A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole

Purple carrots can accumulate large quantities of anthocyanins in their roots and – in some genetic backgrounds-petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F 2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these “root pigmentation” regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis.Fil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute; Estados UnidosFil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; ArgentinaFil: Bolstan, Hamed. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute; Estados UnidosFil: Zhao, Yunyang. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute; Estados UnidosFil: Zhang, Jianhui. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute; Estados UnidosFil: Simon, Philipp W.. United States Department of Agriculture. Agricultural Research Service; Argentina. University of Wisconsin; Estados Unido

Identification of an SCPL gene controlling anthocyanin acylation in carrot (Daucus carota L.) root

Anthocyanins are natural health promoting pigments that can be produced in large quantities in some purple carrot cultivars. Decoration patterns of anthocyanins, such as acylation, can greatly influence their stability and biological properties and use in the food industry as nutraceuticals and natural colorants. Despite recent advances made toward understanding the genetic control of anthocyanin accumulation in purple carrot, the genetic mechanism controlling acylation of anthocyanin in carrot root have not been studied yet. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify the genetic factor conditioning the accumulation of non-acylated (Cy3XGG) versus acylated (Cy3XFGG and Cy3XSGG) cyanidin derivatives, in three carrot populations. Segregation and mapping analysis pointed to a single gene with dominant effect controlling anthocyanin acylation in the root, located in a 576kb region containing 29 predicted genes. Orthologous and phylogenetic analyses enabled the identification of a cluster of three SCPL-acyltransferases coding genes within this region. Comparative transcriptome analysis indicated that only one of these three genes, DcSCPL1, was always expressed in association with anthocyanin pigmentation in the root and was co-expressed with DcMYB7, a gene known to activate anthocyanin biosynthetic genes in carrot. DcSCPL1 sequence analysis, in root tissue containing a low level of acylated anthocyanins, demonstrated the presence of an insertion causing an abnormal splicing of the 3rd exon during mRNA editing, likely resulting in the production of a non-functional acyltransferase and explaining the reduced acylation phenotype. This study provides strong linkage-mapping and functional evidences for the candidacy of DcSCPL1 as a primary regulator of anthocyanin acylation in carrot storage root.Fil: Curaba, Julien. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Bostan, Hamed. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Departamento de Producción Agropecuaria. Cátedra de Horticultura y Floricultura; ArgentinaFil: Senalik, Douglas A.. United States Department of Agriculture. Agricultural Research Service; ArgentinaFil: Mengist, Molla Fentie. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Zhao, Yunyang. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados UnidosFil: Simon, Philipp W.. United States Department of Agriculture. Agricultural Research Service; ArgentinaFil: Iorizzo, Massimo. North Carolina State University. Department Of Food, Bioprocessing And Nutrition Sciences. Plants For Human Health Institute.; Estados Unido

A Cluster of MYB Transcription Factors Regulates Anthocyanin Biosynthesis in Carrot (Daucus carota L.) Root and Petiole

Purple carrots can accumulate large quantities of anthocyanins in their roots and –in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these “root pigmentation” regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis

Testing CMB Anomalies in E-mode Polarization with Current and Future Data

In this paper, we explore the power of the cosmic microwave background (CMB) polarization (E-mode) data to corroborate four potential anomalies in CMB temperature data: the lack of large angular-scale correlations, the alignment of the quadrupole and octupole (Q-O), the point-parity asymmetry, and the hemispherical power asymmetry. We use CMB simulations with noise representative of three experiments -- the Planck satellite, the Cosmology Large Angular Scale Surveyor (CLASS), and the LiteBIRD satellite -- to test how current and future data constrain the anomalies. We find the correlation coefficients $\rho$ between temperature and E-mode estimators to be less than $0.1$, except for the point-parity asymmetry ($\rho=0.17$ for cosmic-variance-limited simulations), confirming that E-modes provide a check on the anomalies that is largely independent of temperature data. Compared to Planck component-separated CMB data (SMICA), the putative LiteBIRD survey would reduce errors on E-mode anomaly estimators by factors of $\sim 3$ for hemispherical power asymmetry and point-parity asymmetry, and by $\sim 26$ for lack of large-scale correlation. The improvement in Q-O alignment is not obvious due to large cosmic variance, but we found the ability to pin down the estimator value will be improved by a factor $\gtrsim100$. Improvements with CLASS are intermediate to these.Comment: 23 pages, 15 figures, 6 table

CLASS Observations of Atmospheric Cloud Polarization at Millimeter Wavelengths

The dynamic atmosphere imposes challenges to ground-based cosmic microwave background observation, especially for measurements on large angular scales. The hydrometeors in the atmosphere, mostly in the form of clouds, scatter the ambient thermal radiation and are known to be the main linearly polarized source in the atmosphere. This scattering-induced polarization is significantly enhanced for ice clouds due to the alignment of ice crystals under gravity, which are also the most common clouds seen at the millimeter-astronomy sites at high altitudes. This work presents a multifrequency study of cloud polarization observed by the Cosmology Large Angular Scale Surveyor (CLASS) experiment on Cerro Toco in the Atacama Desert of northern Chile, from 2016 to 2022, at the frequency bands centered around 40, 90, 150, and 220 GHz. Using a machine-learning-assisted cloud classifier, we made connections between the transient polarized emission found in all four frequencies with the clouds imaged by monitoring cameras at the observing site. The polarization angles of the cloud events are found to be mostly $90^\circ$ from the local meridian, which is consistent with the presence of horizontally aligned ice crystals. The 90 and 150 GHz polarization data are consistent with a power law with a spectral index of $3.90\pm0.06$, while an excess/deficit of polarization amplitude is found at 40/220 GHz compared with a Rayleigh scattering spectrum. These results are consistent with Rayleigh-scattering-dominated cloud polarization, with possible effects from supercooled water absorption and/or Mie scattering from a population of large cloud particles that contribute to the 220 GHz polarization.Comment: 16 pages, 14 figures, submitted to Ap

