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

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.

Comparison of Covariate Balance Weighting Methods in Estimating Treatment Effects

Different covariate balance weighting methods have been proposed by researchers from different perspectives to estimate the treatment effects.This paper gives a brief review of the covariate balancing propensity score method by Imai and Ratkovic(2014),the stable balance weighting procedure by Zubizarreta(2015),the calibration balance weighting approach by Chan,et al.(2016),and the integrated propensity score technique by Sant’Anna,et al.(2020).Simulations are conducted to illustrate the finite sample performance of both the average treatment effect and quantile treatment effect estimators based on different weighting methods.Simulation results show that in general,the covariate balance weighting methods can outperform the conventional maximum likelihood estimation method while the performance of the four covariate balance weighting methods varies with the data generating processes.Finally,the four covariate balance weighting methods are applied to estimate the treatment effects of the college graduate on personal annual income.