Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally c...Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep 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 conditions.Our 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 type.Results 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 traits.Most 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 analysis.Conclusions 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 programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.展开更多
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 provi...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.展开更多
基金supported by Croatian Science Foundation project IP-2018–01-8708-Application of NGS methods in the assessment of genomic variability in ruminants–“ANAGRAMS”the EU Operational Program Competitiveness and Cohesion 2014–2020 project KK.01.1.1.04.0058—Potential of microencapsulation in cheese productionthe project No.QK1919156 of the Ministry of Agriculture,Czech Republic.
文摘Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep 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 conditions.Our 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 type.Results 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 traits.Most 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 analysis.Conclusions 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 programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.
基金supported by the Project of Northern Agriculture and Livestock Husbandry Technology Innovation Center,Chinese Academy of Agricultural Sciences(BFGJ2022002)the National Key Research and Development Program of China(2021YFD1200900,2023YFF1001003,and 2023YFF1000900)+3 种基金Biological Breeding-National Science and Technology Major Project(2023ZD0407106)the National Natural Science Foundation of China(32102511,31661143014,31972527,32320103006,and 32272845)Chinese Universities Scientific Fund(2024TC162)National High Level Hospital Clinical Research Funding(2023-NHLHCRF-YXHZ-TJMS-09)。
文摘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.
