Rare phenotypes in domestic animals: unique resources for multiple applications

Comparison of miR-106b, miR-191, and miR-30d expression dynamics in milk with regard to its composition in Holstein and Ayrshire cows

OBJECTIVE

Milk composition varies considerably and depends on paratypical, genetic, and epigenetic factors. MiRNAs belong to the class of small non-coding RNAs; they are one of the key tools of epigenetic control because of their ability to regulate gene expression at the post-transcriptional level. We compared the relative expression levels of miR-106b, miR-191, and miR-30d in milk to demonstrate the relationship between the content of these miRNAs with protein and fat components of milk in Holstein and Ayrshire cattle.

METHODS

Milk fat, protein, and casein contents were determined in the obtained samples, as well as the content of the main fatty acids (g/100 g milk), including: saturated acids, such as myristic (C14:0), palmitic (C16:0), and stearic (C18:0) acids; monounsaturated acids, including oleic (C18:1) acid; as well as long-, medium- and short-chain, polyunsaturated, and trans fatty acids. Real-time stem-loop one-tube reverse transcription polymerase chain reaction with TaqMan probes was used to measure the miRNA expression levels.

RESULTS

The miRNA expression levels in milk samples were found to be decreased in the first two months in Holstein breed, and in the first four months in Ayrshire breed. Correlation analysis did not reveal any dependence between changes in the expression level of miRNA and milk fat content, but showed a multidirectional relationship with individual milk fatty acids. Positive associations between the expression levels of miR-106b and miR-30d and protein and casein content were found in the Ayrshire breed. Receiver operating characteristic curve analysis showed that miR-106b and miR-30d expression levels can cause changes in fatty acid and protein composition of milk in Ayrshire cows, whereas miR-106b expression level determines the fatty acid composition in Holsteins.

CONCLUSION

The data obtained in this study showed that miR-106b, miR-191, and miR-30d expression levels in milk samples have peculiarities associated with breed affiliation and the lactation period.

Exploring the origin of a unique mutant allele in twin-tail goldfish using CRISPR/Cas9 mutants

Artificial selection has been widely applied to genetically fix rare phenotypic features in ornamental domesticated animals. For many of these animals, the mutated loci and alleles underlying rare phenotypes are known. However, few studies have explored whether these rare genetic mutations might have been fixed due to competition among related mutated alleles or if the fixation occurred due to contingent stochastic events. Here, we performed genetic crossing with twin-tail ornamental goldfish and CRISPR/Cas9-mutated goldfish to investigate why only a single mutated allele-chdS with a E127X stop codon (also called chdAE127X)-gives rise to the twin-tail phenotype in the modern domesticated goldfish population. Two closely related chdS mutants were generated with CRISPR/Cas9 and compared with the E127X allele in F2 and F3 generations. Both of the CRISPR/Cas9-generated alleles were equivalent to the E127X allele in terms of penetrance/expressivity of the twin-tail phenotype and viability of carriers. These findings indicate that multiple truncating mutations could have produced viable twin-tail goldfish. Therefore, the absence of polymorphic alleles for the twin-tail phenotype in modern goldfish likely stems from stochastic elimination or a lack of competing alleles in the common ancestor. Our study is the first experimental comparison of a singular domestication-derived allele with CRISPR/Cas9-generated alleles to understand how genetic fixation of a unique genotype and phenotype may have occurred. Thus, our work may provide a conceptual framework for future investigations of rare evolutionary events in domesticated animals.

