Phenotypic Plasticity, Genetic Networks and Breeding by Design of Polygenic Traits in Diverse Environments

Polygenic traits, which are shaped by numerous loci with minor effects, environmental factors, and epigenetic modifications, play a pivotal role in agriculture. However, their genetic architecture has long been difficult to determine. Our earlier Research Topic, Advances in Statistical Methods for the Genetic Dissection of Complex Traits in Plants, established a compressed variance component mixed model that considers all possible genetic effects and controls for all possible polygenic backgrounds, along with the 3VmrMLM algorithm, and demonstrated their power in dissecting complex traits across diverse plant species. Building on this foundation, a big-data and AI algorithm, Fast3VmrMLM, has since been developed to meet the demands of large-scale genomic datasets. Together, these advances provide new opportunities to decipher the genetic basis and phenotypic plasticity of polygenic traits by identifying quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), QTN-by-meteorological factor interactions (QMIs), and QTN-by-QTN interactions (QQIs). Once a large number of polygenes underlying polygenic traits have been identified, genetic networks constructed from these loci can help researchers pinpoint key hub genes, providing breeders with actionable targets.In crop breeding, varieties are traditionally selected based on observed phenotypes, a process that is both time-consuming and increasingly challenged by climate variability. Integrating these AI-driven methods with the breeding-by-design concept enables us to decipher the genetic basis and phenotypic plasticity of polygenic traits and substantially accelerates the breeding process in the face of increasing climate variability. The aim of this Research Topic is to consolidate cutting-edge work in this field and provide breeders with concrete molecular targets and key hub genes for developing the next generation of crop varieties.We welcome submissions of all article types published by Frontiers in Plant Science on the following themes, including but not limited to:• Reviews and perspectives on GWAS and breeding by design in plants• Deciphering the genetic basis of polygenic traits by identifying QTNs, QEIs, QMIs, and QQIs through genome-wide association studies• Deciphering the phenotypic plasticity of polygenic traits in diverse environments• Implementing breeding by design at low cost, including the mining of novel alleles, superior germplasm, and superior hybrid combinations• Identifying the biological functions and dissecting the molecular mechanisms of novel genes mined by new GWAS methods Topic editors: Yuan-Ming Zhang, Yang-Jun Wen, Zhenyu Jia, Shangqian Xie, Ya-Wen Zhang Source: https://www.frontiersin.org/research-topics/80849/phenotypic-plasticity-genetic-networks-and-breeding-by-design-of-polygenic-traits-in-diverse-environments