The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement

Abstract

After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.

Keywords: domestication; functional genomics; genomics; improvement; maize.

Figure 1

Genomic Sequence Variants in the tb1 Regions of Teosinte and Tropical and Temperate Maize Lines. (A) The red rectangles indicate the position of tb1 and the blue rectangles indicate the position of the Hopscotch TE. This TE is the functional variant of tb1 and is absent in teosinte. This Hopscotch TE is located ∼60 kb upstream of tb1 in temperate line B73 (RefGen_v4, Jiao et al., 2017) and tropical line SK (Yang et al., 2019a). (B–D) The increased expression levels of representative selected genes (tb1 in B, ZmSWEET4c in C, ra1 in D) in modern elite maize lines compared with teosinte, the ancestor of maize. The expression profile was obtained by analyzing RNA-seq data generated by Lemmon et al. (2014).

Figure 2

Examples of Large Structural Variations between Two Maize Lines, B73 and Mo17. (A) An ∼2-Mb inversion on chromosome 7, as indicated by blue dots and dashed box. (B) Two adjacent inversions covering ∼2 Mb on chromosome 1, as indicated by blue dots and dashed boxes. (C) An ∼3-Mb deletion in Mo17, as compared with B73, on chromosome 6. (D) An ∼3-Mb insertion in Mo17, as compared with B73, on chromosome 6. The alignment was performed using MUMMER 3.23 (Kurtz et al., 2004) with a minimum match length of 1 kb.

Figure 3

An Overview of Strategies for Rapid Gene Cloning and Maize Improvement. (A–C) Genetic architecture of a target trait is dissected with, for example, linkage mapping, GWAS, QTG-seq, and QTG-seq. Different selection methods are then used based on the complexity of the genetic architecture of the target trait. For example, MAS is suitable for selection of GLS resistance, whereas GS is much more efficient for selection of hundred-kernel weight. (D–G) After QTLs are mapped, candidate genes are proposed and the mutants for candidate genes are screened from a mutant library generated with CRISPR/Cas9. The causal gene is validated with these mutants. With causal variants and/or favorable alleles generated with CRISPR/Cas9 confirmed, they then can be applied directly in breeding programs. GWAS, genome-wide association study; MAS, marker-assisted selection; GS, genomic selection.