-pathogen interaction and new genes associated with the clinical condition.

Fine-scale genetic diversity of the Brazilian Pantaneiro horse breed adapted to flooded regions.

Among the animal species first introduced in Brazil during the country's discovery, horses (Equus caballus) stand out because of their evolutionary history and relationship with humans. Among the Brazilian horse breeds, the Pantaneiro draws attention due to its adaptative traits. Blood samples of 116 Pantaneiro horses were divided into six populations based on their sampling location, aiming to identify the existence of genetic structure and quantify genetic diversity within and between them. Populations were compared to elucidate genetic variability and differentiation better and assess the impact of Pantanal's natural geographic barriers on gene flow between populations. Data from the GGP Equine BeadChip (Geneseek-Neogen, 65.157 SNPs) was used to assess basic diversity parameters, genetic distance (FST), principal component analysis (PCA), and population structure (ADMIXTURE) for the sampled animals. Mantel test was also performed to investigate the correlation between the populations' genetic and geographic distances. Results showed high genetic variability in all populations, with elevated levels of admixture in their structure. High levels of admixture make it challenging to establish a racial pattern and, consequently, populations within the breed, being that only one of the populations differentiated itself from the others. No significant correlations between genetic and geographic distances were observed, indicating that environmental barriers did not hinder gene flow between populations, and neither farmers' selection practices might have change breed genetic composition significantly. Low genetic distance and similar heterozygosity values were observed among populations, suggesting strong genetic proximity and low differentiation. Thereby, the Pantaneiro breed does not exhibit genetic subpopulations and could be considered, for conservation purposes, a single big population in the Panatnal region. This study will support sampling strategies for National genebank.

Occurrence, morphology, and morphometry of follicles containing multiple oocytes in FecGE mutant Santa Inês ewes.

This study was conducted to characterize the morphology and morphometry of follicles containing multiple oocytes (MOFs) and determine the association with the FecGE mutation in Santa Inês ewes. Based on the genotypes, 65 ewes were characterized as being homozygous wild-type (n = 25; FecG+/+), heterozygous mutant (n = 27, FecG+/E), and homozygous mutant (n = 13, FecGE/E). The variables evaluated were follicle developmental stage, number of oocytes per follicle, morphology, and morphometry of MOFs. The FecGE mutation did not affect the frequency of MOFs (P > 0.05) (3.0 % in FecG+/+; 3.3 % in FecG+/E; and 3.5 % in FecGE/E). The greater viability (P < 0.05) of MOFs was identified in transitory stage of the FecGE/E (95.0 %) and FecG+/E (90.9 %) when compared to the FecG+/+ genotype (73.3 %). Furthermore, the morphology of transitory follicles with two oocytes was the variable and when evaluated was the most reliable determinant for predicting which ewes had an FecGE mutation. In conclusion, the FecGE mutation did not affect the frequency of MOFs. The ewes with FecGE mutation had a greater frequency of morphologically normal MOFs in the transitory stage. Furthermore, the ewes with the FecGE mutation had a greater likelihood of having MOFs containing two morphologically normal oocytes.

Integration of georeferenced and genetic data for the management of biodiversity in sheep genetic resources in Brazil.

There are few animal germplasm/gene bank collections in Brazil, and basic studies are needed to attend the future internal and external demands from international partners. The aim of this work was to validate a "proof of concept" that integrates spatial (georeferenced data) and genetic data regarding the local of origin from 3518 DNA samples from 17 different genetic groups or breeds of sheep in the Brazilian Germplasm bank. Spatialisation shows that not all genetic groups have samples in the bank, and collection is concentrated in the conservation nuclei spread nationwide. Only 21% of states with a specific breed have samples in the gene bank. The mean number of animals sampled per collection was 32, while the mean distance travelled to collect samples was 262 km from the conservation nuclei. For example, the Brazilian Somali were only collected in the conservation nucleus in Ceará State. No samples were collected to date for the Cariri breed, which is recognised by the Brazilian Ministry of Agriculture. Only two farms and one breed in the bank are from the northern region. Of the 27 states, there are samples in the gene bank of sheep from 13, so several states have no samples, requiring collection from herds outside the official system of conservation to make sure that studies using this germplasm realised are not biased. Significant genetic differences are seen above 332 km, which should guide future sampling efforts. Suggestions are given for improving the quantity, quality and diversity of samples in the gene bank.

