scholarly journals Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for QTL mapping in maize

2020 ◽  
Author(s):  
Jiayang Xie ◽  
Dustin Mayfield-Jones ◽  
Gorka Erice ◽  
Min Choi ◽  
Andrew D.B. Leakey
Keyword(s):  
Machine Learning ◽  
Gas Exchange ◽  
Qtl Mapping ◽  
Epidermal Cell ◽  
Genetic Basis ◽  
Stomatal Complex ◽  
Photosynthetic Gas Exchange ◽  
Pavement Cells ◽  
Stomatal Complexes ◽  
Stomatal Patterning

AbstractStomata are adjustable pores on leaf surfaces that regulate the trade-off of CO2 uptake with water vapor loss, thus having critical roles in controlling photosynthetic carbon gain and plant water use. The lack of easy, rapid methods for phenotyping epidermal cell traits have limited the use of quantitative, forward and reverse genetics to discover the genetic basis of stomatal patterning. A new high-throughput epidermal cell phenotyping pipeline is presented here and used for quantitative trait loci (QTL) mapping in field-grown maize. The locations and sizes of stomatal complexes and pavement cells on images acquired by an optical topometer from mature leaves were automatically determined. Computer estimated stomatal complex density (SCD; R2 = 0.97) and stomatal complex area (SCA; R2 = 0.71) were strongly correlated with human measurements. Leaf gas exchange traits correlated with the dimensions and proportion of stomatal complexes but, unexpectedly, did not correlate with SCD. Genetic variation in epidermal traits were consistent across two field seasons. Out of 143 QTLs in total, 36 QTLs were consistently identified for a given trait in both years. 24 hotspots of overlapping QTLs for multiple traits were identified. Orthologs of genes known to regulate stomatal patterning in Arabidopsis were located within some, but not all, of these regions. This study demonstrates how discovery of the genetic basis for stomatal patterning can be accelerated in maize, a model for C4 species where these processes are poorly understood.One sentence summaryOptical topometry and machine learning tools were developed to assess epidermal cell patterning, and applied to analyze its genetic architecture alongside leaf photosynthetic gas exchange in maize.

QTL Mapping for Photosynthetic Gas-Exchange Parameters in Soybean

2010 ◽  
Vol 36 (1) ◽  
pp. 92-100
Author(s):  
Zhi-Tong YIN ◽  
Hai-Na SONG ◽  
Fan-Fan MENG ◽  
Xiao-Ming XU ◽  
De-Yue YU
Keyword(s):  
Gas Exchange ◽  
Qtl Mapping ◽  
Gas Exchange Parameters ◽  
Photosynthetic Gas Exchange ◽  
Exchange Parameters

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

2020 ◽  
Author(s):  
John N. Ferguson ◽  
Samuel B. Fernandes ◽  
Brandon Monier ◽  
Nathan D. Miller ◽  
Dylan Allan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Gas Exchange ◽  
Association Study ◽  
Biomass Production ◽  
Genome Wide Association Study ◽  
Leaf Gas Exchange ◽  
Optical Tomography ◽  
Photosynthetic Gas Exchange ◽  
Biomass Sorghum ◽  
Intrinsic Water Use Efficiency

ABSTRACTSorghum 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.

scholarly journals Fossil evidence for low gas exchange capacities for Early Cretaceous angiosperm leaves

Paleobiology ◽  
2011 ◽  
Vol 37 (2) ◽  
pp. 195-213 ◽  
Author(s):  
Taylor S. Feild ◽  
Garland R. Upchurch ◽  
David S. Chatelet ◽  
Timothy J. Brodribb ◽  
Kunsiri C. Grubbs ◽  
...  
Keyword(s):  
Gas Exchange ◽  
Early Cretaceous ◽  
Leaf Gas Exchange ◽  
Exchange Capacity ◽  
Basal Angiosperm ◽  
Photosynthetic Gas Exchange ◽  
Angiosperm Evolution ◽  
Early Angiosperm ◽  
Fossil Evidence ◽  
Functional Analyses

