114 research outputs found
How to Use Fewer Markers in Admixture Studies
No full textSwiss Fleckvieh has been established from 1970 as a composite of Simmental and Red Holstein Friesian cattle. Breed composition is currently reported based on pedigree information. Information on ancestry informative molecular markers potentially provides more accurate information. For the analysis Illumina Bovine SNP50 Beadchip data for 495 bulls were used. Markers were selected based on difference in allele frequencies in the pure populations, using FST as an indicator. Performance of sets with decreasing number of markers was compared. The scope of the study was to see how much we can reduce the number of markers based on FST to get a reliability that is close to that with the full set of markers. On these sets of markers hidden Markov models (HMM) and methods used in genomic selection (BayesB, partial least squares regression, LASSO variable selection) were applied. Correlations of admixture levels were estimated and compared with admixture levels based on pedigree information. FST chosen SNP gave very high correlations with pedigree based admixture. Only when using 96 and 48 SNP with the highest FST, correlations dropped to 0.92 and 0.90, respectively
High-Density Genomic Characterization of Native Croatian Sheep Breeds
No full textA recent comprehensive genomic analysis based on 50K SNP profiles has shown that the regional Balkan sheep populations have considerable genetic overlap but are distinctly different from surrounding breeds. All eight Croatian sheep breeds were represented by a small number of individuals per breed. Here, we genotyped 220 individuals representing the native Croatian sheep breeds (Istrian Sheep, Krk Island Sheep, Cres Island Sheep, Rab Island Sheep, Lika Pramenka, Pag Island Sheep, Dalmatian Pramenka, Dubrovnik Sheep) and mouflon using the Ovine Infinium ® HD SNP BeadChip (606,006 SNPs). In addition, we included publicly available Balkan Pramenka and other Mediterranean sheep breeds. Our analyses revealed the complex population structure of Croatian sheep breeds and their origin and geographic barriers (island versus mainland). Migration patterns confirmed the historical establishment of breeds and the pathways of gene flow. Inbreeding coefficients (F ROH>2 Mb) between sheep populations ranged from 0.025 to 0.070, with lower inbreeding coefficients observed in Dalmatian Pramenka and Pag Island Sheep and higher inbreeding in Dubrovnik sheep. The estimated effective population size ranged from 61 to 1039 for Krk Island Sheep and Dalmatian Pramenka, respectively. Higher inbreeding levels and lower effective population size indicate the need for improved conservation management to maintain genetic diversity in some breeds. Our results will contribute to breeding and conservation strategies of native Croatian sheep breeds
Advances in Farm Animal Genomic Resources
No full textThe history of livestock started with the domestication of their wild ancestors: a restricted number of species allowed to be tamed and entered a symbiotic relationship with humans. In exchange for food, shelter and protection, they provided us with meat, eggs, hides, wool and draught power, thus contributing considerably to our economic and cultural development. Depending on the species, domestication took place in different areas and periods. After domestication, livestock spread over all inhabited regions of the earth, accompanying human migrations and becoming also trade objects. This required an adaptation to different climates and varying styles of husbandry and resulted in an enormous phenotypic diversity. Approximately 200 years ago, the situation started to change with the rise of the concept of breed. Animals were selected for the same visible characteristics, and crossing with different phenotypes was reduced. This resulted in the formation of different breeds, mostly genetically isolated from other populations. A few decades ago, selection pressure was increased again with intensive production focusing on a limited range of types and a subsequent loss of genetic ADVANCES IN FARM ANIMAL GENOMIC RESOURCES Images 1-3 taken from: http://www.photolibre.fr (retrieved in 2010), image 4 by Stéphane Joost. Cover image by Stéphane Joost, EPFL and http://www.photolibre.fr (retrieved in 2010). Topic Editors: Stéphane Joost, École Polytechnique Fédérale de Lausanne, Switzerland Michael W. Bruford, Cardiff University, UK Ino Curik, University of Zagreb, Croatia Juha Kantanen, Natural Resources Institute Finland, Finland Johannes A. Lenstra, Utrecht University, Netherlands Johann Sölkner, University of Natural Resources and Life Sciences Vienna, Austria Göran Andersson, Swedish University of Agricultural Sciences, Sweden Philippe V. Baret, Université catholique de Louvain, Belgium Nadine Buys, KU Leuven, Belgium Jutta Roosen, Technische Universität München, Germany Michèle Tixier-Boichard, INRA, France Paolo Ajmone Marsan, Università Cattolica del S. Cuore, Italy Frontiers in Genetics 3 January 2016 | Advances in Farm Animal Genomic Resources diversity. For short-term economic reasons, farmers have abandoned traditional breeds. As a consequence, during the 20th century, at least 28% of farm animal breeds became extinct, rare or endangered. The situation is alarming in developing countries, where native breeds adapted to local environments and diseases are being replaced by industrial breeds. In the most marginal areas, farm animals are considered to be essential for viable land use and, in the developing world, a major pathway out of poverty. Historic documentation from the period before the breed formation is scarce. Thus, reconstruction of the history of livestock populations depends on archaeological, archeo-zoological and DNA analysis of extant populations. Scientific research into genetic diversity takes advantage of the rapid advances in molecular genetics. Studies