bioRxiv Science⌕ Search
Home/Archive/bioRxiv

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.
View original source ↗Export metadata ↓

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.

Source connections

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

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

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Ancestral polyploidy and non-linear dosage shifts define the photosynthetic transition in the Heliantheae alliance

Whole-genome duplications (WGDs) have played a central role in plant evolutionary innovation, yet their genome-wide influence on complex physiological traits such as carbon-concentrating mechanisms (CCMs) remains poorly resolved. Here, we present high-quality genome assemblies and annotations for 35 species within the Heliantheae alliance (Asteraceae), spanning the complex photosynthetic spectrum from C3 to C4. Ks-based analyses combined with gene tree-species tree reconciliation identified a shared paleopolyploid event (WGD-2) ~30 million years ago. Using phylogenetically informed association mapping with these species, we detected 451 functional MapMan BINs with copy number variation significantly associated with interspecific variation in the CO2 compensation point. Notably, 303 of these BINs contain greater than 10% WGD-2-derived genes, indicating a strong enrichment of duplicated loci within photosynthetically relevant functional modules. Effect-size analysis revealed that the C3-to-C4 transition is governed by threshold-dependent genomic architecture rather than gradual additive change. Substantial expansions in key transcription factor modules, including HD-ZIP, HSF, LOB, and TCP, were associated with strong non-linear physiological shifts, consistent with genomic tipping points. By integrating comparative genomics, physiological trait variation, and evolutionary analysis, this study establishes a mechanistic link between ancient polyploidy and contemporary photosynthetic diversification. These findings provide a framework for understanding the genetic basis of carbon concentrating mechanism evolution and inform future optimization of photosynthetic efficiency in Asteraceae crops such as sunflower.

plant biology↗
bioRxiv2026

Heat-induced increases in xylem vulnerability: Experimental evidence and possible mechanisms

Hotter droughts driven by global warming are increasing tree mortality worldwide. Here, we propose a theoretical framework that explains how dissolved gas affects the stability of bubbles in xylem sap, and shows that in the presence of gas, sudden increases in temperature can accelerate embolism formation. We then provide experimental evidence that heat exposure can change xylem vulnerability to drought. Using data from seven Australian and European tree species, we assessed how elevated temperature (+15 and +20 {degrees}C above ambient) affects both xylem embolism resistance, measured with the Optical Vulnerability Technique, and VPD-corrected drying times. We found evidence for reduced embolism resistance and accelerated dehydration in heat-exposed plants. On average, trees reached the water potential at 50% loss of xylem function at 0.73 MPa less negative water potentials and 7.8 kPa h earlier, though responses were highly species-specific, and credibly different from zero only in the Australian species. Our results are consistent with the proposed framework and suggest that embolism resistance may not be a static trait, which has important repercussions for studies of plant vulnerability to drought. Further studies are necessary to assess the potential effects of heat-induced reductions in embolism resistance on tree mortality during heatwaves.

plant biology↗
bioRxiv2026

Genome-wide latitudinal variation associated with defence and reproductive pathways linked to Norway spruce adaptation

Environmental cues modulate the natural variations in genes that outline local adaptation in plants for optimal survival. Genome-wide analysis using exome capture dataset in Norway spruce (Picea abies L. Kast) in Sweden revealed natural allelic variation in coding regions of genes associated with defence and reproductive pathways that follow a latitudinal cline, despite of the weak population structure with a low genetic differentiation. Steepest clines in the allele frequencies of missense SNPs from coding region (cSNPs) were detected in 60S RIBOSOMAL PROTEIN L18 (RPL18C), a gene involved in plant survival and defence/stress responses and LONG AFTER FAR-RED 3 (LAF3) that mediates light responses. This was closely followed by cline in ZINC 4 FINGER DNA 3'-PHOSPHOESTERASE (ZDP), involved in DNA repair and DNA demethylation pathways. Flowering genes that displayed latitudinal cline in cSNPs included BARELY ANY MERISTEM 1 (BAM1), REDUCED VERNALIZATION RESPONSE 1 (VRN1), FLOWERING CONTROL LOCUS A (FCA) and TERMINAL FLOWER 1 (TFL1) among few others. These variations may contribute to differential functioning of the defence/flowering genes, enabling the tree to thrive at its best under given local environmental conditions. The clines provide evidence towards local adaptation in these Norway spruce populations across Sweden; it coincides with the latitudinal variation in climatic conditions including temperature, day length and light quality, along with existing cline e.g. differential growth and defence response, and bud-burst/bud-set. The knowledge can be applied in forest industry to design future sustainable breeding strategies e.g. assisted migration, in the context of inevitable climate change.

plant biology↗