Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data of 373 animals belonging to 23 sheep breeds of different geographic origins using the Rsb (extended haplotype homozygosity) and F ST statistical approaches, to identify loci associated with the fat-tail phenotype. We also checked if these putative selection signatures overlapped with regions of high-homozygosity (ROH). The analyses identified novel signals and confirmed the presence of selection signature in genomic regions that harbor candidate genes known to affect fat deposition. Several genomic regions that frequently appeared in ROH were also identified within each breed, but only two ROH islands overlapped with the putative selection signatures. The results reported herein provide the most complete genome-wide study of selection signatures for fat-tail in African and Eurasian sheep breeds; they also contribute insights into the genetic basis for the fat tail phenotype in sheep, and confirm the great complexity of the mechanisms that underlie quantitative traits, such as the fat-tail.

A meta-analysis including 36 different results of statistic models from 14 papers was conducted. It evaluated the association between elevated non-esterified fatty acids and/or β-hydroxybutyrate (BHB) on the reproduction outcomes that were pregnancy at first insemination, estrous cyclicity, time to pregnancy, metritis and placental retention. Each association between BHB or NEFA and an outcome reported in literature was a model considered as raw-data for the meta-regression. For each outcome, the meta-regression adjusted the odds ratio, relative risk or hazard ratio with various moderators to reduce the heterogeneity among the studies. The relative risk for metritis and placental retention in case of high BHB or NEFA was in accordance to previous meta-regression and was 1.91 (IC95 = 1.72 to 2.12) and 1.51 (95%CI = 1.19 to 1.92), respectively. The relative risk for pregnancy at first insemination in case of high BHB was assessed to be 0,62 (95%CI = 0,41 to 0,93). The hazard ratio for time to pregnancy in case of high BHB and NEFA was 0.77 (95%CI = 0.61 to 0.97). The present meta-analysis failed to clearly conclude on the association between estrus cyclicity and high BHB or NEFA. The present work allowed a new overview on the association between hyperketonemia and reproductive performance and disorders. It updated the previous meta-regression and included new outcomes. It highlighted the urgent need of further intensive epidemiologic studies on this topic.

One strategy for improving fertility in cattle is administration of GnRH or human chorionic gonadotropin (hCG) during the luteal phase, which increases progesterone (P4) secretion and delays luteolysis. To provide an overview of how GnRH or hCG treatment between 4 and 15 d after artificial insemination (AI) improves pregnancy per AI (P/AI) in cows, a metaanalysis was performed on 107 different trials from 52 publications. Data from 18,082 treated cows and 18,385 untreated controls were meta-analyzed. The meta-analysis explained the relative risk for P/AI with GnRH or hCG treatment under various circumstances. The results did not show any difference in P/AI between cows treated with hCG and cows treated with GnRH. Compared with no treatment, treatment with GnRH or hCG improved the chances of P/AI in cows with very poor (<30%) and poor (30.1 to 45%) fertility, whereas treatment did not benefit cows with very good fertility (>60.1%). Moreover, treatment with GnRH and hCG improved the chances of P/AI in primiparous cows. The improvement was much better in primiparous cows with very low fertility. Treatment with buserelin at a dose above 10 µg and with hCG at a dose above 2,500 IU was associated with increased chances of P/AI compared with lower doses. Treatment with GnRH 10 d after AI was also associated with increased chances of P/AI compared with earlier treatment. The present meta-analysis showed that the use of GnRH and hCG after AI should be focused on cows expected to have low or moderate fertility. Day and dose of treatment have to be considered as well.

Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global F ST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region’s history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector.

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number.