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

Ferguson, John N, Fernandes, Samuel B, Monier, Brandon , Miller, Nathan D, Allen, Dylan, Dmitrieva, Anna, Schmuker, Peter, Lozano, Roberto, Valluru, Ravi, Buckler, Edward S, Gore, Michael A, Brown, Patrick J, Spalding, Edgar P and Leakey, Andrew D B (2021) Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions. Plant Physiology . ISSN 0032-0889

Full content URL: https://doi.org/10.1093/plphys%2Fkiab346

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

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a 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 the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 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 Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

Keywords:Machine-learning, WUE, GWAS, TWAS, Sorghum, phenotyping
Subjects:C Biological Sciences > C400 Genetics
D Veterinary Sciences, Agriculture and related subjects > D412 Crop Physiology
D Veterinary Sciences, Agriculture and related subjects > D400 Agriculture
D Veterinary Sciences, Agriculture and related subjects > D710 Agricultural Biology
Divisions:College of Science > Lincoln Institute for Agri-Food Technology
ID Code:46378
Deposited On:08 Sep 2021 11:35

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