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High-throughput sequencing is a revolutionary technological innovation in DNA sequencing.This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output.High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics.Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, muitifaceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding.In this Topic,we review the application of high-throughput sequencing technologies and big data to plant breeding.