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Bread wheat (Triticum aestivum L) is one of main staple food crops worldwide contributing 20% calories in human diet. Drought stress is the main factor limiting yields and threatening to food security, with climate change resulting in more frequent and intense drought. Developing drought-tolerant wheat cultivars is a promising way forward. The use of a holistic approaches that include high-throughput phenotyping and genetic makers in selection could help in accelerating genetic gains. Fifty advanced breeding lines were selected from the CIMMYT Turkey winter wheat breeding program and studied under irrigated and semiarid conditions for two years. High-throughput phenotyping were done for wheat crown root traits using shovelomics techniques and canopy green area and senescence dynamics using vegetation indices (green area using RGB images and Normalized Difference Vegetation Index using spectral reflectance). In addition, genotyping by KASP markers for adaptability genes was done. Overall, under semiarid conditions compared to irrigated conditions yield reduced by 3.09 t ha−1 (−46.8%). Significant difference between the treatment and genotype was observed for grain yield and senescence traits. Genotypes responded differently under drought stress. Root traits including shallower nodal root angle under irrigated conditions and root number per shoot under semiarid conditions were associated with increased grain yield. RGB based vegetation index measuring canopy green area at anthesis was more strongly associated with GY than NDVI under drought. Five established functional genes (PRR73.A1 – flowering time, TEF-7A – grain size and weight, TaCwi.4A - yield under drought, Dreb1-drought tolerance, and ISBW11.GY.QTL.CANDIDATE- grain yield) were associated with different drought-tolerance traits in this experiment. We conclude that a combination of high-throughput phenotyping and selection for genetic markers can help to develop drought-tolerant wheat cultivars.