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Universitat Politècnica de València (2020)

Evaluation of the genetic progress and changes in genome structure of sheep under community-based breeding programs in Ethiopia

Rekik, Emna

Titre : Evaluation of the genetic progress and changes in genome structure of sheep under community-based breeding programs in Ethiopia

Estimaciones de tendencias genéticas para el rendimiento del crecimiento y la evaluación genómica de programas comunitarios de cría de ovejas en Etiopía

Auteur : Rekik, Emna

Université de soutenance : Universitat Politècnica de València

Grade : Máster Universitario en Mejora Genética Animal y Biotecnología de la Reproducción 2020

Several pilot community-based breeding programs (CBBPs) were established since 2009 for various sheep breeds in Ethiopia. In these CBBPs, the main selection trait identified through participatory approaches was six months weight (SMWT). The purpose of this study was to contribute to an understanding of the results of CBBP practices for two breeds (Bonga and Menz) by addressing (i) Estimation of the correlation between phenotypic based selection and BLUP-EBV ; (ii) Assessment of the effect of selection based on SMWT on other productive and reproductive traits ; (iii) Quantification of genetic trend for growth traits ; and (iv) Screening for genomic changes induced by CBBPs. Data of 10877 lamb records for Bonga and 16245 for Menz were collected between 2009 and 2018. Performance data from the breeding programs were analysed using Average Information Restricted Maximum Likelihood method (AI-REML). For Menz, heritability estimates of 0.04, 0.18 and 0.39 were obtained for Birth Weight (BWT), Weaning weight (WWT) and (SMWT), respectively. for Bonga, corresponding values were 0.17, 0.42 and 0.32. For Menz, genetic correlation estimates of 0.90, 0.53 and 0.88 were obtained between SMWT and WWT, SMWT and YWT and WWT and BWT, respectively. For Bonga, high to moderate genetic correlations of 0.97 and 0.42 were obtained between SMWT and WWT and litter size (LS) and SMWT, respectively. Over the years, there was a sustained genetic progress in SMWT for both breeds, being in average 0.12 ± 0.022 and 0.04 ± 0.003 kg/year for Bonga and Menz, respectively. Genetic progress in BWT was not observed in Bonga, but a significant increase occurred in Menz. For both breeds, WWT showed a significant increase reaching 0.09 ± 0.012 and 0.02 ± 0.018 kg/year for Bonga and Menz, respectively. Considering that there was no direct selection on WWT in the community flocks, the calculated increased weights are due to correlated responses. The genetic trend for LS over the years in Bonga was positive and significant (P < 0.01). To understand how selection on weight traits impacted the genomic structure, we assessed genomic diversity, population structure, and genomic selection among Menz and Bonga sheep breeds using 600K high density SNP genotyping. A total of 182 animals of the two breeds were sampled from participating and non-participating flocks in CBBPs. In Menz, the observed heterozygosity HO and Expected heterozygosity HE were 0.31 and 0.32, respectively while for Bonga, a lower similar value of 0.3 was calculated for HO and HE. The average pairwise population differentiation (FST) between the two breeds was 0.083%, ranging from 0.078% to 0.087%, indicating their low to moderate differentiation. The FST within the same breed but between CBBP and control animals was 0.007%. PCA and ADMIXTURE analyses revealed a clustering pattern of the two sheep breeds according to their geographical distribution. The genomic regions under putative selection identified by FST approaches revealed genes associated with adaptation to environments, metabolism, immune responses, growth and reproduction traits. Outputs of this study are to be used to develop optimum alternative improvement and dissemination schemes for Menz and Bonga sheep and a model scheme for other sheep breeds. Though preliminary, the genomic findings may represent in the future a breakthrough in improving the design of CBBP¿s for increased performance of local sheep breeds in Ethiopia

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