Phylogeography of feral Monteiro pig in the Brazilian Pantanal Ecosystem.

The Monteiro is a feral pig found in the Brazilian Pantanal ecosystem. The goal of this research is to generate data and knolewdge related to animal populations wich can be used for management and development of an in vitro conservation program for animal resourses at Pantanal ecosystem. The present study evaluated animals sampled from 10 distinct locations within the region, using 19 microsatellite markers (N = 189) and the control region of mitochondrial DNA (mtDNA) (N = 392). Low genetic differences were found between populations with the microsatellite data. The FST range was between 0.009 and 0.063 (p-value < 0.05). The Mantel test corroborated with previous results, as low correlations between genetic and geographic distances were observed (r2 = 0.2309, p = 0.06). Bayesian analysis for genetic structure identification placed the Monteiro pigs into three main clusters (MOB, Pop 1 and all others Pantanal populations). Most of the Monteiro pigs share a single European haplotype as seen by mtDNA analyses. This haplotype is not exclusive, as it is shared with other swine populations (commercial and other locally adapted breeds). Monteiro populations from different geographic locations within Pantanal are not isolated and can be considered as a large unique population. Since animals roam freely to seek food and water, or even due to seasonal flooding of their habitat, the Monteiro populations presented absence of major genetic structure and evidence of high gene flow. These results can be used to create a management plan and in situ and ex situ conservation program for conservation and use of the Monteiro breed in the Pantanal ecosystem.

Paternal Origins and Migratory Episodes of Domestic Sheep.

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle.

Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.

Heat stress effects on sheep: Are hair sheep more heat resistant?

Climatic variables can trigger physiological, biochemical, haematological and hormonal alterations that influence the maintenance of homeothermy and can affect production and productivity in sheep. Different mechanisms are responsible for tolerance to heat stress (HS) including coat and skin colour, body size, fat distribution, physiological reactions and not just coat type (hair/wool). This review looks at physical, physiological, molecular and genetic aspects of heat tolerance in sheep and how they affect hair and wool sheep. We propose that it is the adaptation to hot environments and not the type of coat (wool/hair) itself that determines the capacity of the resistance of the animal to HS, due to modifications in essential pathways such as energy metabolism, physiological responses and body size. When studied in similar environments, commercial wool breeds tend to show higher heat stress, but hair breeds tend not to differ from wool breeds that are adapted to hot environments.

Low mtDNA diversity in a highly differentiated population of spinner dolphins (Stenella longirostris) from the Fernando de Noronha Archipelago, Brazil.

Spinner dolphins (Stenella longirostris, Gray 1828) are widely distributed in tropical waters around the world. Although they occur in large, pelagic groups in the Eastern Tropical Pacific, elsewhere in the Pacific they are found in small and genetically isolated populations associated with islands. This species is considered to be "Least Concern" (LC) by the World Conservation Union (IUCN). To assess genetic diversity and population structure of an island-associated population in the South Atlantic Ocean we surveyed 162 spinner dolphins throughout the Fernando de Noronha Archipelago of the northeast coast of Brazil using ten microsatellite loci and sequencing a 413-bp section of the mitochondrial DNA (mtDNA) control region. Eleven mtDNA haplotypes were identified and haplotype diversity (h) and nucleotide diversity (π) were 0.3747 and 0.0060, respectively. Median-Joining Network revealed the presence of two very divergent haplotypes and F-statistics indicated some heterogeneity between two sampling years. All microsatellite loci were polymorphic (Ho: 0.767; He: 0,764) but, revealed no detectable substructure. We also compared the mtDNA haplotypes from Noronha to 159 haplotypes representing 893 individuals from 14 locations worldwide. We found that the two common haplotypes from the Fernando de Noronha Archipelago were absent in all other populations. These comparisons showed that Noronha spinner dolphins are likely more differentiated than other island populations, suggesting that they form societies with strong site fidelity mediated by females.

