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

Assessing the Genomics Structure of Dorper and White Dorper Variants, and Dorper Populations in South Africa and Hungary

Dorper sheep was developed for meat production in arid and semi-arid regions under extensive production systems in South Africa. Two variants with distinct head and neck colors were bred during their development process. White Dorper have a white coat while Dorper have a black head and neck. Both variants have grown in popularity around the world. Therefore, understanding the genomic architecture between South African Dorpers and Dorper populations adapted to other climatic regions, as well as genomic differences between Dorper and White Dorper variants is vital for their molecular management. Using the ovine 50K SNP chip, this study compared the genetic architecture of Dorper variants between populations from South Africa and Hungary. The Dorper populations in both countries had high genetic diversity levels, although Dorper in Hungary showed high levels of inbreeding. White Dorpers from both countries were genetically closely related, while Dorpers were distantly related according to principal component analysis and neighbor-joining tree. Additionally, whereas all groups displayed unique selection signatures for local adaptation, Dorpers from Hungary had a similar linkage disequilibrium decay. Environmental differences and color may have influenced the genetic differentiation between the Dorpers. For their molecular management and prospective genomic selection, it is crucial to understand the Dorper sheep’s genomic architecture, and the results of this study can be interpreted as a step in this direction.

A Phylogenetic and Morphological Evolution Study of Ribes L. in China Using RAD-Seq

Ribes L. belongs to the Grossulariaceae family and has important edible, medicinal, ornamental, and landscaping values. Taxonomic classification within this genus is difficult due to its large variety of species, wide distribution, large morphological variations, and presence of two complex taxonomic groups with bisexual or unisexual flowers. Our study aims to clarify the phylogenetic relationships of Ribes L. taxa in China, and further, to provide a reference for a revised global classification of it. The phylogenetic analysis of 52 Ribes L. samples from 30 species was constructed based on restriction site-associated DNA sequencing and single nucleotide polymorphisms. Afterward, two important taxonomic characters were selected for ancestral state reconstruction over the molecular phylogeny. The results showed that the 52 samples could be divided into six branches, i.e., six subgenera, which caused some controversy regarding the morphological classification of Ribes L. in China. The molecular phylogeny supported the separation of subg. Coreosma from subg. Ribesia and subg. Hemibotrya from subg. Berisia and validated the rationale for recognizing subg. Grossularia as an independent subgenus, the rationality of which was further verified by the reconstruction of ancestor traits. Gene flow among Ribes L. was identified and further confirmed our results.

Comprehensive assessment of genetic diversity, structure, and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis

There are four unique cattle breeds in Japan: Japanese Black, Japanese Brown, Japanese Polled, and Japanese Shorthorn. The objective of this study was to comprehensively assess the genetic diversity, structure, relationship, and the degree of influence from foreign breeds (Angus, Simmental, Hanwoo, Shorthorn, Ayrshire, Brown Swiss, and Devon) in the Japanese cattle breeds using Illumina 50 K SNP array. In principal component analysis, each Japanese breed was separately clustered except for Japanese Shorthorn and Shorthorn. Japanese cattle breeds also showed different genetic components from each other at K ≥ 5 in population structure analysis. Japanese Shorthorn, on the other hand, had a very similar structure to Shorthorn at K ≤ 9, and Japanese Polled had a partially similar component with Angus at K = 3-7. Such close relationships were also observed in the phylogenetic tree. These findings imply that Japanese cattle breeds share genetic components with European cattle breeds to some extent while they have been almost differentiated. In population structure analysis, Japanese Black cattle shared little genetic component (3.5%) with European breeds. This is the first study to determine the extent to which European breeds impact Japanese breeds.

Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle

Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures on the genome, rather many loci experience small allele frequency shifts, resulting in large cumulative phenotypic changes. Directional selection and local adaptation are changing populations; but, identifying loci underlying polygenic or environmental selection has been difficult. We use genomic data on tens of thousands of cattle from three populations, distributed over time and landscapes, in linear mixed models with novel dependent variables to map signatures of selection on complex traits and local adaptation. We identify 207 genomic loci associated with an animal's birth date, representing ongoing selection for monogenic and polygenic traits. Additionally, hundreds of additional loci are associated with continuous and discrete environments, providing evidence for historical local adaptation. These candidate loci highlight the nervous system's possible role in local adaptation. While advanced technologies have increased the rate of directional selection in cattle, it has likely been at the expense of historically generated local adaptation, which is especially problematic in changing climates. When applied to large, diverse cattle datasets, these selection mapping methods provide an insight into how selection on complex traits continually shapes the genome. Further, understanding the genomic loci implicated in adaptation may help us breed more adapted and efficient cattle, and begin to understand the basis for mammalian adaptation, especially in changing climates. These selection mapping approaches help clarify selective forces and loci in evolutionary, model, and agricultural contexts.

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.

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.

