Multi-trait multi-environment selection using BLUP and BLUP-derived indices for identification of compact and high-yielding cotton ideotypes under rainfed environments

Developing compact, high-yielding cotton genotypes for rainfed conditions is a key breeding objective to enhance suitability for high-density planting and mechanical harvesting. This study evaluated 24 compact to semi-compact genotypes across three rainfed environments in Tamil Nadu, India, during kharif 2024 to identify consistent ideotypes combining yield potential and optimal plant architecture using BLUP and BLUP-derived selection indices (FAI-BLUP, MTSI, MTMPS, MGIDI). BLUP-based joint ANOVA revealed highly significant ( p < 0.001) genotype, environment, and GEI effects for all traits. Mean seed cotton yield (SCY) was 115.57 g plant⁻¹, with heritability ranging from 0.23 (NSB) to 0.72 (SCY). Genotypic variance contributed 71.99% to SCY and 42.12% to boll weight (BW), indicating strong genetic control. BLUP-based predictions identified Suraksha, Subiksha, and Suraj as high-yielding genotypes, while CO17, Nano, and TVH002 exhibited compact architecture and high selection accuracy. FAI-BLUP index identified Suraksha, Suraj, CO17, and Bt/C-62 as top ideotypes with high yield efficiency and compact growth. MTSI explained 70.78% of variation, selecting Suraj, Subiksha, F2383, and RS2818 as superior genotypes with positive selection gains for SCY (+ 4.73%) and BW (+ 4.24%) and negative gains for plant height (PH) and branching traits, confirming progress toward compactness. MTMPS and MGIDI indices confirmed the consistent performance of Suraksha, Suraj, Subiksha, CO17, and F2383, with mean gains of + 8.72% (SCY) and − 8.12% (PH), highlighting a balance between yield and architecture and consistency under rainfed. Strong positive correlations between BW and SCY ( r = 0.78) and negative correlations of excessive vegetative traits (PH, SBL, MIL) with yield emphasized the importance of compact ideotypes. All BLUP-derived indices consistently identified compact, high-yielding, and consistent genotypes across locations, demonstrating that integrating BLUP with multi-trait, multi-environment indices is an effective strategy for selecting rainfed cotton ideotypes suitable for high-density planting and mechanized cultivation.