25 research outputs found
Dual origins of dairy cattle farming : evidence from a comprehensive survey of European Y-Chromosomal variation
Background - Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages.
Methodology and Principal Findings - Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula.
Conclusions - We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries
Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources
The genetic diversity of the world!s livestock populations is decreasing, both within and
across breeds. A wide variety of factors has contributed to the loss, replacement or genetic
dilution of many local breeds. Genetic variability within the more common commercial
breeds has been greatly decreased by selectively intense breeding programmes. Conservation
of livestock genetic variability is thus important, especially when considering possible future
changes in production environments. The world has more than 7500 livestock breeds and
conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of
this article is to review the state of the art in approaches for prioritization of breeds for
conservation, particularly those approaches that consider molecular genetic information,
and to identify any shortcomings that may restrict their application. The Weitzman method
was among the first and most well-known approaches for utilization of molecular genetic
information in conservation prioritization. This approach balances diversity and extinction
probability to yield an objective measure of conservation potential. However, this approach
was designed for decision making across species and measures diversity as distinctiveness.
For livestock, prioritization will most commonly be performed among breeds within species,
so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have
been proposed. Although these methods are technically sound, their application has generally
been limited to research studies; most existing conservation programmes have
effectively primarily based decisions on extinction risk. The development of user-friendly
software incorporating these approaches may increase their rate of utilization
Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025
Livestock conservation practice is changing rapidly in light of policy developments, climate
change and diversifying market demands. The last decade has seen a step change in
technology and analytical approaches available to define, manage and conserve Farm
Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for
FAnGR conservation in terms of technological continuity, analytical capacity and integrative
methodologies needed to fully exploit new, multidimensional data. The final conference of the
ESF Genomic Resources program aimed to address these interdisciplinary problems in an
attempt to contribute to the agenda for research and policy development directions during the
coming decade. By 2020, according to the Convention on Biodiversity’s Aichi Target 13,
signatories should ensure that “… the genetic diversity of … farmed and domesticated
animals and of wild relatives … is maintained, and strategies have been developed and
implemented for minimizing genetic erosion and safeguarding their genetic diversity.”
However, the real extent of genetic erosion is very difficult to measure using current data.
Therefore, this challenging target demands better coverage, understanding and utilization of
genomic and environmental data, the development of optimized ways to integrate these data
with social and other sciences and policy analysis to enable more flexible, evidence-based
models to underpin FAnGR conservation. At the conference, we attempted to identify the
most important problems for effective livestock genomic resource conservation during the
next decade. Twenty priority questions were identified that could be broadly categorised into
challenges related to methodology, analytical approaches, data management and
conservation. It should be acknowledged here that while the focus of our meeting was
predominantly around genetics, genomics and animal science, many of the practical
challenges facing conservation of genomic resources are societal in origin and are
predicated on the value (e.g. socio-economic and cultural) of these resources to farmers,
rural communities and society as a whole. The overall conclusion is that despite the fact that
the livestock sector has been relatively well-organised in the application of genetic
methodologies to date, there is still a large gap between the current state-of-the-art in the
use of tools to characterise genomic resources and its application to many non commercial
and local breeds, hampering the consistent utilisation of genetic and genomic data as
indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to
make a concerted effort in the coming decade to enable to the democratisation of the
powerful tools that are now at its disposal, and to ensure that they are applied in the context
of breed conservation as well as development
Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers
Articles in International JournalsBackground: Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions.
Methods: A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAOrecommended
microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity.
Results: Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in
breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships
revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion.
However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and
between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher
priority for conservation than the European groups of breeds.
Conclusions: Conservation priorities differed significantly according to the weight given to within- and betweenbreed
genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their
products should be taken into consideration to ensure their long-term survival
The Agersoe cattle : the last remnants of the Danish island cattle (Bos taurus)?
The following members of the European Cattle Genetic diversity consortium contributed to this study: Lenstra, J. A., Nijman, I. J. (both Utrecht University, The Netherlands); Moazami-Goudarzi, K. (INRA, Jouy-en-Josas, France); Erhardt, G., Wiemann, C., Prinzenberg, E.-M. (Justus-Liebig Universität, Germany); Harlizius, B. (School of Vetenary Medicine, Germany); Looft, C., Kalm, E. (Christian-Albrechts, Universität, Germany); Kantanen, J. (MTT, Finland); Olsaker, I. (Norwegian School of Vetenary Sciences); Holm, L. E. (Danish Institute of Agricultural Sciences, Denmark).vo
Microsatellite genotyping of medieval cattle from central italy suggests an old origin of chianina and romagnola cattle
Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archeological site in central Italy. Amplification of 15 microsatellite FAO-recommended markers with PCR products yielded g84923667239enotypes for four markers. Expected heterozygosity was comparable with values of modern breeds, but observed heterozygosity was underestimated due to allelic loss. Genetic distances suggested a position intermediate between (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the Iberian, North-European and Central-European cattle, but also a clear relationship with two central-Italian breeds, Chianina and Romagnola. This suggests that these breeds are derived from medieval cattle living in the same area. Our results illustrate the potential of ancient DNA for reconstructing the history of local cattle husbandry
Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle
Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archeological site in central Italy. Amplification of 15 microsatellite FAO-recommended markers with PCR products yielded genotypes for four markers. Expected heterozygosity was comparable with values of modern breeds, but observed
heterozygosity was underestimated due to allelic loss. Genetic distances suggested a position intermediate between (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the Iberian, North-European and Central-European cattle, but also a clear relationship with two central-Italian breeds, Chianina and Romagnola. This suggests that these breeds are derived from medieval cattle living in the same area. Our results illustrate the potential of ancient DNA for reconstructing the history of local cattle husbandry
Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds
Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n = 54) were found, but many correlations were non-significant (n = 100) or significantly negative (n = 11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds