| 1. |
- Wade, C. M., et al.
(författare)
-
Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse
- 2009
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 326:5954, s. 865-867
-
Tidskriftsartikel (refereegranskat)abstract
- We report a high-quality draft sequence of the genome of the horse ( Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
|
|
| 2. |
- Androsiuk, P., et al.
(författare)
-
Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden
- 2013
-
Ingår i: Silvae Genetica. - : J.D. Sauerlaender's Verlag. - 0037-5349. ; 62:3, s. 127-136
-
Tidskriftsartikel (refereegranskat)abstract
- Efficient use of any breeding resources requires a good understanding of the genetic value of the founder breeding materials for predicting the gain and diversity in future generations. This study evaluates the distribution of genetic variation and level of relatedness among and within nine breeding populations of Norway spruce for Northern Sweden using nuclear microsatellite markers. A sample set of 456 individuals selected from 140 stands were genotyped with, 15 SSR loci. Over all loci each individual was identified with unique multilocus genotype. High genetic diversity (average H-e=0.820) and low population differentiation (F-ST = 0.0087) characterized this material. Although low in F-ST, the two northernmost populations were clustered as a distinct group diverged from the central populations. The population differentiation pattern corresponds well with the post glacial migration history of Norway spruce and the current gene flow and human activity in the region. The average inbreeding coefficient was 0.084 after removal loci with high frequency of null alleles. The estimated relatedness of the trees gathered in the breeding populations was very low (average kinship coefficient 0.0077) and not structured. The high genetic variation and low and not structured relatedness between individuals found in the breeding populations confirm that the Norway spruce breeding stock for northern Sweden represent valuable genetic resources for both long-term breeding and conservation programs.
|
|
| 3. |
|
|
| 4. |
- Staiger, E. A., et al.
(författare)
-
The evolutionary history of the DMRT3 'Gait keeper' haplotype
- 2017
-
Ingår i: Animal Genetics. - : WILEY. - 0268-9146 .- 1365-2052. ; 48:5, s. 551-559
-
Tidskriftsartikel (refereegranskat)abstract
- A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3: Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.
|
|
| 5. |
- Jäderkvist Fegraeus, Kim, et al.
(författare)
-
A potential regulatory region near the EDN3 gene may control both harness racing performance and coat color variation in horses
- 2018
-
Ingår i: Physiological Reports. - : Wiley. - 2051-817X. ; 6:10
-
Tidskriftsartikel (refereegranskat)abstract
- The Swedish‐Norwegian Coldblooded trotter and the heavier North‐Swedish draught horse both descend from the North‐Swedish horse, but the Coldblooded trotters have been selected for racing performance while the North‐Swedish draught horse is mainly used for agricultural and forestry work. By comparing the genomes of Coldblooded trotters, North‐Swedish draught horses and Standardbreds for a large number of single‐nucleotide polymorphisms (SNPs), the aim of the study was to identify genetic regions that may be under selection for racing performance. We hypothesized that the selection for racing performance, in combination with unauthorized crossbreeding of Coldblooded trotters and Standardbreds, has created regions in the genome where the Coldblooded trotters and Standardbreds are similar, but differ from the North‐Swedish draught horse. A fixation index (Fst) analysis was performed and sliding window Delta Fst values were calculated across the three breeds. Five windows, where the average Fst between Coldblooded trotters and Standardbreds was low and the average Fst between Coldblooded trotters and North‐Swedish draught horses was high, were selected for further investigation. Associations between the most highly ranked SNPs and harness racing performance were analyzed in 400 raced Coldblooded trotters with race records. One SNP showed a significant association with racing performance, with the CC genotype appearing to be negatively associated. The SNP identified was genotyped in 1915 horses of 18 different breeds. The frequency of the TT genotype was high in breeds typically used for racing and show jumping while the frequency of the CC genotype was high in most pony breeds and draught horses. The closest gene in this region was the Endothelin3 gene (EDN3), a gene mainly involved in melanocyte and enteric neuron development. Both functional genetic and physiological studies are needed to fully understand the possible impacts of the gene on racing performance.
|
|
| 6. |
|
|
| 7. |
- Kaspersson, A., et al.