The photosynthetic gas exchange capacities of early angiosperms remain enigmatic. Nevertheless, many hypotheses about the causes of early angiosperm success and how angiosperms influenced Mesozoic ecosystem function hinge on understanding the maximum capacity for early angiosperm metabolism. We applied structure-functional analyses of leaf veins and stomatal pore geometry to determine the hydraulic and diffusive gas exchange capacities of Early Cretaceous fossil leaves. All of the late Aptian—early Albian angiosperms measured possessed low vein density and low maximal stomatal pore area, indicating low leaf gas exchange capacities in comparison to modern ecologically dominant angiosperms. Gas exchange capacities for Early Cretaceous angiosperms were equivalent or lower than ferns and gymnosperms. Fossil leaf taxa from Aptian to Paleocene sediments previously identified as putative stem-lineages to Austrobaileyales and Chloranthales had the same gas exchange capacities and possibly leaf water relations of their living relatives. Our results provide fossil evidence for the hypothesis that high leaf gas exchange capacity is a derived feature of later angiosperm evolution. In addition, the leaf gas exchange functions of austrobaileyoid and chloranthoid fossils support the hypothesis that comparative research on the biology of living basal angiosperm lineages reveals genuine signals of Early Cretaceous angiosperm ecophysiology.

Types of photosynthetic gas exchange of leaves of beet and maize in relation to the CO2 regimes in their crop stands

1973 ◽  
Vol 1 (10) ◽  
pp. 399-403 ◽  
Author(s):  
A.A. Nichiporovich ◽  
S.N. Chmora ◽  
G.A. Slobodskaya ◽  
T.A. Avdeyeva
Keyword(s):  
Gas Exchange ◽  
Photosynthetic Gas Exchange

scholarly journals Analysis of the genetic basis of plant height-related traits in response to ethylene by QTL mapping in maize (Zea mays L.)

PLoS ONE ◽  
2018 ◽  
Vol 13 (2) ◽  
pp. e0193072
Author(s):  
Weiqiang Zhang ◽  
Zhi Li ◽  
Hui Fang ◽  
Mingcai Zhang ◽  
Liusheng Duan
Keyword(s):  
Zea Mays ◽  
Qtl Mapping ◽  
Plant Height ◽  
Genetic Basis ◽  
Zea Mays L

scholarly journals Alterations in Gas Exchange and Oxidative Metabolism in Rice Leaves Infected by Pyricularia oryzae are Attenuated by Silicon

2015 ◽  
Vol 105 (6) ◽  
pp. 738-747 ◽  
Author(s):  
Gisele Pereira Domiciano ◽  
Isaías Severino Cacique ◽  
Cecília Chagas Freitas ◽  
Marta Cristina Corsi Filippi ◽  
Fábio Murilo DaMatta ◽  
...  
Keyword(s):  
Gas Exchange ◽  
Photochemical Efficiency ◽  
Pyricularia Oryzae ◽  
Gas Exchange Parameters ◽  
Photosynthetic Gas Exchange ◽  
Exchange Performance ◽  
Rice Leaves ◽  
Maximum Photochemical Efficiency ◽  
Important Disease ◽  
Exchange Parameters

Rice blast, caused by Pyricularia oryzae, is the most important disease in rice worldwide. This study investigated the effects of silicon (Si) on the photosynthetic gas exchange parameters (net CO2 assimilation rate [A], stomatal conductance to water vapor [gs], internal-to-ambient CO2 concentration ratio [Ci/Ca], and transpiration rate [E]); chlorophyll fluorescence a (Chla) parameters (maximum photochemical efficiency of photosystem II [Fv/Fm], photochemical [qP] and nonphotochemical [NPQ] quenching coefficients, and electron transport rate [ETR]); concentrations of pigments, malondialdehyde (MDA), and hydrogen peroxide (H2O2); and activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione reductase (GR), and lypoxigenase (LOX) in rice leaves. Rice plants were grown in a nutrient solution containing 0 or 2 mM Si (−Si or +Si, respectively) with and without P. oryzae inoculation. Blast severity decreased with higher foliar Si concentration. The values of A, gs and E were generally higher for the +Si plants in comparison with the −Si plants upon P. oryzae infection. The Fv/Fm, qp, NPQ, and ETR were greater for the +Si plants relative to the −Si plants at 108 and 132 h after inoculation (hai). The values for qp and ETR were significantly higher for the –Si plants in comparison with the +Si plants at 36 hai, and the NPQ was significantly higher for the –Si plants in comparison with the +Si plants at 0 and 36 hai. The concentrations of Chla, Chlb, Chla+b, and carotenoids were significantly greater in the +Si plants relative to the –Si plants. For the –Si plants, the MDA and H2O2 concentrations were significantly higher than those in the +Si plants. The LOX activity was significantly higher in the +Si plants than in the –Si plants. The SOD and GR activities were significantly higher for the –Si plants than in the +Si plants. The CAT and APX activities were significantly higher in the +Si plants than in the –Si plants. The supply of Si contributed to a decrease in blast severity, improved the gas exchange performance, and caused less dysfunction at the photochemical level.

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