Effect of Breed and Non-genetic Factors on Body Weight and Average Daily Gains of Goats in Tunisia

The present study was carried out to evaluate growth performance of three goat breeds in Tunisia (Alpine, Boer and Damascus) from birth to 90 days and to investigate the effect of non- genetic factors on birth weight (BW), weight at 10 days (W10), weight at 30 days (W30), weight at 70 days (W70), weight at 90 days (W90) and average daily weight gains from birth to 30 days (ADG0-30), from 10 to 30 days (ADG10-30), from 30 to 70 days (ADG30-70), from 30 to 90 days (ADG30-90), from 70 to 90 days (ADG7090). A total of 3198 goats including Alpine (n%253D1030), Boer (n%253D2084) and Damascene (n%253D84), born during the period 2004-2016 were used. Data analysis showed non-significant effect of breed on growth traits. However Damascus goats had the heaviest overall live weight at birth (3.99plusmn%253B0.05kg) followed by Alpine (3.94plusmn%253B0.02kg) and Boer (3.90plusmn%253B0.02kg) until 90 days (13.25plusmn%253B0.66, 12.13plusmn%253B0.35, 12.07plusmn%253B0.35kg respectively ).Average daily weight gains followed the same trend as weights. Overall, sex-type of birth, season and the combined year of birth-farm-herd influenced growth traits. Higher performances were recorded in males born as singles, during the rainy season (November to March), in 2007 and 2008, belonging to herd1of Chenchou experimental station and herd 5 belonging to a private farm respectively. In conclusion, our study confirms that non-genetic factors affect these three goat breeds. Adjustments for those factors are necessary to provide standard comparisons among breeds under challenging Tunisian conditions

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

INTRODUCTION: The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale. METHODS: In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context. RESULTS AND DISCUSSION: We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian F ST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism ( BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation ( SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity

Estimation of Genetic Parameters for Litter Size and Growth Traits in a Prolific Line of Tunisian Barbarine Sheep

This study aimed to assess genetic parameters for ewe productivity in a Tunisian Barbarine sheep line. The traits studied were litter size (LS), birth weight (BW), weight at 90 days (W90), and average daily gain between 10 and 30 days (ADG13). A total of 3804 growth and 2726 lambing records were used. Bivariate linear and threshold animal models were fitted and analyzed using the Gibbs sampling methodology. Heritabilities for LS obtained with univariate threshold, bivariate linear, and threshold models were around 0.15, higher than the estimate obtained by a univariate linear model (0.09 ± 0.03). Direct heritability for growth traits remained consistent across models, except for W90 in the bivariate linear threshold model. Maternal heritability for growth traits was higher than direct heritability, ranging from 0.07 to 0.15, except for BW. The covariances between the direct and maternal effects of growth traits were slightly negative. Repeatability oscillated between 0.16 and 0.62. Direct genetic correlations between LS and the other traits were negative, varying from −0.18 (LS-BW) to −0.83 (LS-W90). Our results suggest that the threshold model may be the most appropriate for LS. A selection index including LS and growth traits may be proposed for routine genetic evaluation in this population

Simplification of milk recording in dairy cattle for low input systems.

The simplification of recording procedures constitutes an economic alternative to reduce operational costs when national recording programs are concerned in low input production systems. A total of 54 940 daily milk yields from a herd of 63 Holstein cows recorded in 3 years were used in this study. The effect of reducing tests to measure the accuracy of 305 milk yields was investigated. Two methods of total milk yield computation (the Test Interval Method (TIM) and the Interpolation using Standard Lactation Curves (ISLC)) were compared based on 495 combinations of milk recording alternatives. These alternatives were based on 2 milkings/day, one alternated milking (AM/PM) and one non-alternated milking (AM or PM). All of them were used with 9 intervals between consecutive tests (3 to 11 weeks) and 11 intervals between calving date and the first test day. Results showed that the differences between the actual 305 d milk yield and milk estimated by TIM were the smallest on consecutive test days of maximum 6 weeks of intervals. Differences increased in both sides positively back to A3 and negatively toward A11. Standard estimation errors increased from 4 to 9 from A3 to A11. Phenotypic correlations decreased from .99 to .94 when intervals between the calving date and the first test day increased and this for all test methods (A3-A 11). The ISLC led to a better accuracy of milk yield estimation when intervals between consecutive tests got longer

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic “hypericum perforatum” weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker FST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l’ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding

FecX(Bar) a Novel BMP15 mutation responsible for prolificacy and female sterility in Tunisian Barbarine Sheep

Naturally occurring mutations in growth and differentiation factor 9 (GDF9) or bone morphogenetic protein 15 (BMP15) genes are associated with increased ovulation rate (OR) and litter size (LS) but also sterility. Observing the Tunisian Barbarine ewes of the "W" flock selected for improved prolificacy, we found prolific and infertile ewes with streaky ovaries. Blood genomic DNA was extracted from a subset of low-ovulating, prolific and infertile ewes of the "W" flock, and the entire coding sequences of GDF9 and BMP15 were sequenced. We evidenced a novel polymorphism in the exon 1 of the BMP15 gene associated with increased prolificacy and sterility. This novel mutation called FecX(Bar) is a composite polymorphism associating a single nucleotide substitution (c.301G > T), a 3 bp deletion (c. 302_304delCTA) and a C insertion (c. 310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101. Calculated in the "W" flock, the FecX(Bar) allele increased OR by 0.7 ova and LS by 0.3 lambs (p = 0.08). As for already identified mutations, homozygous females carrying FecX(Bar) exhibited streaky ovaries with a blockade at the primary stage of folliculogenesis as shown by histochemistry. Our investigation demonstrates a new mutation in the BMP15 gene providing a valuable genetic tool to control fecundity in Tunisian Barbarine, usable for diffusion program into conventional flocks looking for prolificacy improvement

Table_2_Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data.docx

IntroductionThe development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.MethodsIn this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.Results and discussionWe revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east–west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino’s European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.</p

Table_1_Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data.xlsx

IntroductionThe development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.MethodsIn this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.Results and discussionWe revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east–west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino’s European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.</p

Image_2_Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data.pdf

IntroductionThe development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.MethodsIn this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.Results and discussionWe revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east–west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino’s European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.</p