Advanced high-throughput plant phenotyping techniques for genome-wide association studies: A review

Abstract

Linking phenotypes and genotypes to identify genetic architectures that regulate important traits is crucial for plant breeding and the development of plant genomics. In recent years, genome-wide association studies (GWASs) have been applied extensively to interpret relationships between genes and traits. Successful GWAS application requires comprehensive genomic and phenotypic data from large populations. Although multiple high-throughput DNA sequencing approaches are available for the generation of genomics data, the capacity to generate high-quality phenotypic data is lagging far behind. Traditional methods for plant phenotyping mostly rely on manual measurements, which are laborious, inaccurate, and time-consuming, greatly impairing the acquisition of phenotypic data from large populations. In contrast, high-throughput phenotyping has unique advantages, facilitating rapid, non-destructive, and high-throughput detection, and, in turn, addressing the shortcomings of traditional methods. Aim of Review: This review summarizes the current status with regard to the integration of high-throughput phenotyping and GWAS in plants, in addition to discussing the inherent challenges and future prospects. Key Scientific Concepts of Review: High-throughput phenotyping, which facilitates non-contact and dynamic measurements, has the potential to offer high-quality trait data for GWAS and, in turn, to enhance the unraveling of genetic structures of complex plant traits. In conclusion, high-throughput phenotyping integration with GWAS could facilitate the revealing of coding information in plant genomes.

Keywords: Gene; Imaging; Phenotype; Spectroscopy; Traits.

Graphical abstract

Fig. 1

General analysis process of GWAS equipped with high-throughput phenotyping.

Fig. 2

Schematic overview of high throughput phenotyping used in GWAS studies for rice.

Fig. 3

The current status of GWAS equipped with high-throughput phenotyping in plants. (a) The proportion of studies using GWAS combined with high-throughput phenotyping in plant species (based on searched articles); (b) The main focus of searched articles for various plants. The bigger font size corresponding to the more high attention.