Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Ferguson, J.; Fernandes, S.; Monier, B.; Miller, N. D.; Allan, D.; Dmitrieva, A.; Schmuker, P.; Lozano, R.; Valluru, R.; Buckler, E. S.; Gore, M. A.; Brown, P.; Spalding, E. P.; Leakey, A.

doi:10.1101/2020.11.02.365213

bioRxiv · 10.1101/2020.11.02.365213

Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Ferguson, J.·Fernandes, S.·Monier, B.·Miller, N. D.·Allan, D.·Dmitrieva, A.·Schmuker, P.·Lozano, R.·Valluru, R.·Buckler, E. S.·Gore, M. A.·Brown, P.·Spalding, E. P.·Leakey, A.

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Abstract

Sorghum is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is also studied as a feedstock for biofuel and forage. Mechanistic modelling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping for discovery of genotype to phenotype associations remain bottlenecks in efforts to understand the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a novel machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were then the subject of genome-wide association study (GWAS) and transcriptome-wide association study (TWAS) across 869 field-grown biomass sorghum accessions. SD was correlated with plant height and biomass production. Plasticity in SD and SLA were interrelated with each other, and productivity, across wet versus dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population supported identification of associations between DNA sequence variation, or RNA transcript abundance, and trait variation. 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose orthologs in Arabidopsis have functions related to stomatal or leaf development and leaf gas exchange. These advances in methodology and knowledge will aid efforts to improve the WUE of C4 crops.

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Ferguson, J., Fernandes, S., Monier, B., Miller, N. D., Allan, D., Dmitrieva, A., Schmuker, P., Lozano, R., Valluru, R., Buckler, E. S., Gore, M. A., Brown, P., Spalding, E. P., Leakey, A.. 2020-11-03. Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. https://doi.org/10.1101/2020.11.02.365213

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