In recent years, new plant breeding technologies (NPBT) have had enormous effects on breeding and the agricultural industry. In particular, genome editing technology, including site-directed nuclease technologies, has progressed dramatically since the first-generation Zinc finger nucleases to the third-generation clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9). CRISPR/Cas9 technology has yielded a revolutionary breakthrough in the accurate, efficient, and user-friendly genome editing of eukaryotes. Several methods for basic research and applications, such as knock-out, base editing, gene targeting, and transcriptional activation or repression have been derived from CRISPR/Cas9 technology. Herein, we will describe the current progress in NPBTs and also summarize the crops developed by NPBTs. After analyzing the current status of NPBTs and crop development, we have proposed potential strategies for crop development using NPBTs.

Hexaploid wheat (common wheat/bread wheat) is one of the most important cereal crops in the world and a model for research of an allopolyploid plant with a large, highly repetitive genome. In the heritability of agronomic traits, variation in gene presence/absence plays an important role. However, there have been relatively few studies on the variation in gene presence/absence in crop species, including common wheat. Recently, a reference genome sequence of common wheat has been fully annotated and published. In addition, advanced next-generation sequencing (NGS) technology provides high quality genome sequences with continually decreasing NGS prices, thereby dawning full-scale wheat functional genomic studies in other crops as well as common wheat, in spite of their large and complex genomes. In this review, we provide information about the available tools and methodologies for wheat functional genomics research supported by NGS technology. The use of the NGS and functional genomics technology is expected to be a powerful strategy to select elite lines for a number of germplasms.