Exploiting morphobiometric and genomic variability of African indigenous camel populations-A review

Camels (Camelus dromedarius) in Africa are adapted to arid and the semi-arid environmental conditions, and are valuable for meat, milk and fiber production. On account of the growing demand for camels in this continent, there is a need for knowledge on their phenotypic and genetic diversity. This is fundamental to sustainable herd management and utilization including the design of appropriate breeding and conservation strategies. We reviewed studies on the phenotypic and genetic characterization, breeding objectives, systems of production, productive and reproductive performances, and pathways for the sustainable rearing and use of camels in Africa. The morphological and genetic diversity, productive and reproductive abilities of African camels suggest the existence of genetic variations that can be utilized for breeds/ecotypes' genetic improvement and conservation. Possible areas of intervention include the establishment of open nucleus and community-based breeding schemes and utilization of modern reproductive technologies for the genetic improvement of milk and meat yields, sustainable management of rangelands, capacity building of the pastoralists and agro-pastoralists, institutional supports, formation of centralized conservation centres and efficient and effective marketing systems.

Opportunities of Genomics for the Use of Semen Cryo-Conserved in Gene Banks

Shortly after the introduction of cryo-conserved semen in the main farm animal species, gene banks were founded. Safeguarding farm animal genetic diversity for future use was and is the main objective. A sampling of sires was based on their pedigree and phenotypic information. Nowadays, DNA information from cryo-conserved sires and from animals in the living populations has become available. The combination of their DNA information can be used to realize three opportunities: 1) to make the gene bank a more complete archive of genetic diversity, 2) to determine the history of the genetic diversity from the living populations, and 3) to improve the performance and genetic diversity of living populations. These three opportunities for the use of gene bank sires in the genomic era are outlined in this study, and relevant recent literature is summarized to illustrate the great value of a gene bank as an archive of genetic diversity.

Livestock Management for the Delivery of Ecosystem Services in Fire-Prone Shrublands of Atlantic Iberia

In the northwest of the Iberian Peninsula, characterized by its humid climate, large rural areas are being abandoned, mostly in less-favoured areas covered by heathlands, which present a low nutritive quality for livestock production. The high combustibility of these shrublands is driving a high wildfire incidence with negative environmental and economic effects. In this review, some aspects on wildfire occurrence and the potential of grazing livestock to reduce woody phytomass and fire risk in heathland-dominated areas whilst maintaining quality production and preserving biodiversity are summarized. Heathlands may be partially improved—converted to grassland—to better meet animals’ nutritional requirements while acting as ‘natural’ firebreaks. The specific grazing behaviour offers the opportunity to combine different domestic herbivores (mixed grazing) to achieve sustainable systems utilizing heterogeneous resources. Cattle, sheep, goats, and horses may have a role in the provision of different ecosystem services such as food production and biodiversity conservation. Genotype x environment interactions shape the ability of animals to cope with poor vegetation conditions, with smaller species and breeds performing better than larger animals. Goats and horses are indicated to arrest woody encroachment. Sustainable grazing systems are affordable in heathland–grassland mosaics by selecting appropriate livestock species and breeds for quality production, thus favouring rural economies and lowering fire risk.

Automated Processing and Phenotype Extraction of Ovine Medical Images Using a Combined Generative Adversarial Network and Computer Vision Pipeline

The speed and accuracy of phenotype detection from medical images are some of the most important qualities needed for any informed and timely response such as early detection of cancer or detection of desirable phenotypes for animal breeding. To improve both these qualities, the world is leveraging artificial intelligence and machine learning against this challenge. Most recently, deep learning has successfully been applied to the medical field to improve detection accuracies and speed for conditions including cancer and COVID-19. In this study, we applied deep neural networks, in the form of a generative adversarial network (GAN), to perform image-to-image processing steps needed for ovine phenotype analysis from CT scans of sheep. Key phenotypes such as gigot geometry and tissue distribution were determined using a computer vision (CV) pipeline. The results of the image processing using a trained GAN are strikingly similar (a similarity index of 98%) when used on unseen test images. The combined GAN-CV pipeline was able to process and determine the phenotypes at a speed of 0.11 s per medical image compared to approximately 30 min for manual processing. We hope this pipeline represents the first step towards automated phenotype extraction for ovine genetic breeding programmes.

