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Equine athletes have a genetic heritage that has been evolved for millions of years, which provides an opportunity to study the genetics of locomotion pattern and performance in mammals. The Hanoverian, a breed originating in Germany, is arguably among the most athletic of horse breeds, as well as possessing a balanced character and beautiful appearance. Here, we compared the whole genomes of Hanoverian with three other horse breeds (Akhal-Teke, Franches-Montagnes, and Standardbred), using the fixation index ([F.sub.st]) and cross-population composite likelihood ratio (XP-CLR) methods for testing the multi-locus allele frequency differentiation between populations. We identified 299 and 485 positively selected genes using the [F.sub.st] and XP-CLR methods, respectively. Further functional analyses showed that the ACTA1 gene is potentially involved in athletic performance in the Hanoverian breed, consistent with its role observed in human population. In addition, three other loci on chromosomes 1 and 20 were identified to be potentially involved in equine physical performance. The selected candidate genes identified in this study may be useful in current breeding efforts to develop improved breeds in regard to athletic performance. Key words: whole genome analysis, athletic performance, ACTA1 gene, Hanoverian horse. Les chevaux de course ont un heritage genetique qui est le produit de millions d'annees d'evolution, ce qui fournit une opportunite d'etudier la genetique de la locomotion et de la performance chez les mammiferes. Le Hanovrien, une race provenant de l'Allemagne, est possiblement parmi les races les plus athletiques en raison de son caractere equilibre et de sa belle apparence. Dans ce travail, les auteurs comparent les sequences genomiques du Hanovrien avec celles de trois autres races (Akhal-Teke, Franches-Montagnes et Standardbred) au moyen de l'indice de fixation ([F.sub.st]) et du ratio de vraisemblance composite entre populations (XP-CLR;<< cross-population composite likelihood ratio >>) pour mesurer la differentiation des frequences alleliques multi-locus entre differentes populations. Les auteurs ont identifie respectivement 299 et 485 genes ayant fait l'objet d'une selection positive au moyen des methodes Fst et XP-CLR. Des analyses fonctionnelles additionnelles ont montre que le gene ACTA1 serait potentiellement implique dans la performance sportive de la race Hanovrienne, ce qui est conforme a son role au sein de la population humaine. De plus, trois autres locus sur les chromosomes 1 et 20 ont ete identifies comme etant potentiellement impliques dans la performance physique chez les chevaux. Les genes candidats identifies dans ce travail seront peut-etre utiles en selection et pour developper des races ameliorees pour leurs performances sportives. [Traduit par la Redaction] Mots-cles : analyse genomique complete, performance sportive, gene ACTA1, cheval Hanovrien., Introduction During the last decades, efforts to genetically improve horse breeds for their abilities in sport competitions has been growing (Tomasz et al. 2015). Performance in show jumping is an [...]

Objectives: Pistacia genus belongs to the flowering plants in the cashew family and contains at least 11 species. The whole-genome resequencing data of different species from Pistacia genus are described herein. The data reported here will be useful for better understand the adaptive evolution, demographic history, genetic diversity, population structure, and domestication of pistachio. Data description: Genomic DNA was isolated from fresh leaves and used to construct libraries with insert size of 350 bp. Sequence libraries were made and sequenced on the Illumina Hiseq 4000 platform to produce 150 bp paired-end reads. A total number of 4,851,118,730 billion reads (ranging from 33,305,900 to 34,990,618 reads per sample) were created across all samples. We produced a total of 727.67 Gbp data which have been deposited in the Genome Sequence Archive (GSA) database with the Accession of CRA000978. All of the data are also available as the sequence read archive (SRA) format in the National Center for Biotechnology Information (NCBI) with identifier of SRP189222, mirroring our deposited data in GSA. [ABSTRACT FROM AUTHOR]

Runs of homozygosity (ROH) stretches are continuous homozygous fragments of the genome, which are more suitable for calculating the genomic inbreeding, identifying footprints involved in economic traits and understanding the population history in livestock species. In this study, using a dataset of Ovine SNP50 BeadChip genotypes, the distribution of ROH in nine sheep populations (Soay n= 110, Australian Poll Dorset n=108, Australian Suffolk n=109, Finn sheep n= 99, Scottish Texel n= 80, Scottish Blackface n= 56, Galway n= 49, Border Leicester n= 48, German Texel n=46) from Europe were investigated. ROHs were detected by using PLINK v1.09 with the minimal number of SNPs in ROH set at 40; the maximal gap between the adjacent SNPs was set to 1Mb; the minimum SNP density per ROH was set to 1/100 kb and no heterozygote less than 16 Mb was allowed. The detected ROHs were specified to four categories, based on their length: 1–4 Mb, 4–8 Mb, 8–16 Mb and above 16 Mb. A total of 22,204 ROHs were identified, in which ~ 92 – 98 % were less than 16 Mb in length, covering 4.6% to 12.9% of the entire genome. The inbreeding coefficient based on ROH (FROH) varied among populations (ranging from 0.05 to 0.14). The highest inbreeding rate was found in Border Leicester and Soay breeds. In addition, we detected 90 possible ROH Islands that overlapped with candidate genes associated with different economic traits such as the body weight, meat production, fat deposition, horn-less, and coat color in sheep. Our results suggested that although genetic selection for meat and wool traits in these breeds have been extensively carried out during the last decades, the autozygotic proportion of the genome is still considerably low, and it could lead to an acceptable response to selection in breeding schemes. [ABSTRACT FROM AUTHOR]

Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we used 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found convergent signature of positive selection at the gene level, particularly the EPAS1 gene in these Tibetan domestic mammals. We also reported a potential function in response to hypoxia for the gene C10orf67 , which underwent positive selection in three of the domestic mammals. Our data provide an insight into adaptive evolution of high-altitude domestic mammals, and should facilitate the search for additional novel genes involved in the hypoxia response pathway. [ABSTRACT FROM AUTHOR]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective: The data provided herein represent the whole-genome resequencing data related to three wolves and three Iranian local dogs. The understanding of genome evolution during animal domestication is an interesting subject in genome biology. Dog is an excellent model for understanding of domestication due to its considerable variety of behavioral and physical traits. The Zagros area of current day Iran has been identified as one of the initial centers of animal domestication. The availability of the complete genome sequences of Iranian local canids can be a valuable resource for researchers to address questions and testing hypotheses on the dog domestication process. Data description: We collected blood samples from six Iranian local canids including two hunting dogs (Saluki breed), a mastiff dog (Qahderijani ecotype) and three wolves. We extracted genomic DNA from blood samples. Sequence data were produced using the Illumina HiSeq 2500 system. All sequence data are available in the National Genomics Data Center (NGDC), Genome Sequence Archive (GSA) database under the accession of CRA001324 and the National Center for Biotechnology Information (NCBI) under the accession of PRJNA639312. The short-read sequences with the mean depth of 16X were aligned to the dog reference genome (CanFam3.1) and achieved 99% coverage of the reference assembly. The obtained information from this experiment will be useful in evolutionary biology. [ABSTRACT FROM AUTHOR]