The Qinghai Plateau’s high-altitude conditions present significant challenges for wheat cultivation, demanding varieties with enhanced adaptability and stress resistance. However, the genetic basis for key traits like grain yield and stress tolerance in wheat adapted to these conditions remains poorly understood. This knowledge is crucial for developing wheat varieties that can thrive in the harsh environment of the Qinghai Plateau.This study aimed to uncover the genetic foundation of key traits by analyzing five F2 populations from crosses between Qinghai Plateau spring wheat varieties and CIMMYT germplasm. We used a target sequencing breeder chip to assess phenotypic variation in six parental lines. We identified potential genes for all-stage resistance (APR) and adult plant resistance (ASR) to stripe rust. Genotyping lines across the F2 populations revealed 99 loci/genes associated with ten key traits, with 35 showing genetic separation. Notably, the number of stripe rust resistance genes in the parental lines ranged from 4 to 9, with the F2 lines aggregating between 0 and 9 genes. Grainrelated genes were aggregated in varying numbers, with the majority of lines carrying two genes. Gene frequency analysis revealed significant variation across populations, contributing valuable data for marker-assisted breeding and advancing wheat molecular breeding research.