Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Baseggio, Matheus; Murray, Matthew; Magallanes‐Lundback, Maria; Kaczmar, Nicholas; Chamness, James; Buckler, Edward S.; Smith, Margaret E.; DellaPenna, Dean; Tracy, William F.; Gore, Michael A.

doi:10.1002/tpg2.20008

Cited by 42 publications

(100 citation statements)

References 80 publications

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“…Carotenoids are responsible for the yellow or orange color of egg yolk [1], corn kernels [2], vegetables and fruits [3,4], and flowers [5,6]. The largest fraction of carotenoids, however, is masked by chlorophyll (see Sections 3 and 4 below) in photosynthetic organisms.…”

Section: Overview Of Sources and Roles Of Carotenoidsmentioning

confidence: 99%

Zeaxanthin, a Molecule for Photoprotection in Many Different Environments

et al. 2020

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Conversion of sunlight into photochemistry depends on photoprotective processes that allow safe use of sunlight over a broad range of environmental conditions. This review focuses on the ubiquity of photoprotection associated with a group of interconvertible leaf carotenoids, the xanthophyll cycle. We survey the striking plasticity of this process observed in nature with respect to (1) xanthophyll cycle pool size, (2) degree and speed of interconversion of its components, and (3) flexibility in the association between xanthophyll cycle conversion state and photoprotective dissipation of excess excitation energy. It is concluded that the components of this system can be independently tuned with a high degree of flexibility to produce a fit for different environments with various combinations of light, temperature, and other factors. In addition, the role of genetic variation is apparent from variation in the response of different species growing side-by-side in the same environment. These findings illustrate how field studies can generate insight into the adjustable levers that allow xanthophyll cycle-associated photoprotection to support plant photosynthetic productivity and survival in environments with unique combinations of environmental factors.

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Section: Overview Of Sources and Roles Of Carotenoidsmentioning

confidence: 99%

Zeaxanthin, a Molecule for Photoprotection in Many Different Environments

et al. 2020

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“…2019). The procedure of Baseggio et al . (2020) for SNP calling, filtering, and imputing missing genotypes was used to construct a SNP marker dataset for the genetic dissection and prediction of fresh kernel elemental phenotypes.…”

Section: Methodsmentioning

confidence: 99%

“…A GWAS was conducted across and within locations to identify SNP markers significantly associated with each elemental phenotype following the methods of Baseggio et al . (2020) with minor modifications.…”

Section: Methodsmentioning

confidence: 99%

“…2019) could potentially lead to spurious associations with su1 and sh2 as shown for tocotrienols and certain carotenoids (Baseggio et al . 2019, 2020), endosperm mutation type ( su1 , sh2 , or su1sh2 ) was also tested with the BIC for inclusion as a covariate in the model. Of the 401 inbred lines, 384 lines had endosperm mutation type scores available from Baseggio et al .…”

Section: Methodsmentioning

confidence: 99%

“…To approximate the amount of phenotypic variation explained by a significantly associated SNP, we calculated the difference between the likelihood-ratio-based R 2 statistic (R 2 LR ) of Sun et al . (2010) from a mixed linear model with or without the given SNP, following Baseggio et al . (2020).…”

Section: Methodsmentioning

confidence: 99%

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Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

Baseggio

Murray

et al. 2021

Preprint

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Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel. In concordance with mapping results from mature maize kernels, we detected a probable pleiotropic association of zinc and iron concentrations with nicotianamine synthase5 (nas5), which purportedly encodes an enzyme involved in synthesis of the metal chelator nicotianamine. Additionally, a pervasive association signal was identified for cadmium concentration within a recombination suppressed region on chromosome 2. The likely causal gene underlying this signal was heavy metal ATPase 3 (hma3), whose counterpart in rice, OsHMA3, mediates vacuolar sequestration of cadmium and zinc in roots, whereby regulating zinc homeostasis and cadmium accumulation in grains. Consistent with transgenic studies in rice, we detected an association of hma3 with cadmium but not zinc accumulation in fresh kernels. This finding implies that selection for low cadmium will not affect zinc levels in fresh kernels. Although less resolved association signals were detected for boron, nickel, and calcium, all 15 elements were shown to have moderate predictive abilities via whole-genome prediction. Collectively, these results help improve our genomics-assisted breeding efforts centered on improving the elemental profile of fresh sweet corn kernels.

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Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels

et al. 2022

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Sweet corn (Zea mays L.) is consistently one of the most highly consumed vegetables in the United States, providing a valuable opportunity to increase nutrient intake through biofortification. Significant variation for carotenoid (provitamin A, lutein, zeaxanthin) and tocochromanol (vitamin E, antioxidants) levels is present in temperate sweet corn germplasm, yet previous genome‐wide association studies (GWAS) of these traits have been limited by low statistical power and mapping resolution. Here, we employed a high‐quality transcriptomic dataset collected from fresh sweet corn kernels to conduct transcriptome‐wide association studies (TWAS) and transcriptome prediction studies for 39 carotenoid and tocochromanol traits. In agreement with previous GWAS findings, TWAS detected significant associations for four causal genes, β‐carotene hydroxylase (crtRB1), lycopene epsilon cyclase (lcyE), γ‐tocopherol methyltransferase (vte4), and homogentisate geranylgeranyltransferase (hggt1) on a transcriptome‐wide level. Pathway‐level analysis revealed additional associations for deoxy‐xylulose synthase2 (dxs2), diphosphocytidyl methyl erythritol synthase2 (dmes2), cytidine methyl kinase1 (cmk1), and geranylgeranyl hydrogenase1 (ggh1), of which, dmes2, cmk1, and ggh1 have not previously been identified through maize association studies. Evaluation of prediction models incorporating genome‐wide markers and transcriptome‐wide abundances revealed a trait‐dependent benefit to the inclusion of both genomic and transcriptomic data over solely genomic data, but both transcriptome‐ and genome‐wide datasets outperformed a priori candidate gene‐targeted prediction models for most traits. Altogether, this study represents an important step toward understanding the role of regulatory variation in the accumulation of vitamins in fresh sweet corn kernels.

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Natural variation for carotenoids in fresh kernels is controlled by uncommon variants in sweet corn

Cited by 42 publications

References 80 publications

Zeaxanthin, a Molecule for Photoprotection in Many Different Environments

Zeaxanthin, a Molecule for Photoprotection in Many Different Environments

Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels

Transcriptome‐wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels

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