Genome editing and chromosome engineering in plants

In the last two decades, innovations in genomics (genome reading) have advanced crop breeding and have played a central role crop improvement. Since first crop genome (rice) was published, several crop genomes are out in the public domain with an exponential increase in the number of samples per genome, improved genome assembly and development of PAN genomes (Figure 1). The availability of reference, whole genome re-sequencing (WGRS) and PAN-genomes are essential to map allelic variants (single base pair to large variations) and have advanced our knowledge toward precise gene discovery, marker development, and trait introgression (Bevan et al., 2017; Kadam et al., 2016; Patil et al., 2016; Valliyodan et al., 2021). WGRS and development of PAN genomes is one of the many payoffs of trait discovery programs and has been conducted in a variety of organism including humans, animals, and several crop species (Figure 1). The dense variation data integrated with other omics platforms (transcriptomics, phenomics, and metabolomics) improves the understanding of phenotype–genotype relationship and essential for marker-assisted breeding and gene mapping. Several crop-specific databases have been developed to accelerate the trait mapping, and this information has become an integral part of all aspects of biological research, including basic and applied plant biology (Deshmukh et al., 2021; Matthews et al., 2009). With integrated genomic technologies, researchers can now effectively identify casual genetic variants from wild/landrace relatives. Application of robust and high throughput genome engineering technologies will be essential to understand gene function and achieve targeted modification of desirable agronomic traits in a wide range of plants, especially crop species.