Random regression of Hereford percentage intramuscular fat on geographical coordinates

Accounting for genotype-environment interactions may improve genetic prediction and parameter estimation. The objective was to use random regression analyses to estimate variances and thereby heritability for intramuscular fat (IMF) across longitude and latitude coordinates within the continental United States. Records from the American Hereford Association (n = 169,440) were used. Analyses were first conducted using the continental United States in its entirety, and then as subdivided into two or four regions. Data were analyzed with an animal model, and linear and quadratic random regressions of additive genetic merit on longitude or latitude as covariate (separately). Subdivided data were analyzed with linear random regressions unique to regions. Regions were North and South separated at 40°N latitude, or West and East separated at 99°W longitude using longitude or latitude as covariate, respectively. Further subdivision to four regions included additional boundaries of 44.46° and 36.46°N latitude and 104.55° and 92.22°W longitude. The estimated heritability of IMF from the traditional model was 0.19 ± 0.004. Without regional subdivision of data, quadratic random regression had the best fit for the data based on likelihood ratio tests using longitude or latitude as covariate (P < 0.01). Estimates of heritability from quadratic random regression on latitude ranged from 0.12 in the South to a high of 0.27 at the extreme Northern latitude. Estimates of heritability from quadratic random regression on longitude ranged from 0.17 in the middle of the parameter space (corresponding to the central United States) to 0.37; higher estimates were noted at the extremes, that is, the far West and East longitudes. Random regression analyses of data divided into regions were conducted with a linear coefficient, as increasing to a quadratic polynomial was never accomplished. Results from random regression on latitude in the East region were similar to results from analyses without regions (h2 ranged from 0.09 to 0.32); however, estimates of heritability in the West region had a lower range from South to North (0.14 to 0.27). Estimates of heritability from random regression on longitude with data divided into two regions were similar to those from analyses that did not include region. Estimates in the South region were somewhat lower and had a lower range (0.15 to 0.31) than those from the North region (0.19 to 0.47). When data were further subdivided, estimation of only a subset of covariances among random regression coefficients was possible, that is, within-region covariances of intercept and linear terms (latitude); those and covariances between all linear random regression coefficients were estimated when longitude was the covariate. Results from random regression analyses of data with four regions modeled produced very high estimates of heritability in low latitudes in the furthest West and high latitudes in the furthest East region, with approximate difference of 0.3 and 0.2 between estimates in the two West regions and the two East regions, respectively. Results from random regression on longitude indicated higher estimates of heritability in North region, especially at the furthest East longitudes of the most Northern region. There appeared to be substantial additive genetic variance differences, as well as estimates of heritability, that correspond to different geographical environments as modeled by random regressions on within-region latitude or longitude coordinates.

Conservation and Utilization of Livestock Genetic Diversity in the United States of America through Gene Banking

A germplasm collection curated by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Animal Germplasm Program contains of over one million samples from over 55,000 animals, representing 165 livestock and poultry breeds. The collection was developed to provide genetic conservation and security for the U.S. livestock sector. Samples in the collection span 60 years, suggesting a wide range of genetic diversity and genetic change is represented for rare and major breeds. Classifying breeds into four groups based upon registration or census estimates of population size of < 1000, < 5000, < 20,000, and > 20,000 indicated that 50% of the collection is comprised of rare breeds in the < 1000 category. As anticipated, collections for breeds in the < 20,000 and > 20,000 are more complete (86% and 98%, respectively) based upon an index combining the number of germplasm samples and the number of animals. For the rarest breeds (< 1000), collection completeness was 45%. Samples from over 6000 animals in the collection have been used for adding diversity to breeds, genomic evaluation, reconstituting populations, or various research projects. Several aspects of collecting germplasm samples from rare breeds are discussed. In addition, approaches that could be used to enhance the status of rare breeds via the repository use are presented. However, given the array of obstacles confronting rare breeds, the gene bank may be the most secure prospect for the long-term conservation of rare breed genetics.

Morphological divergence in the West African shorthorn Lagune cattle populations from Benin

This study explored the potential role of agro-ecology in shaping the morphology of Lagune cattle population of Benin. A total of 708 adult Lagune cattle were sampled randomly from nine provenances in two agro-ecological zones (AEZs) and were assessed for eight qualitative and twelve linear body measurements. Data were analyzed using generalized linear model procedures (PROC GLM) followed by the multiple comparison of least square means (LSMEAN) according to the Tukey-Kramer method and multivariate analytical methods, including canonical discrimination analysis (CDA) and hierarchical ascendant classification. Irrespective of AEZ and sex, the body length (102.3 ± 9.31 cm) was greater than the wither height (93.1 ± 7.39 cm) and the body index smaller than 0.85. However, there were significant differences between the two AEZs for most of the measured morphometric and qualitative traits. Moreover, a male-biased sexual size dimorphism was recorded. The CDA based on only four basic body measurements (rump height, body length, heart girth, and ear length) and the calculated Mahalanobis distances suggest that the populations from the two AEZs are distinct and could be further considered ecotypes. Nevertheless, the overall moderate classification rate (70%) of the individual animals into their group of origin indicates interbreeding between the two populations. The pairwise Mahalanobis distances between provenances in the same AEZ were also significant. Together, these results provide supporting evidence for the existence of subdivisions in the Lagune cattle populations from South Benin. The high morphological diversity in the Lagune cattle recorded in the present study could serve as a starting point for the development of efficient selection and sound subpopulation management strategies but also for further phenotypic and genetic characterizations.

