Plant biology research has currently entered the post-genomics era with the advances in genomic technologies. The unprecedented development of genomics and application in crops is driving a new “green revolution” in agriculture. With the high-quality genomes of many important crops (for example, rice, wheat, maize, soybean, and vegetables), numerous genes controlling the agronomically important traits have been identified and the underlying mechanisms have been revealed. Modern plant genomics can boost research progress in several aspects:(1) omics data provide a comprehensive exploration of a given gene family in a genome-wide, sometimes genus-wide manner;(2) high-quality genomes and large-scale sequencing data allow the identification of single nucleotide polymorphism (SNP) and structural variations, facilitating quantitative trait loci (QTL) or genome-wide association (GWAS) studies to rapidly identify genetic loci for agronomic traits;(3) combining with other omics, such as metabolomics, quantitative proteomics, epigenomics and epitranscriptomics, multi-omic approaches can gain new insights into a biological question even without an available reference genome.

In this context, the present Topic “Plant Functional Genomics and Crop Genetic Improvement” provides a forum for researchers to communicate their latest findings related to plant functional genomics and the corresponding applications in crop genetic improvement. We collaborate with several related journals, including Agronomy, Crops, International Journal of Molecular Sciences, Life and Plants, to cover such a broad-range theme. This Topic has collected a set of 51 papers (three reviews and 48 research articles) with a relatively low acceptance rate (~ 25%), covering several species including wheat (Triticum aestivum L.), rice (Oryza sativa L.), maize (Zea mays L.), soybean (Glycine max L.), cotton (Gossypium hirsutum L.), rapeseed (Brassica napus L.), tea plant (Camellia sinensis (L.) O. Kuntze), flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) and many others. These studies fall into four themes of plant genetics and genomics:(1) Genome-wide characterization of gene families in plants;(2) Functional studies of genes regulating various traits in plants;(3) Dissecting important agronomic traits through population genetics;(4) Multi-omic analysis facilitates plant functional genomic and genetic improvement studies. This Editorial paper aims to showcase the Topic and discuss the related perspectives.