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Approximately one million in vitro produced (IVP) cattle embryos are transferred world-wide each year as a way to improve the rates of genetic gain. The most advanced programmes also apply genomic selection at the embryonic stage by SNP genotyping and the calculation of genomic estimated breeding values (GEBVs). However, a high proportion of cattle embryos fail to establish a pregnancy. Here, we demonstrate that further interrogation of the SNP data collected for GEBVs can effectively remove aneuploid embryos from the pool, improving live births per embryo transfer (ET). Using three preimplantation genetic testing for aneuploidy (PGT-A) approaches, we assessed 1713 cattle blastocysts in a blind, retrospective analysis. Our findings indicate aneuploid embryos have a 5.8% chance of establishing a pregnancy and a 5.0% chance of given rise to a live birth. This compares to 59.6% and 46.7% for euploid embryos (p < 0.0001). PGT-A improved overall pregnancy and live birth rates by 7.5% and 5.8%, respectively (p < 0.0001). More detailed analyses revealed donor, chromosome, stage, grade, and sex-specific rates of error. Notably, we discovered a significantly higher incidence of aneuploidy in XY embryos and, as in humans, detected a preponderance of maternal meiosis I errors. Our data strongly support the use of PGT-A in cattle IVP programmes.

AdaptMap Consortium.

Additional file 3: Figure S3. Relationship between observed heterozygosity versus (left) ROH coverage or (right) within-population allele-sharing distances. Red and dark blue indicate insular and continental breeds, respectively, with high homozygosity. Pink and light blue indicate insular and continental breeds, respectively, with low or modest homozygosity.

Additional file 3: Table S1. Environmental variables considered for the landscape genomic analysis. Table S2. FLK and hapFLK windows for the sub-continental groups after filtering steps. Overlapping or partially overlapping regions across the different geographical subdivisions are reported with the same letter as used for the population group (from a to m). Table S3. Selective sweeps of early adaptation. The bold values indicate overlap or partial overlap between comparisons. Table S4 Common regions between ROH and XP-EHH and/or FST analyses for the group of “fiber-producing” goat breeds and genes within these regions. Table S5. Common regions between ROH and XP-EHH and/or FST analyses for the group of “meat-producing” goat breeds and genes within these regions. Table S6. Common regions between ROH and XP-EHH and/or FST analyses for the group of “milk-producing” goat breeds and genes within these regions. Table S7. Top four regions detected for the coat color groups (Black, White and Red), indicated comparisons between the groups and genes located nearby these regions. Table S8. Results of the most significant associations involving the 57 filtered SNPs. For each SNP: SNP probe, genotype, genomic coordinate, associated environmental variable (“Env”) and scores and statistical test output values (“Gscore”, “WaldScore”, “Efron”, “AIC”, “Beta_0” and “Beta_1”) are reported. Table S9. List of genes located nearby (± 100 kb) the 57 filtered SNPs obtained by the landscape genomics analysis. Table S10. GO term biological processes. Table S11. MAF (minor allele frequency) and major allele of the 13 SNPs shared by Dry and Temperate/Continental groups. Table S12. Samβada significant results for the SNPs of the FST analyses. For each SNP probe: chromosome and position are reported, as well as Environment, G score, Wald Score, AIC, Abs_Beta1 and the Köppen group in which the SNP was detected by the FST analyses. Table S13. List of genes located nearby (± 100 kb) of the 65 SNPs selected with the FST approach and confirmed by Samβada. The * symbol indicates the SNPs with the highest value (> 0.999) also in landscape genomic analysis

Additional file 3. Comparison of ROH across the breeds raised in different countries. The higher the value on the y axis, the bigger is the difference. The threshold of Hâ =â 5 is indicated with a red line.