Morphological variability within the indigenous sheep population of Benin

Knowledge of both the genetic diversity and geographical distribution of animal genetic resources is a prerequisite for their sustainable utilization, improvement and conservation. The present study was undertaken to explore the current morphological variability within the sheep population in Benin as a prelude for their molecular characterization. From November 2018 to February 2020, 25 quantitative linear body measurements and 5 qualitative physical traits were recorded on 1240 adult ewes from the 10 phytogeographic zones that comprise the three vegetation zones of Benin. Fourteen morphological indices were calculated based on the linear body measurements. The collected data were first analyzed using multiple comparisons of least-square means (LSmeans), followed by generalized linear model (GLM) procedures, to explore the relationships among the measured morphometric traits and the 10 phytogeographic zones. Next, the presence of any genetic sub-populations was examined using multivariate analytical methods, including canonical discriminant analysis (CDA) and ascending hierarchical clustering (AHC). Univariate analyses indicated that all quantitative linear body measurements varied significantly (P<0.05) across the phytogeographic zones. The highest values (LSmean± standard error) of withers height (68.3±0.47 cm), sternum height (46.0±0.35 cm), and rump height (68.8±0.47 cm) were recorded in the Mekrou-Pendjari zone, the drier phytogeographic zone in the North, whereas the lowest values, 49.2±0.34, 25.9±0.26, and 52.0±0.35 cm, respectively, were recorded in the Pobe zone in the South. Multivariate analyses revealed the prevalence of four distinct sheep sub-populations in Benin. The sub-population from the South could be assimilated to the short-legged and that from the North to the West African long-legged sheep. The two other sub-populations were intermediate and closer to the crossbreeds or another short-legged sub-breed. The proportion of individuals correctly classified in their group of origin was approximately 74%. These results uncovered a spatial morphological variation in the Beninese sheep population along a South-North phytogeographic gradient.

Tracing selection signatures in the pig genome gives evidence for selective pressures on a unique curly hair phenotype in Mangalitza

Selection for desirable traits and breed-specific phenotypes has left distinctive footprints in the genome of pigs. As representative of a breed with strong selective traces aiming for robustness, health and performance, the Mangalitza pig, a native curly-haired pig breed from Hungary, was investigated in this study. Whole genome sequencing and SNP chip genotyping was performed to detect runs of homozygosity (ROH) in Mangalitza and Mangalitza-crossbreeds. We identified breed specific ROH regions harboring genes associated with the development of the curly hair type and further characteristics of this breed. Further analysis of two matings of Mangalitza with straight-coated pig breeds confirmed an autosomal dominant inheritance of curly hair. Subsequent scanning of the genome for variant effects on this trait revealed two variants potentially affecting hair follicle development and differentiation. Validation in a large sample set as well as in imputed SNP data confirmed these variants to be Mangalitza-specific. Herein, we demonstrated how strong artificial selection has shaped the genome in Mangalitza pigs and left traces in the form of selection signatures. This knowledge on genomic variation promoting unique phenotypes like curly hair provides an important resource for futures studies unraveling genetic effects for special characteristics in livestock.

Recent land use and management changes decouple the adaptation of livestock diversity to the environment

Native livestock breeds, i.e. those autochthonous to a specific region, are locally adapted domesticated animals that conserve genetic resources, guaranty food security and provide agroecosystem services. Native breeds are largely threatened worldwide by agricultural intensification and rural areas abandonment processes related to recent changes in production schemes and planning. Yet, our gap of knowledge regarding livestock breed-environment relationships may prevent the design of successful conservation measures. In this work, we analyse the links between livestock diversity -i.e. richness of native breeds- and a selection of environmental factors that express at broad scales, with a temporal perspective. We compare native breeds distributional patterns before and after the agricultural intensification, in the context of land-use change in mainland Spain. Our results confirm the existence of strong associations between the distribution of native livestock breeds and environmental factors. These links, however, weaken for contemporary distributions. In fact, changes in breed distribution reflect a shift towards more productive environments. Finally, we found that the areas having higher breed richness are undergoing land abandonment processes. Succeeding in the conservation of threatened native breeds will require going beyond merely genetic and production-oriented views. Ecological and sociocultural perspectives should also be accounted for as global change processes are determinant for livestock agrobiodiversity.