(författare)
-
Microbial dynamics in barley grain stored under controlled atmosphere
- 1988
-
Ingår i: Animal Feed Science and Technology. - : Elsevier BV. - 0377-8401 .- 1873-2216. ; 19:4, s. 299-312
-
Tidskriftsartikel (refereegranskat)abstract
- Barley of 2 moisture contents, 20-23% and 26-28%, was stored airtight for 2 separate seasons in 2 full-scale silos, and for 3 separate seasons in 12-16 pilot silos (1.25 m3). The microbial dynamics were studied, using colony-forming units (CFU) of microorganisms, the proportion of internally-invaded kernels and ATP content. The ATP content was a good measure of the microbial activity, which decreased after loading and was very low during the winter period. Field-associated moulds and yeasts decreased in numbers of CFU and in the amount of invaded kernels. Fusarium species survived more satisfactorily than most field fungi. The temperature rise in spring caused an increase in ATP content, as a result of extensive growth of yeast of the genera Hansenula and Candida. This activity started earlier in the high-moisture grain (March). In May, a significant increase in CFU of Penicillium was observed and, during May to July, in many silos, all kernels were invaded, mostly by P. roqueforti. In an attempt to increase the time of safe storage, some technical improvements and gaseous and liquid chemical additives were tested. Attachment of "lungs" to the silos, and addition of organic acids or gases (CO2, N2, NH3) to the grain, increased the safe storage time by one to several months. The aerobic storage stability of rolled barley taken in July from the full-scale silos was tested. The rapid deterioration following unloading limited the aerobic storage stability to a few days. © 1988.
|
|
| 8. |
- Brandariz-Fontes, Claudia, et al.
(författare)
-
Y-Chromosome Analysis in Retuertas Horses
- 2013
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:5, s. e64985-
-
Tidskriftsartikel (refereegranskat)abstract
- Several studies based on a variety of genetic markers have attempted to establish the origins of horse domestication. Thus far a discrepancy between the results of mitochondrial DNA analysis, which show high levels of diversity, and results from the Y-chromosome, with almost no genetic variability, has been identified. Most previous work on the horse Y-chromosome has focused on widespread, popular breeds or local Asian breeds. It is possible that these breeds represent a reduced set of the genetic variation present in the species. Additional genetic variation may be present in local breeds and ancient feral populations, such as the Retuertas horse in Spain. In this study we analyzed the Y-chromosome of the Retuertas horse, a feral horse population on the Iberian Peninsula that is at least several hundred years old, and whose genetic diversity and morphology suggests that it has been reproductively isolated for a long time. Data from the Retuertas horse was compared to another 11 breeds from the region (Portugal, Spain and France) or likely of Iberian origin, and then to data from 15 more breeds from around the globe. We sequenced 31 introns, Zinc finger Y-chromosomal protein (ZFY) and anonymous Y-linked fragments and genotyped 6 microsatellite loci found on the Y-chromosome. We found no sequence variation among all individuals and all breeds studied. However, fifteen differences were discovered between our data set and reference sequences in GenBank. We show that these likely represent errors within the deposited sequences, and suggest that they should not be used as comparative data for future projects.
|
|
| 9. |
- Brunet, Jörg, et al.
(författare)
-
Immigration credit of temperate forest herbs in fragmented landscapes—Implications for restoration of habitat connectivity
- 2021
-
Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 58:10, s. 2195-2206
-
Tidskriftsartikel (refereegranskat)abstract
- In many agricultural landscapes, it is important to restore networks of forests to provide habitat and stepping stones for forest specialist taxa. More knowledge is, however, needed on how to facilitate the immigration of such taxa in restored forest patches. Here, we present the first chronosequence study to quantify the dynamics of immigration credits of forest specialist plants in post-arable forest patches.We studied the distribution of herbaceous forest specialist plant species in 54 post-arable broadleaved forest patches along gradients of age (20–140 years since forest establishment), distance from ancient forest (0–2,600 m) and patch area (0.5–9.6 ha). With linear mixed models, we estimated the effects of these factors on species richness, patch means of four dispersal-related plant traits and with generalized linear models on the occurrence of 20 individual species.Post-arable forest patch age and spatial isolation from ancient forest, but not patch size, were important predictors for species richness of forest specialists, suggesting that also small patches are valuable for habitat connectivity. Compared to species richness in ancient forest stands, the immigration credit was reduced by more than 90% after 80 years in post-arable forest patches contiguous to ancient forest compared to 40% after 80 years and 60% after 140 years in isolated patches (at least 100 m to next forest). Tall-growing species with adaptations to long-distance dispersal were faster colonizers, whereas species with heavy diaspores and clonal growth were slower to colonize.Synthesis and applications. We show that post-arable oak plantations have a high potential for restoration of forest herb vegetation. Dispersal-related plant traits play a key role in explaining interspecific differences among forest specialists. To facilitate forest herb immigration across all functional groups in agricultural landscapes, we suggest to create clusters of relatively small new forest patches nearby older forest with source populations.
|
|
| 10. |
- McCue, Molly E., et al.
(författare)
-
A High Density SNP Array for the Domestic Horse and Extant Perissodactyla : Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies
- 2012
-
Ingår i: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 8:1, s. e1002451-
-
Tidskriftsartikel (refereegranskat)abstract
- An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of similar to 43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of similar to 750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
|
|