of mitochondrial DNA, microsatellite DNA profiling and Y-chromosomes have revealed details on the process of domestication, on the diversity retained by breeds and on relationships between breeds. However, we only see a small part of the genetic information and the advent of new technologies is most timely in order to answer many essential questions. High-throughput single-nucleotide polymorphism genotyping is about to be available for all major farm animal species. The recent development of sequencing techniques calls for new methods of data management and analysis and for new ideas for the extraction of information. To make sense of this information in practical conditions, integration of geo-environmental and socio-economic data are key elements. The study and management of farm animal genomic resources (FAnGR) is indeed a major multidisciplinary issue. The goal of the present Research Topic was to collect contributions of high scientific quality relevant to biodiversity management, and applying new methods to either new genomic and bioinformatics approaches for characterization of FAnGR, to the development of FAnGR conservation methods applied ex-situ and in-situ, to socio-economic aspects of FAnGR conservation, to transfer of lessons between wildlife and livestock biodiversity conservation, and to the contribution of FAnGR to a transition in agriculture (FAnGR and agro-ecology)
Advances in farm animal genomic resources
No full textThe history of livestock started with the domestication of their wild ancestors: a restricted number of species allowed to be tamed and entered a symbiotic relationship with humans. In exchange for food, shelter and protection, they provided us with meat, eggs, hides, wool and draught power, thus contributing considerably to our economic and cultural development. Depending on the species, domestication took place in different areas and periods. After domestication, livestock spread over all inhabited regions of the earth, accompanying human migrations and becoming also trade objects. This required an adaptation to different climates and varying styles of husbandry and resulted in an enormous phenotypic diversity. Approximately 200 years ago, the situation started to change with the rise of the concept of breed. Animals were selected for the same visible characteristics, and crossing with different phenotypes was reduced. This resulted in the formation of different breeds, mostly genetically isolated from other populations. A few decades ago, selection pressure was increased again with intensive production focusing on a limited range of types and a subsequent loss of genetic diversity. For short-term economic reasons, farmers have abandoned traditional breeds. As a consequence, during the 20th century, at least 28% of farm animal breeds became extinct, rare or endangered. The situation is alarming in developing countries, where native breeds adapted to local environments and diseases are being replaced by industrial breeds. In the most marginal areas, farm animals are considered to be essential for viable land use and, in the developing world, a major pathway out of poverty. Historic documentation from the period before the breed formation is scarce. Thus, reconstruction of the history of livestock populations depends on archaeological, archeo-zoological and DNA analysis of extant populations. Scientific research into genetic diversity takes advantage of the rapid advances in molecular genetics. Studies of mitochondrial DNA, microsatellite DNA profiling and Y-chromosomes have revealed details on the process of domestication, on the diversity retained by breeds and on relationships between breeds. However, we only see a small part of the genetic information and the advent of new technologies is most timely in order to answer many essential questions. High-throughput single-nucleotide polymorphism genotyping is about to be available for all major farm animal species. The recent development of sequencing techniques calls for new methods of data management and analysis and for new ideas for the extraction of information. To make sense of this information in practical conditions, integration of geo-environmental and socio-economic data are key elements. The study and management of farm animal genomic resources (FAnGR) is indeed a major multidisciplinary issue. The goal of the present Research Topic was to collect contributions of high scientific quality relevant to biodiversity management, and applying new methods to either new genomic and bioinformatics approaches for characterization of FAnGR, to the development of FAnGR conservation methods applied ex-situ and in-situ, to socio-economic aspects of FAnGR conservation, to transfer of lessons between wildlife and livestock biodiversity conservation, and to the contribution of FAnGR to a transition in agriculture (FAnGR and agro-ecology).LASI
Genomic dissection of inbreeding depression: a gate to new opportunities
No full textABSTRACT Inbreeding depression, reduction in performance of quantitative traits, including reproduction and survival, caused by inbreeding, is a well-known phenomenon observed in almost all experimental, domesticated, and natural populations. In spite of its importance to the fate of a small population and numerous research performed in the last century, the genetic basis of inbreeding depression is still unclear. Recent fast development of molecular techniques has enabled estimation of a genomic inbreeding coefficient (FROH), which reflects realized autozygosity and can be further partitioned to chromosomes and chromosomal segments. In this review, we first describe classical approach used in the estimation of inbreeding in livestock populations, followed by early concepts of replacing pedigree inbreeding coefficient by individual heterozygosity. Then, we explain runs of homozygosity as key approach in estimating realized autozygosity. Furthermore, we present two different concepts of analysing regions that substantially contribute to the inbreeding depression. Thus, we describe how to identify or map mutations that result in the reduction of performance and, in terms of quantitative genetics, how to analyse the architecture of inbreeding depression. At the end, we discuss future perspectives in eliminating deleterious mutations from livestock populations
