An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Morphometry and depth of inseminating catheter penetration in prolific and non- prolific ewes at different ages: A post mortem study.

The ewe's cervix structure is highly variable among females, which may limit the application of transcervical artificial insemination (TCAI). This work aimed to study the variation in cervix anatomy in two different prolificacy breeds (D'man a prolific and Boujaâd a non-prolific sheep). Reproductive tracts were collected from D'man (n = 64) and Boujaâd (n = 187) females aged between 1 and 4 years. The weight of the uterus, length of the cervix and depth of penetration of the inseminating pipette were recorded. The number of cervical rings was counted and their arrangement graded. The cervix anatomy of D'man ewes differs from that of Boujaâd. The cervix morphology of Boujaâd ewes is more complex compared to D'man ewes; this complexity depends on the age of the ewe. No significant difference was found regarding the depth of penetration of the insemination catheter for the two breeds at 1, 2 and 4 years old (P > 0.05). However, at 3 years old, the highest depth of penetration (P < 0.05) was recorded in D'man ewes. In addition, for both breeds, grade 2 was the most frequent (P < 0.05), and the cervix became less complicated for TCAI with advanced age (4 years old). To conclude, the cervix of D'man ewes is less complex and more favorable to TCAI. In addition, to overcome the complexity of the cervix in Boujaâd sheep, a selection of 4-year-old ewes will make the penetration of the artificial insemination catheter possible.

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12× coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g., panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.

Effect of some non-genetic factors on milk yield and composition of Draa indigenous goats under an intensive system of three kiddings in 2 years.

With 5 millions heads, goats occupy the second place after sheep in Morocco. The indigenous populations are generally raised for meat, except Draa goat that is raised as a dual purpose doe. The objective of this study was to assess milk yield and composition of Draa indigenous goat breed under an intensive system of three kiddings in 2 years and to evaluate the effects of non-genetic factors. Data were collected on 381 lactations between 2006 and 2012 and on 174 samples for milk composition between 2008 and 2010. The highest milk yield was recorded in does of 36-48 months old (84.3 ± 4.78), those suckling more than one kid (80.0 ± 3.39) and those kidding in spring (80.4 ± 3.60) and summer (79.9 ± 3.67). Except protein content, milk composition was not affected by age of does. Dry matter and fat content increased significantly with the lactation stage, protein content decreased from early to middle/late lactation, and lactose content was high in middle lactation. The highest dry matter and fat and lactose contents were obtained for summer kiddings, while the highest percent of protein was recorded for autumnal kiddings. It was concluded that under the three kiddings in 2-year system, Draa does produce enough milk with an interesting milk composition, indicating that this system may be used with success to improve farmers' income.

Genetic and environmental factors affecting perinatal and preweaning survival of D'man lambs.

This study examined the viability of 4,554 D'man lambs born alive at Errachidia research station in south-eastern Morocco between 1988 and 2009. Lamb survival to 1, 10, 30 and 90 days old was 0.95, 0.93, 0.93 and 0.92, respectively. The majority of deaths (85.7%) occurred before 10 days of age. Type and period of birth both had a significant effect on lamb survival traits, whereas age of dam and sex of lamb did not. The study revealed a curvilinear relationship between lamb's birth weight and survival traits from birth to 90 days, with optimal birth weights for maximal perinatal and preweaning survival varying according to type of birth from 2.6 to 3.5 kg. Estimation of variance components, using an animal model including direct and maternal genetic effects, the permanent maternal environment as well as fixed effects, showed that direct and maternal heritability estimates for survival traits between birth and 90 days were mostly low and varied from 0.01 to 0.10; however, direct heritability for survival at 1 day from birth was estimated at 0.63. Genetic correlations between survival traits and birth weight were positive and low to moderate. It was concluded that survival traits of D'man lambs between birth and 90 days could be improved through selection, but genetic progress would be low. However, the high proportion of the residual variance to total variance reinforces the need to improve management and lambing conditions.