Selection Response in the Genomic Era: Recent Advances in Quantitative Genetics, Genomic Selection, and Evolutionary Genomics

Abstract

Selection theory has remained the cornerstone of quantitative genetics, evolutionary biology, and genetic improvement programs in plants and animals. This review synthesizes the historical development and recent advances in selection theory, highlighting the transition from the classical breeder's equation to modern genomic prediction frameworks. Classical quantitative genetic principles, including genetic variance partitioning, heritability, genetic advance, correlated response, and selection index theory, are discussed as the theoretical basis for predicting response to selection. The review further examines the limitations of conventional phenotypic selection, particularly under complex genotype × environment (G×E) interactions, changing allele frequencies, and low-heritability traits. Recent developments in genomic selection (GS), genomic prediction (GP), genome-wide association studies (GWAS), high-throughput phenotyping, and whole-genome sequencing have substantially enhanced the accuracy of breeding value estimation while shortening breeding cycles. Special emphasis is placed on multi-trait and multi-environment genomic prediction models that integrate genomic, phenotypic, and environmental information to improve prediction accuracy and accelerate sustainable genetic gain under diverse environments. The review also discusses the contributions of evolutionary genomics in understanding polygenic adaptation, balancing selection, domestication, and convergent evolution, thereby bridging evolutionary theory with applied breeding. Finally, current challenges, including climate change, narrowing genetic diversity, complex G×E interactions, and regulatory and ethical considerations associated with genome-edited crops, are highlighted. Overall, this review demonstrates that integrating quantitative genetics with advanced genomic technologies provides a powerful framework for accelerating crop improvement and developing climate-resilient, high-yielding cultivars capable of meeting future global food security demands.