Govinal Badiger Bhaskara, Jesse R. Lasky, Samsad Razzaque, Li Zhang, Taslima Haque, Jason E. Bonnette, Guzide Zeynep Civelek, Paul E. Verslues, and Thomas E. Juenger

PNAS August 10, 2022; 119 (33) e2205305119

Significance

Sustainable water use is critical for agricultural productivity. Most of the water that plants take up from soil is transpired through stomatal pores while CO₂ enters the leaf. Thus, plants trade water for photosynthetic carbon. Balancing the amount of water lost relative to biomass accumulated, usually referred to as water-use efficiency (WUE), is a critical determinant of crop performance in water-limited environments. We used GWAS and reverse genetics to discover genes underlying WUE variation in Arabidopsis thaliana. These genes affected WUE by altering biomass accumulation or altering water consumption (or both in some cases). These results greatly expand the range of genes that may be manipulated to enhance WUE and contribute to sustainable water use in agriculture.

Abstract

Water-use efficiency (WUE) is the ratio of biomass produced per unit of water consumed; thus, it can be altered by genetic factors that affect either side of the ratio. In the present study, we exploited natural variation for WUE to discover loci affecting either biomass accumulation or water use as factors affecting WUE. Genome-wide association studies (GWAS) using integrated WUE measured through carbon isotope discrimination (δ¹³C) of Arabidopsis thaliana accessions identified genomic regions associated with WUE. Reverse genetic analysis of 70 candidate genes selected based on the GWAS results and transcriptome data identified 25 genes affecting WUE as measured by gravimetric and δ¹³C analyses. Mutants of four genes had higher WUE than wild type, while mutants of the other 21 genes had lower WUE. The differences in WUE were caused by either altered biomass or water consumption (or both). Stomatal density (SD) was not a primary cause of altered WUE in these mutants. Leaf surface temperatures indicated that transpiration differed for mutants of 16 genes, but generally biomass accumulation had a greater effect on WUE. The genes we identified are involved in diverse cellular processes, including hormone and calcium signaling, meristematic activity, photosynthesis, flowering time, leaf/vasculature development, and cell wall composition; however, none of them had been previously linked to WUE. Thus, our study successfully identified effectors of WUE that can be used to understand the genetic basis of WUE and improve crop productivity.

See https://www.pnas.org/doi/10.1073/pnas.2205305119

Figure 1: Natural variation, GWAS analysis, and reverse genetic tests of candidate genes for WUE by gravimetric and δ¹³C analyses. (A) Plastic response of 185 Arabidopsis accessions to terminal drought. WUE (δ¹³C of above-ground biomass) values are pooled accession values within each treatment. (B) Distribution of WUE (δ¹³C) plasticity (difference in δ¹³C between drought and wet) for 185 Arabidopsis accessions. Blue vertical line indicates the median. (C) Manhattan plot of SNP P values from the GWAS analysis using the WUE plasticity data shown in A. The blue horizontal line indicates the cutoff for the top 500 low P-value SNPs. The vertical lines indicate the genomic positions for the prioritized GWAS candidates for which we analyzed WUE (biomass produced per unit of water consumed) using reverse genetics. Gray lines indicate location of genes where the T-DNA mutant(s) did not have significantly altered WUE and orange dotted lines indicate genes where the T-DNA mutant(s) did have significant effect on WUE. (D) Distribution of gravimetric WUE (g/L, ratio of biomass to water consumed) for 88 T-DNA mutants from high throughput screening using small containers (n = 3 to 10 biological replicates per genotype). Blue vertical line indicates the mean of Col-0 wild type.