Food securers or invasive aliens? Trends and consequences of non-native livestock introgression in developing countries

Importation of livestock genetic resources from industrialized countries for introgression of specific traits and other forms of crossbreeding is often indicative of a shift in production systems toward greater intensification and specialization. In developing countries, imported genetic resources are regarded as both a solution to improve the performance of local livestock and as one of the main threats to local populations. Using international databases, censuses and technical reports, we investigate ongoing trends and consequences of these two phenomena in 40 countries from Africa, Asia and Latin America. In these countries, the share of locally adapted breeds within species has decreased by an average of 0.76% per year over the last 20 years. The corresponding increase has been distributed between pure exotic breeds and crossbred animals, with differences across regions. In several countries, increased utilization of exotic cattle breeds and crossbreeding has been accompanied by a trend in increased milk yield per cow. The shift from local genetic resources to crossbred and exotic animals must be considered in the context of challenges such as food security, erosion of agrobiodiversity, interactions with other agricultural production, reduction of poverty and provision of ecosystem services, as well as resilience to and mitigation of climate change.

Genome-wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Simple Summary

In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also contribute insights into the genetic basis for plumage color in poultry, and confirm the great complexity of the mechanisms that control this trait.

Abstract

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (F_ST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and F_ST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

Organization and Management of Conservation Programs and Research in Domestic Animal Genetic Resources

Creating national committees for domestic animal genetic resources within genetic resource national commissions is recommended to organize in situ and ex situ conservation initiatives. In situ conservation is a high priority because it retains traditional zootechnical contexts and locations to ensure the long-term survival of breeds. In situ actions can be based on subsidies, technical support, structure creation, or trademark definition. Provisional or permanent relocation of breeds may prevent immediate extinction when catastrophes, epizootics, or social conflicts compromise in situ conservation. Ex situ in vivo (animal preservation in rescue or quarantine centers) and in vitro methods (germplasm, tissues/cells, DNA/genes storage) are also potential options. Alert systems must detect emergencies and summon the national committee to implement appropriate procedures. Ex situ coordinated centers must be prepared to permanently or provisionally receive extremely endangered collections. National germplasm banks must maintain sufficient samples of national breeds (duplicated) in their collections to restore extinct populations at levels that guarantee the survival of biodiversity. A conservation management survey, describing national and international governmental and non-governmental structures, was developed. Conservation research initiatives for international domestic animal genetic resources from consortia centralize the efforts of studies on molecular, genomic or geo-evolutionary breed characterization, breed distinction, and functional gene identification. Several consortia also consider ex situ conservation relying on socioeconomic or cultural aspects. The CONBIAND network (Conservation for the Biodiversity of Local Domestic Animals for Sustainable Rural Development) exemplifies conservation efficiency maximization in a low-funding setting, integrating several Latin American consortia with international cooperation where limited human, material, and economic resources are available.

An exploratory analysis on how geographic, socioeconomic, and environmental drivers affect the diversity of livestock breeds worldwide

This study investigates the relationships between various environmental and geographic, demographic, and socioeconomic factors with the diversity of livestock breeds reported within countries across the world. Statistical analyses were performed considering the numbers of breeds reported by 158 countries for 4 livestock mammalian species (cattle, sheep, goats, and pigs). Organization for Economic Cooperation and Development (OECD) countries reported more breeds than non-OECD countries in general. Strong and positive correlations were found between agricultural area, human population size, species population size, and number of breeds per country. When considering regression models, the species population size was found as the most important explanatory factor for the number of breeds reported by countries in the 4 species. Diversity of production systems in the country had a significant association with the number of breeds reported for sheep, goats, and pigs. The number of ruminant breeds was positively associated with the size of agricultural area and the diversity of land cover in the country. While demographic and cultural importance of a given species is a major factor associated with the number of livestock breeds within countries, this diversity is also connected to the variability in environmental and production conditions.