Runs of homozygosity have been used for genomic characterization and inbreeding estimation, or to detect selective signatures in the genome of mammal and avian species. Here we report runs of homozygosity and heterozygosity in the turkey genome (Meleagris gallopavo). A total of 5,297 turkeys from one commercial line collected between 2010 and 2016 were genotyped using a proprietary 60k array, and pedigree records of 773,414 individuals were available. Runs of both homozygosity and heterozygosity were detected. Relatively long and abundant runs of homozygosity were detected, with comparatively few runs of heterozygosity. Inbreeding coefficients calculated using ROH were higher than those calculated using pedigree. These results provide a preliminary characterization of the turkey genome in terms of runs of homozygosity and heterozygosity-rich genomic regions.

Additional file 5: Table S3. List of markers and genes identified by both CDA and FST approaches. This table reports the markers and the genes in common between the two considered approaches for detection of selection signatures.

Aim of the present thesis is to study the genetic variability of cattle breeds farmed in Italy. These were selected in order to represent different origin, selection history and production aptitudes. The variation at genome level was investigated by using three approaches that allow for disentangling different aspects of the genetic difference between animal populations. One approach checked the difference between two breeds by using a modification of the Fst metric methodology, developed in order to make the signal pattern more readable through a local regression smoothing and to identify outlier signals based on statistical evidence. This study was focused a identifying genomic regions that harbor genes involved in the differences between dairy and beef cattle. Then a multi-breed investigation was performed based on the comparison between allele frequencies under the hypothesis of the binomial distributions. The research was mainly aimed at looking for genes shared between breeds grouped according to production aptitudes. Finally a third study was carried out to analyse the structural differences in the genome by investigating the variation of the distribution of ROH between breeds. Relationships between runs of homozygosity features and inbreeding coefficients have been investigated within and between breeds.

BACKGROUND Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats. RESULTS The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e. short ROH ( 0.20) F values. For populations from Asia, the average number of ROH is smaller and their coverage is lower in goats from the Near East than in goats from Central Asia, which is consistent with the role of the Fertile Crescent as the primary centre of goat domestication. We also observed that local breeds with small population sizes tend to have a larger fraction of the genome covered by ROH compared to breeds with tens or hundreds of thousands of individuals. Five regions on three goat chromosomes i.e. 11, 12 and 18, contain ROH hotspots that overlap with signatures of selection. CONCLUSIONS Patterns of homozygosity (average number of ROH of 77 and genome coverage of 248 Mb; F

BACKGROUND Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. RESULTS Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. CONCLUSIONS These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.

BACKGROUND Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. RESULTS Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and F values (P value

Purpose: The increasing need for disposal of lake-dredged material (LDM) as a consequence of intensified natural and/or anthropogenically mediated erosion processes has lead the scientific community to find new strategies for its reuse. The aim of this study is to investigate the effect of LDM use on the biochemical and functional performance of a degraded soil affected by erosion and entisolization processes. Materials and methods: As a paradigmatic case study, a hydrographic basin located in Sardinia (Italy) was investigated. Severe soil degradation processes affect this area and have resulted in intensive sheet and rill water erosion. In contrast, an increase in sedimentation has been recorded on the bottom of an artificial lake. A degraded soil, collected in this area, were treated by co-utilization of LDM, other mineral matrices (a zeolitized tuff), organic amendment (a commercial manure), and mineral fertilizer (urea, triple superphosphate, and potassium sulfate) for the growth of a pasture grass under controlled (pot) conditions. The evolution of nine different model proto-horizons (MPH) was monitored through a series of biochemical parameters and techniques (total/extracellular enzymatic activity, isoelectric focusing, and gas chromatography) to assess the potential of LDM in soil biochemical recovery. Results and discussion: On the whole, treatments containing LDM resulted in good recovery of degraded soils, as shown by a general enhancement in biochemical functionality. Application of LDM increased the more stable fraction of organic matter and its active biochemical fraction, showing the highest stable humic carbon content and humic activity. Such outcomes seem to represent a long-term beneficial effect on soil functionality. Conclusions: This study demonstrates that LDM could be a useful pedotechnomaterial (PTM) for improving the biochemical functionality of extremely degraded soils. Additionally, the use of LDM as a PTM has the ecological advantage of recycling what is often considered as a “waste material.” From a socioeconomic point of view, the reuse of LDM in pedotechnique could represent a new low-cost alternative to the complex and expensive management and disposal of this material.