A Natural Major Module Confers the Trade‐Off between Phenotypic Mean and Plasticity of Grain Chalkiness in Rice

This study reveals the genetic and molecular mechanisms controlling the general trade‐off between phenotypic mean and plasticity of grain chalkiness in rice and identifies two major external drivers (high temperature and wide grain) and a natural major module (GCP6‐MPC5) that control this trade‐off. This work holds significant implications for a proof‐of‐concept breeding strategy in integrating both phenotypic mean and plasticity. Abstract A critical challenge in crop breeding is the trade‐off between improving the mean of an important trait and maintaining its phenotypic plasticity. Grain chalkiness is a key cereal grain‐quality trait highly susceptible to environments. However, the genetic and molecular mechanisms controlling the trade‐off between phenotypic mean and plasticity of grain chalkiness remain unknown. Here, utilizing comprehensive genome‐wide association studies on ten grain chalkiness traits over five years in a mini‐core collection, substantial phenotypic plasticity of grain chanlkiness is found, which declines during modern breeding. A general trade‐off between phenotypic mean and plasticity of grain chalkiness is demonstrated, which are controlled by distinct genetic architectures revealed through a detailed QTL atlas. High temperature and wide grain significantly increase grain chalkiness mean but decrease its plasticity and genetic dissection, representing two major external drivers for the trade‐off. Two key quantitative trait genes MPC5 and GCP6 are identified to control this trade‐off. The transcription factor GCP6 biochemically and genetically inhibits MPC5 expression, forming a key module that confers the mean‐plasticity trade‐off of both grain chalkiness and width. Finally, minimal marker sets for molecular breeding accounted for two thirds of grain chalkiness variation. These findings elucidate the genetic architecture of the mean‐plasticity trade‐off in grain chalkiness and offer a proof‐of‐concept breeding strategy to simultaneously optimize both phenotypic mean and plasticity in crop improvement. This study reveals the genetic and molecular mechanisms controlling the general trade-off between phenotypic mean and plasticity of grain chalkiness in rice and identifies two major external drivers (high temperature and wide grain) and a natural major module (GCP6- MPC5 ) that control this trade-off. This work holds significant implications for a proof-of-concept breeding strategy in integrating both phenotypic mean and plasticity. Abstract A critical challenge in crop breeding is the trade-off between improving the mean of an important trait and maintaining its phenotypic plasticity. Grain chalkiness is a key cereal grain-quality trait highly susceptible to environments. However, the genetic and molecular mechanisms controlling the trade-off between phenotypic mean and plasticity of grain chalkiness remain unknown. Here, utilizing comprehensive genome-wide association studies on ten grain chalkiness traits over five years in a mini-core collection, substantial phenotypic plasticity of grain chanlkiness is found, which declines during modern breeding. A general trade-off between phenotypic mean and plasticity of grain chalkiness is demonstrated, which are controlled by distinct genetic architectures revealed through a detailed QTL atlas. High temperature and wide grain significantly increase grain chalkiness mean but decrease its plasticity and genetic dissection, representing two major external drivers for the trade-off. Two key quantitative trait genes MPC5 and GCP6 are identified to control this trade-off. The transcription factor GCP6 biochemically and genetically inhibits MPC5 expression, forming a key module that confers the mean-plasticity trade-off of both grain chalkiness and width. Finally, minimal marker sets for molecular breeding accounted for two thirds of grain chalkiness variation. These findings elucidate the genetic architecture of the mean-plasticity trade-off in grain chalkiness and offer a proof-of-concept breeding strategy to simultaneously optimize both phenotypic mean and plasticity in crop improvement. Advanced Science, Volume 12, Issue 42, November 13, 2025.