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine.

Invasive alien species are a significant threat to both economic and ecological systems. Identifying the processes that give rise to invasive populations is essential for implementing effective control strategies. We conducted an ancestry analysis of invasive feral swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is widely distributed throughout the contiguous United States, to describe introduction pathways, sources of newly emergent populations and processes contributing to an ongoing invasion. Comparisons of high-density single nucleotide polymorphism genotypes for 6,566 invasive feral swine to a comprehensive reference set of S. scrofa revealed that the vast majority of feral swine were of mixed ancestry, with dominant genetic associations to Western heritage breeds of domestic pig and European populations of wild boar. Further, the rapid expansion of invasive feral swine over the past 30 years was attributable to secondary introductions from established populations of admixed ancestry as opposed to direct introductions of domestic breeds or wild boar. Spatially widespread genetic associations of invasive feral swine to European wild boar deviated strongly from historical S. scrofa introduction pressure, which was largely restricted to domestic pigs with infrequent, localized wild boar releases. The deviation between historical introduction pressure and contemporary genetic ancestry suggests wild boar-hybridization may contribute to differential fitness in the environment and heightened invasive potential for individuals of admixed domestic pig-wild boar ancestry.

Ovarian and follicular variables used to determine ewes with different FecGE genotypes.

Based on ovarian and follicular variables, there was determination of ewes with different FecGE genotypes. Based on the FecGE genotype, 65 Santa Inês ewes were assigned to three experimental groups: homozygous wild-type (n = 25; FecG+/+), mutant heterozygous (n = 27; FecG+/E) and mutant homozygous (n = 13; FecGE/E). The ewe's ovaries were weighed and measured, then the follicles (oocyte, nucleus and nucleolus) were histologically evaluated for morphometry and morphology. Morphologically normal follicles, in the primordial and transitional stages, explained 70.18% of the variability morphological characteristics between mutant and wild-type ewes. Conducting the morphometric evaluation resulted in a more precise determination of the genotype groups when there was assessment of the primordial and secondary follicular developmental stages. The diameter of the oocyte and the oocyte nucleus of the primordial follicles explained 36.76% of the variability in follicular morphology between ewes with the mutation and those with the wildtype group. Similarly, the core diameter of oocytes in secondary follicles explained 10.63% of the variability in follicular morphology among FecGE/E, FecG+/E and FecG+/+ ewes. Thus, morphologically normal follicles in the primordial and transitional stages of development are the variables that allow for a more precise differentiation of Santa Inês ewes with the FecGE mutation. These variables may be evaluated to make more efficient the adoption of biotechniques that when conducted there is utilisation of follicles in the initial developmental stages as a physiological basis for classifying whether specific follicles are useful when conducting the techniques.

Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection.

Human migration and trade facilitated domesticated livestock movement, gene flow and development of diverse populations upon which agriculture is based. In addition, varying USA ecological conditions has led to a diverse set of livestock populations to utilize. Quantifying genetic diversity of these populations is incomplete. This paper quantifies genetic diversity captured by the National Animal Germplasm Program and explores genetic structure and differences among 19 pig populations (feral populations from Pacific islands, continental US, and Chinese breeds) using 70,231 SNP from 500 animal samples. Among continental US breeds Fis was consistently low suggesting genetic variability is sufficiently available for breeders to use. A unique population structure using principal component analysis illustrated clear distinctions between Duroc, Yorkshire, Hampshire, breeds of Chinese origin, and feral Pacific Island populations were identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian waves of gene flow. Quantifying diversity and potential origin of Pacific populations provides insight for future uses, and the need for preservation. Viewing gene bank holdings in context of diversity measures we found a lack of inbreeding within breeds, suggesting the collection represents a wide sampling of individual breeds.