Development of germplasm repositories to assist conservation of endangered fishes: Examples from small-bodied livebearing fishes

Germplasm repositories are a necessary tool for comprehensive conservation programs to fully preserve valuable genetic resources of imperiled animals. Cryopreserved germplasm can be used in the future to produce live young for integration into other conservation projects, such as habitat restoration, captive breeding, and translocations; thus compensating for genetic losses or negative changes that would otherwise be permanent. Although hundreds of cryopreservation protocols for various aquatic species have been published, there are great difficulties in moving such research forward into applied conservation projects. Successful freezing of sperm in laboratories for research does not guarantee successful management and incorporation of genetic resources into conservation programs in reality. The goal of the present review is to provide insights and practical strategies to apply germplasm repositories as a real-world tool to assist conservation of imperiled aquatic species. Live-bearing (viviparous) fishes are used as models herein to help explain concepts because they are good examples for aquatic species in general, especially small-bodied fishes. Small live-bearing fishes are among the most at-risk fish groups in the world, and need urgent conservation attention. However, development of germplasm repositories for small live-bearing fishes is challenged by their unusual reproductive characteristics, such as formation of sperm bundles, initiation of spermatozoa motility in an isotonic environment, internal fertilization and gestation, and the bearing of live young. The development of germplasm repositories for goodeids and Xiphophorus species can provide examples for addressing these challenges. Germplasm repositories must contain multiple basic components, including frozen samples, genetic assessment and information systems. Standardization and process generalization are important strategies to help develop reliable and efficient repositories. An ideal conservation or recovery program for imperiled species should include a comprehensive approach, that combines major concerns such as habitat (by restoration projects), population propagation and maintenance (by captive breeding or translocation projects), and preservation of genetic diversity (by repository projects). In this context, strong collaboration among different sectors and people with different expertise is a key to the success of such comprehensive programs.

Genome-wide associations and detection of potential candidate genes for direct genetic and maternal genetic effects influencing dairy cattle body weight at different ages

Background

Body weight (BW) at different ages are of increasing importance in dairy cattle breeding schemes, because of their strong correlation with energy efficiency traits, and their impact on cow health, longevity and farm economy. In total, 15,921 dairy cattle from 56 large-scale test-herds with BW records were genotyped for 45,613 single nucleotide polymorphisms (SNPs). This dataset was used for genome-wide association studies (GWAS), in order to localize potential candidate genes for direct and maternal genetic effects on BW recorded at birth (BW0), at 2 to 3 months of age (BW23), and at 13 to 14 months of age (BW1314).

Results

The first 20 principal components (PC) of the genomic relationship matrix (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}$$\end{document}G) grouped the genotyped cattle into three clusters. In the statistical models used for GWAS, correction for population structure was done by including polygenic effects with various genetic similarity matrices, such as the pedigree-based relationship matrix (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{A}}$$\end{document}A), the \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}$$\end{document}G-matrix, the reduced \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}$$\end{document}G-matrix LOCO (i.e. exclusion of the chromosome on which the candidate SNP is located), and LOCO plus chromosome-wide PC. Inflation factors for direct genetic effects using \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{A}}$$\end{document}A and LOCO were larger than 1.17. For \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathbf{G}}$$\end{document}G and LOCO plus chromosome-wide PC, inflation factors were very close to 1.0. According to Bonferroni correction, ten, two and seven significant SNPs were detected for the direct genetic effect on BW0, BW23, and BW1314, respectively. Seventy-six candidate genes contributed to direct genetic effects on BW with four involved in growth and developmental processes: FGF6, FGF23, TNNT3, and OMD. For maternal genetic effects on BW0, only three significant SNPs (according to Bonferroni correction), and four potential candidate genes, were identified. The most significant SNP on chromosome 19 explained only 0.14% of the maternal de-regressed proof variance for BW0.

Conclusions

For correction of population structure in GWAS, we suggest a statistical model that considers LOCO plus chromosome-wide PC. Regarding direct genetic effects, several SNPs had a significant effect on BW at different ages, and only two SNPs on chromosome 5 had a significant effect on all three BW traits. Thus, different potential candidate genes regulate BW at different ages. Maternal genetic effects followed an infinitesimal model.

Electronic supplementary material

The online version of this article (10.1186/s12711-018-0444-4) 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.