The rapid advances of new-generation sequencing technologies and available genome sequences of common wheat and its relatives greatly promote fine mapping and map-based cloning of wheat genes, providing a great number of gene-specific markers for wheat breeding. During the past years, we developed 160 high-throughput kompetitive allele-specific PCR (KASP) and 56 semi-thermal asymmetric reverse PCR (STARP) markers for genes underpinning economically important traits in wheat, and established a genotyping by target sequencing (GBTS) technology for the gene-specific markers. The KASP and STARP markers have been validated in over 300 Chinese wheat cultivars. In addition, we also developed a 50K SNP array, containing 135 gene-specific markers and 750 markers tightly linked with known QTL, which can be used both in QTL mapping and molecular breeding. The gene-specific markers have been successfully used in wheat breeding, and five wheat cultivars, including Zhongmai 996, Zhongmai 998, Zhongmai 1062, Jimai 23, and Zhongmai 578, have been released in the wheat grown areas of North Plain or Yellow and Huai River Valley in China.