Mitochondrial DNA Diversity in Wild Boars from the Istria and Cres Island
No full textThe aim of study was to analyze the nucleotide diversity of mitochondrial DNA control region (CR–mtDNA) of 33 wild boars hunted in Istria and Cres Island (Croatia) in order to prove the presence of clade E2 haplotypes outside the Italian Peninsula and Sardinia. Outside of Italy haplotypes from clade E2 have been found only in Istria (Pupcina Cave) on archaeological samples dating to 9000 years BC. Among 21 haplotypes found on a 428–bp sequence fragment representing European wild boars, with 227 sequences additionally retrieved from the GeneBank, our wild boars were assigned in two haplotypes classified in clade E1. Two wild boars, from Oprtalj and Grožnjan, were distributed in the haplotype H2 while the other 31 samples were distributed in the haplotype H6. On the analyzed fragment, observed haplotypes were two (T→C at 15714 and 15758) and one (T→C at 15758) transversions remote from the reference sequence reported in the GenBank under accession number AJ002189 (Ursing and Arnason, 1998). The H2 and H6 haplotypes were both previously found in European wild boars, most frequently in haplotypes from Portugal and Spain. In conclusion, the results obtained were concordant to the hypothesis that clade E2 haplotypes are indigenous to Italy and Sardinia. According to the maternal origin, the Istrian and Cres Island wild boars are close to the Gorizia region (north–east Italy) population as well as to wild boars from Portugal and Spain
Analysis of mitochondrial DNA in Adriatic sardine (Sardina pilchardus): a preliminary study
No full textTo determine the phylogenetic history of sardines researchers use mitochondrial DNA (mtDNA). Mitochondrial DNA contains highly informative polymorphic sites. The cytochrome b (cyt b) gene has been especially used by investigators because of its sufficient point mutation rate, enabling discrimination of closely related fish species, and determination of interspecific variability in pelagic fish species for population identification. Scientific surveys based on meristic, morphometric, and reproductive data suggested that two subpopulations of sardines coexisted in the Northern-Middle Adriatic Sea. Mitochondrial DNA analysis of sardines from the Adriatic Sea has never been conducted in the Republic of Croatia. This study included 14 sardine samples from three separate locations, as well as 30 different haplotype sequences retrieved from GenBank. The aim of this study was to determine the number of haplotypes in sardine populations from the Adriatic Sea, as well as to determine differences between populations. Mitochondrial DNA sequence analysis revealed 11 different haplotypes of sardines from the Adriatic Sea. The differences between samples from different locations were not scientifically significant, and the results of this study indicate homogeneity in the Adriatic sardine stock. However, three parsimony informative mutations found in our samples produce a clearly visible distinction between the Adriatic sardine samples and samples obtained from the seas adjacent to the Adriatic. This distinction of the Adriatic sardine samples can have applications in fisheries and fishery product quality testing
Variance Estimation of Maternal Lineage Effect on Milk Traits in Croatian Holstein Cattle
No full textThe effect of maternal lineage (ML) on milk production traits: milk, fat and protein yield (MY, FY, and PY), fat and protein content (FC and PC) was evaluated in the Croatian Holstein cattle. Data included 102,961 records for 46,696 cows calved from January 2000 to July 2015 taken from the Central database of the Croatian Agricultural Agency. Pedigree file consisted of 77,398 animals. Variance components were estimated by REML method using VCE-6 program. Statistical model included parity, region, and calving season as fixed class effects, while age at first calving was fitted as quadratic regression. Random effects were: interaction herd-year, permanent environment, maternal lineage, and direct additive genetic effect. Identification of ML was based on the pedigree information. The contribution of ML to the phenotypic variance was 2% for FC and PC and 3% for MY, FY, and PY. The estimates of ML for milk traits were within the range of other studies
Influence of Sodium and Potassium Chloride on Rennet Coagulation and Curd Firmness in Bovine Milk
No full textOne of the salting methods in cheese production implies salting the milk before coagulation used in making Domiati-type cheeses and a variety of autochthonous “Lički Škripavac” cheese. The most used sodium replacer is potassium. This study investigated the influence of different added salt concentrations (1%, 1.5%, and 2%) and NaCl to KCl ratios (100%, 50:50%, 25:75%) on the rennet coagulation and curd firmness in bovine milk. The milk coagulation parameters were determined with a computerized renneting meter, Lactodinamograph. The results showed significant interactions between the salt concentrations and NaCl to KCl ratios (p 20, a30, a60, amax) were closest to the control (without salt) and had the best results among all treatments in the lower (1%) and medium (1.5%) salt concentration (p > 0.0001, α = 0.05) while in the highest salt concentration (2%) the treatment effect was nonsignificant (p > 0.05). These results should help future studies make a lower sodium product appealing to consumers without losing quality
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