The goal of much of plant biology research is to understand and thus be able to manipulate phenotypes of important crop species. Decoding crop genomes has been a formidable challenge for many years due to their typically huge sizes, abundant repetitive regions, heterozygosity, and polyploidy. Therefore, plant biologists have heavily relied on studies of the reference plant, Arabidopsis, which has been the subject of a multitude of physiological, genetic, biochemical, molecular, and genomic studies. In recent years, next generation sequencing (NGS) has been a game changer in the field of crop science. NGS-based genomics overcomes many long-standing technical barriers that have made crop genomic challenging. Furthermore, NGS technologies can be used to generate unprecedented amounts of genotypic and transcriptomic data. Integrating these data with high-resolution phenotypes and with other molecular profiling data has enabled identification of genes and molecules associated with crop phenotypes. Indeed, these new high-throughput technologies and approaches have paved the way for understanding genotype-to-phenotype (and phenotype-to-genotype) relationships in crops.

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