ALTERED MERISTEM PROGRAM 1 promotes growth and biomass accumulation influencing guard cell aperture and photosynthetic efficiency in Arabidopsis

López-García, Claudia Marina; Ruíz-Herrera, León Francisco; López‐Bucio, Jesús Salvador; Huerta-Venegas, Pedro Iván; Peña-Uribe, César Arturo; López‐Bucio, José

doi:10.1007/s00709-019-01458-z

Cited by 9 publications

(6 citation statements)

References 51 publications

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“…Putative SD candidates in this gene set included a cell wall expansion-type protein ( EXPB2 (Marowa et al, 2016), an ABA-sensitive MAP KINASE ( RAF10 (Lee et al, 2015)), the PAP10 purple acid phosphatase (Hepworth et al, 2016), and an asparagine-rich protein ( NRP ) that is documented to positively regulate the expression of CRY2 (Zhou et al, 2017), a blue light receptor which in turn increases stomatal index (Kang et al, 2009) (Figure 6, Table S9). Further genes with known roles in stomatal development identified via alternative mapping approaches included AMP1 (Shi et al, 2013; López-García et al, 2020), ATE1 (Movahedi, 2013; Vicente et al, 2019), and TED5 (Tossi et al, 2014; Zoulias et al, 2020). Additionally, through mapping for SD we identified multiple genes with putative and known roles in stomatal behavior, e.g.…”

Section: Discussionmentioning

confidence: 99%

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

Ferguson

Fernandes

Monier

et al. 2020

Preprint

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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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Section: Discussionmentioning

confidence: 99%

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

Ferguson

Fernandes

Monier

et al. 2020

Preprint

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“…amp1 plants also generate more but smaller leaves whereas ubiquitous overexpression of AMP1 did not produce a significant plastochron or leaf size phenotype in our hands. However, recently it was reported that AMP1 overexpressors have an increased rosette size but leaf formation rate was not quantified in this study [43]. Thus, more comprehensive studies including tissue specific overexpression of AMP1 combined with detailed leaf growth analysis are required to assess its role in organ size control and its interaction with CYP78A5 in this process.…”

Section: Plos Geneticsmentioning

confidence: 83%

AMP1 and CYP78A5/7 act through a common pathway to govern cell fate maintenance in Arabidopsis thaliana

et al. 2020

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Higher plants can continuously form new organs by the sustained activity of pluripotent stem cells. These stem cells are embedded in meristems, where they produce descendants, which undergo cell proliferation and differentiation programs in a spatiotemporally-controlled manner. Under certain conditions, pluripotency can be reestablished in descending cells and this reversion in cell fate appears to be actively suppressed by the existing stem cell pool. Mutation of the putative carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) in Arabidopsis causes defects in the suppression of pluripotency in cells normally programmed for differentiation, giving rise to unique hypertrophic phenotypes during embryogenesis as well as in the shoot apical meristem. A role of AMP1 in the miRNAdependent control of translation has recently been established, however, how this activity is connected to its developmental functions is not resolved. Here we identify members of the cytochrome P450 clade CYP78A to act in parallel with AMP1 to control cell fate in Arabidopsis. Mutation of CYP78A5 and its close homolog CYP78A7 in a cyp78a5,7 double mutant caused suspensor-to-embryo conversion and ectopic stem cell pool formation in the shoot meristem, phenotypes characteristic for amp1. The tissues affected in the mutants showed pronounced expression levels of AMP1 and CYP78A5 in wild type. A comparison of mutant transcriptomic responses revealed an intriguing degree of overlap and highlighted alterations in protein lipidation processes. Moreover, we also found elevated protein levels of selected miRNA targets in cyp78a5,7. Based on comprehensive genetic interaction studies we propose a model in which both enzyme classes act on a common downstream process to sustain cell fate decisions in the early embryo and the shoot apical meristem.

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“…Putative SD candidates also included a cell wall expansin-type protein EXPANSIN B2 ( EXPB2 ; Marowa et al, 2016 ), an ABA-sensitive MAP KINASE ( RAF10 ; Lee et al, 2015 ), the PAP10 purple acid phosphatase ( Hepworth et al, 2016 ), and an asparagine-rich protein ( NRP ) that is documented to positively regulate the expression of CRYPTOCHROME 2 ( CRY2 ; Zhou et al, 2017 ), a blue light receptor which in turn increases stomatal index ( Kang et al., 2009 ; Figure 5; Supplemental Table S10 ). Further genes with known roles in stomatal development identified via GWAS/TWAS hits for multiple leaf physiological traits included ALTERED MERISTEM PROGRAM 1 ( AMP1 ; Shi et al, 2013 ; López-García et al, 2020 ), ATPASE E1 ( ATE1 ; Movahedi, 2013 ; Vicente et al, 2019 ), and REVERESAL OF THE DET PHENOTYPE 5 ( TED5 ; Tossi et al, 2014 ; Zoulias et al, 2020 ). EPF 2 was identified via GWAS for A N and contained a putative deleterious mutation ( Supplemental Table S10 ).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

View full text Add to dashboard Cite

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 modelling 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 (GWAS) and transcriptome-wide association study (TWAS) across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 (ci/ca) was genetically correlated with SD, SLA, gs and biomass production. Plasticity in SD and SLA were 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. 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 non-synonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

show abstract

ALTERED MERISTEM PROGRAM 1 promotes growth and biomass accumulation influencing guard cell aperture and photosynthetic efficiency in Arabidopsis

Cited by 9 publications

References 51 publications

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

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

AMP1 and CYP78A5/7 act through a common pathway to govern cell fate maintenance in Arabidopsis thaliana

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

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