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Genomic signatures of selection,local adaptation and production type characterisation of East Adriatic sheep breeds

Journal of Animal Science and Biotechnology 2024年第2期15卷 546-562页

作者： Boris Lukic ino curik Ivana Drzaic Vlatko Galić Mario Shihabi LubošVostry Vlatka Cubric-curik Faculty of Agrobiotechnical Sciences Osijek J.JStrossmayer University of OsijekVladimira Preloga 131000 OsijekCroatia Department of Animal Science Faculty of AgricultureUniversity of ZagrebSvetošimunska Cesta 2510000 ZagrebCroatia Department of Maize Breeding and Genetics Agricultural Institute OsijekJužno predgrađe 1731000 OsijekCroatia Czech University of Life Sciences Prague Kamycka 12916500 PraqueCzech Republic

Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic *** production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production(carcass,wool and milk yield).Therefore,eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation(EAS),are generally considered as multipurpose breeds(milk,meat and wool),not specialised for a particular type of production,but known for their robustness and resistance to certain environmental *** objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures,decipher their biological and productive functionality,and provide a"genomic"characterization of EAS adaptation and determine its production *** We identified positive selection signatures in EAS using several methods based on reduced local variation,linkage disequilibrium and site frequency spectrum(eROHi,iHS,nSL and CLR).Our analyses identified numerous genomic regions and genes(e.g.,desmosomal cadherin and desmoglein gene families)associated with environmental adaptation and economically important *** candidate genes were related to meat/production and health/immune response traits,while some of the candidate genes discovered were important for domestication and evolutionary processes(e.g.,HOXa gene family and FSIP2).These results were also confirmed by GO and QTL enrichment *** Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type,ultimately providing a new opportunity for future breeding *** the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.

关键词： Composite-likelihood ratio East Adriatic sheep Extreme ROH islands Genomic selection signatures Integrated haplotype score Number of segregating sites by length

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Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations

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Science China Life Sciences 2024年

作者： Songsong Xu Zhanerke Akhatayeva Jiaxin Liu Xueyan Feng Yi Yu Bouabid Badaoui Ali Esmailizadeh Juha Kantanen Marcel Amills Johannes A. Lenstra Anna M. Johansson David W. Coltman George E. Liu ino curik Pablo Orozco-terWengel Samuel R. Paiva Natalia A. Zinovieva Linwei Zhang Ji Yang Zhihong Liu Yachun Wang Ying Yu Menghua Li Faculty of Veterinary Medicine Utrecht University Department of Animal Breeding and Genetics Faculty of Veterinary Medicine and Animal Science Swedish University of Agricultural Sciences Department of Biological Sciences University of Alberta Edmonton Department of Biology Western University Animal Genomics and Improvement Laboratory BARC USDA-ARS Department of Animal Science Faculty of Agriculture University of Zagreb Institute of Animal Sciences Hungarian University of Agriculture and Life Sciences (MATE) School of Biosciences Cardiff University Embrapa Genetic Resources and Biotechnology Laboratory of Animal Genetics L.K. Ernst Federal Science Center for Animal Husbandry Moscow Region Frontiers Science Center for Molecular Design Breeding (MOE) Department of Neurology China-Japan Friendship Hospital College of Animal Science Inner Mongolia Agricultural University Sanya Institute of China Agricultural University State Key Laboratory of Animal Biotech Breeding College of Animal Science and Technology China Agricultural University Institute of Grassland Research Chinese Academy of Agricultural Sciences Laboratory of Biodiversity Ecology and Genome Department of Biology Faculty of Sciences Rabat Mohammed V University Department of Animal Science Faculty of Agriculture Shahid Bahonar University of Kerman Production Systems Natural Resources Institute Finland (Luke) Department of Animal Genetics Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB Campus de la Universitat Autònoma de Barcelona Departament de Ciència Animal i dels Aliments Universitat Autònoma de Barcelona

Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield,horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere(T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.

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