Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays

Area of Science:

• Plant genetics and genomics
• Agricultural biotechnology
• Quantitative trait genetics

Background:

• Improving complex traits in crops traditionally relies on genetic markers.
• New technologies enable large-scale measurement of biological intermediates (endophenotypes).
• The utility of endophenotypes for plant trait dissection is underexplored.

Purpose of the Study:

• To illustrate the utility of a large-scale gene expression resource for dissecting plant traits.
• To investigate the role of transcript abundance in maize kernel and agronomic traits.
• To compare the efficacy of transcriptome-wide association studies (TWAS) with genome-wide association studies (GWAS).

Main Methods:

• Utilized a large-scale gene expression resource across 299 maize genotypes and seven tissues.
• Performed single-tissue and multi-tissue transcriptome-wide association studies (TWAS).
• Employed genome-wide association studies (GWAS) and an ensemble approach combining TWAS and GWAS.
• Used variance partitioning in the maize Nested Association Mapping (NAM) population.

Main Results:

• Approximately half of functional variation for maize kernel traits (carotenoids, tocochromanols) and agronomic traits acts through altered transcript abundance.
• Combining TWAS with GWAS increased the power to detect known genes and prioritize causal genes.
• Genes identified by combined GWAS and TWAS explained more heritable trait variance than those from GWAS or TWAS alone.

Conclusions:

• Gene expression endophenotypes significantly improve the ability to link genes to complex phenotypes in plants.
• Integrating TWAS and GWAS enhances the genetic dissection of complex traits.
• Regulatory variation has substantial phenotypic consequences for agricultural species.