Crop seeds are important sources of protein, oil, and carbohydrates for food, animal feeds, and industrial products. Recently, much attention has been paid to quality and functional properties of crop seeds. However, seed traits possess some distinct genetic characteristics in comparison with plant traits, which increase the difficulty of genetically improving these traits. In this study, diallel analysis for seed models with genotype by environment interaction (GE) effect was applied to estimate the variance-covariance components of seed traits. Mixed linear model approaches were used to estimate the genetic covariances between pair-wise seed and plant traits. The breeding values (BV) were divided into two categories for the seed models. The first category of BV was defined as the combination of direct additive, cytoplasmic, and maternal additive effects, which should be utilized for selecting stable cultivars over multi-environments. The three genetic effects, together with their GE interaction, were included in the second category of BV for selecting special lines to be grown in specific ecosystems. Accordingly, two types of selection indices for seed traits, i.e., general selection index and interaction selection index, were developed and constructed on the first and the second category BV, respectively. These proposed selection indices can be applied to solve the difficult task of simultaneously improving multiple seed traits in various environments. Data of crop seeds with regard to four seed traits and four yield traits based on the modified diallel crosses in Upland cotton (Gossypium hirsutum L.) were used as an example for demonstrating the proposed methodology. Crop seeds are important sources of protein, oil, and carbohydrates for food, animal feeds, and industrial products. Recently, much attention has been paid to quality and functional properties of crop seeds. However, seed traits possess some distinct genetic characteristics in comparison with plant traits, which increase the difficulty of genetically improving these traits. In this study, diallel analysis for seed models with genotype by environment interaction (GE) effect was applied to estimate the variance-covariance components of seed traits. to estimate the genetic covariances between pair-wise seed and plant traits. The first category of BV was defined as the combination of direct additive, cytoplasmic, and maternal additive effects , which should be utilized for selecting stable cultivars over multi-environments. The three genetic effects, together with their GE interaction, were included in the second category of: BV, for types of selection indices for seed traits, ie, general selection index and interaction selection index, were developed and constructed on the first and the second category BV, respectively. These proposed selection indices can be applied to solve the difficult task of and more multiple seed traits in various environments. Data of crop seeds with regard to four seed traits and four yield traits based on the modified diallel crosses in Upland cotton (Gossypium hirsutum L.) were used as an example for demonstrating the proposed methodology.