Detection of selection signatures for ear carriage in Maltese goat breed

Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity

The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions

The Valdostana goat is an alpine breed, raised only in the northern Italian region of the Aosta Valley. This breed\u2019s main purpose is to produce milk and meat, but is peculiar for its involvement in the \u201cBatailles de Ch\ue8vres,\u201d a recent tradition of non-cruel fight tournaments. At both the genetic and genomic levels, only a very limited number of studies have been performed with this breed and there are no studies about the genomic signatures left by selection. In this work, 24 unrelated Valdostana animals were screened for runs of homozygosity to identify highly homozygous regions. Then, six different approaches (ROH comparison, Fst single SNPs and windows based, Bayesian, Rsb, and XP-EHH) were applied comparing the Valdostana dataset with 14 other Italian goat breeds to confirm regions that were different among the comparisons. A total of three regions of selection that were also unique among the Valdostana were identified and located on chromosomes 1, 7, and 12 and contained 144 genes. Enrichment analyses detected genes such as cytokines and lymphocyte/leukocyte proliferation genes involved in the regulation of the immune system. A genetic link between an aggressive challenge, cytokines, and immunity has been hypothesized in many studies both in humans and in other species. Possible hypotheses associated with the signals of selection detected could be therefore related to immune-related factors as well as with the peculiar battle competition, or other breed-specific traits, and provided insights for further investigation of these unique regions, for the understanding and safeguard of the Valdostana breed

Initial genomic characterization of Italian, Egyptian and Pakistani goat breeds

Selection and breeding practices in goats have differed greatly among countries and populations. These processes, together with natural selection and regional drift, have shaped the phenotypic variability of goat breeds (Kim et al., 2015). The availability of improved genomic analysis tools for this species may provide useful information on the history of selection, adaptation and differentiation of goats from different areas of the world, that can be evaluated by the study of gene frequencies and length of the Runs of Homozigosity (contiguous length of homozygous genotypes, ROH; Purfield et al., 2012). In current study, we examined using a goat medium density SNP chip animals from three different countries: Egypt (with lack of selection scheme), Italy (with several standardized breeds; Nicoloso et al., 2015) and Pakistan (with several breeds showing peculiar phenotypes) to produce a genomic landscape of goats breeds in these countries. A total of 1,123 animals of 39 different populations, and 48,895 SNP markers were analyzed. Genotypes were imputed on a country-based approach, and markers without known position in the genome were excluded from the analysis. MDS and ADMIXTURE plots confirmed the good differentiation among populations from the three countries. Runs of Homozygosity (ROH) were performed for each country and population allowed the detection of genomic regions with high homozygosity levels, common in at least two out of three sampling areas. These results provide new insights into goat genome structure within and among breeds and countries. The detection of conserved regions with different lengths may explain recent selection strategies or adaptation to different, extreme environmental conditions. The research was funded by INNOVAGEN project. Support by Iowa State University and the Ensminger funds for AE and AT as well as support by the Fulbright Foundation for AE are gratefully acknowledged. Sampling from Pakistan was funded by PAK-USAID project

Electronic excitations of α- Fe2 O3 heteroepitaxial films measured by resonant inelastic x-ray scattering at the Fe L edge

Resonant inelastic x-ray scattering (RIXS) spectra of hematite (α-Fe2O3) were measured at the Fe L3 edge for heteroepitaxial thin films which were undoped and doped with 1% Ti, Sn, or Zn, in the energy-loss range in excess of 1 eV to study electronic transitions. The spectra were measured for several momentum transfers q, conducted at both low temperature (T=14 K) and room temperature. While we cannot rule out dispersive features possibly owing to propagating excitations, the coarse envelopes of the general spectra did not appreciably change shape with q, implying that the bulk of the observed L-edge RIXS intensity originates from (mostly) nondispersive ligand field excitations. Summing the RIXS spectra over q and comparing the results at T=14 K to those at T=300 K revealed pronounced temperature effects, including an intensity change and energy shift of the ≈1.4 eV peak, a broadband intensity increase of the 3-4 eV range, and higher energy features. The q-summed spectra and their temperature dependencies are virtually identical for nearly all of the samples with different dopants, save for the temperature dependence of the Ti-doped sample's spectrum, which we attribute to being affected by a large number of free charge carriers. Comparing with magnetization measurements for different temperatures and dopings likewise did not show a clear correlation between the RIXS spectra and the magnetic ordering states. To clarify the excited states, we performed spin multiplet calculations which were in excellent agreement with the RIXS spectra over a wide energy range and provide detailed electronic descriptions of the excited states. The implications of these findings to the photoconversion efficiency of hematite photoanodes is discussed