Microwave Observations of Venus with CLASS

We report on the disk-averaged absolute brightness temperatures of Venus measured at four microwave frequency bands with the Cosmology Large Angular Scale Surveyor (CLASS). We measure temperatures of 432.3 $\pm$ 2.8 K, 355.6 $\pm$ 1.3 K, 317.9 $\pm$ 1.7 K, and 294.7 $\pm$ 1.9 K for frequency bands centered at 38.8, 93.7, 147.9, and 217.5 GHz, respectively. We do not observe any dependence of the measured brightness temperatures on solar illumination for all four frequency bands. A joint analysis of our measurements with lower frequency Very Large Array (VLA) observations suggests relatively warmer ($\sim$ 7 K higher) mean atmospheric temperatures and lower abundances of microwave continuum absorbers than those inferred from prior radio occultation measurements.Comment: 10 pages, 3 figures, published in PS

CLASS Angular Power Spectra and Map-Component Analysis for 40 GHz Observations through 2022

Measurement of the largest angular scale ($\ell < 30$) features of the cosmic microwave background (CMB) polarization is a powerful way to constrain the optical depth to reionization, $\tau$, and search for the signature of inflation through the detection of primordial $B$-modes. We present an analysis of maps covering nearly 75% of the sky made from the ground-based $40\,\mathrm{GHz}$ channel of the Cosmology Large Angular Scale Surveyor (CLASS) from August 2016 to May 2022. Using fast front-end polarization modulation from the Atacama Desert in Chile, we show this channel achieves higher sensitivity than the analogous frequencies from satellite measurements in the range $10 < \ell < 100$. After a final calibration adjustment, noise simulations show the CLASS linear (circular) polarization maps have a white noise level of $125 \,(130)\,\mathrm{\mu K\, arcmin}$. We measure the Galaxy-masked $EE$ and $BB$ spectra of diffuse synchrotron radiation and compare to space-based measurements at similar frequencies. In combination with external data, we expand measurements of the spatial variations of the synchrotron spectral energy density (SED) to include new regions of the sky and measure the faint diffuse SED in the harmonic domain. We place a new upper limit on a background of circular polarization in the range $5 < \ell < 125$ with the first bin showing $D_\ell < 0.023$ $\mathrm{\mu K^2_{CMB}}$ at 95% confidence. These results establish a new standard for recovery of the largest-scale CMB polarization from the ground and signal exciting possibilities when the higher sensitivity and higher frequency CLASS channels are included in the analysis.Comment: 36 pages, 24 figures, 6 tables. Submitted to The Astrophysical Journa

Two Year Cosmology Large Angular Scale Surveyor (CLASS) Observations: Long Timescale Stability Achieved with a Front-End Variable-delay Polarization Modulator at 40 GHz

The Cosmology Large Angular Scale Surveyor (CLASS) is a four-telescope array observing the largest angular scales ($2 \lesssim \ell \lesssim 200$) of the cosmic microwave background (CMB) polarization. These scales encode information about reionization and inflation during the early universe. The instrument stability necessary to observe these angular scales from the ground is achieved through the use of a variable-delay polarization modulator (VPM) as the first optical element in each of the CLASS telescopes. Here we develop a demodulation scheme used to extract the polarization timestreams from the CLASS data and apply this method to selected data from the first two years of observations by the 40 GHz CLASS telescope. These timestreams are used to measure the $1/f$ noise and temperature-to-polarization ($T\rightarrow P$) leakage present in the CLASS data. We find a median knee frequency for the pair-differenced demodulated linear polarization of 15.12 mHz and a $T\rightarrow P$ leakage of $<3.8\times10^{-4}$ (95\% confidence) across the focal plane. We examine the sources of $1/f$ noise present in the data and find the component of $1/f$ due to atmospheric precipitable water vapor (PWV) has an amplitude of $203 \pm 12 \mathrm{\mu K_{RJ}\sqrt{s}}$ for 1 mm of PWV when evaluated at 10 mHz; accounting for $\sim32\%$ of the $1/f$ noise in the central pixels of the focal plane. The low level of $T\rightarrow P$ leakage and $1/f$ noise achieved through the use of a front-end polarization modulator enables the observation of the largest scales of the CMB polarization from the ground by the CLASS telescopes.Comment: Submitted to Ap

The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids

Sulfoquinovose (SQ) is the anionic headgroup of the ubiquitous plant sulfolipid, sulfoquinovosyl diacylglycerol (SQDG). SQDG can undergo delipidation to give sulfoquinovosyl glycerol (SQGro) and further glycoside cleavage to give SQ, which can be metabolized through microbial sulfoglycolytic pathways. Exogenous SQDG metabolites are imported into bacteria through membrane spanning transporter proteins. The recently discovered sulfoglycolytic sulfoquinovose monooxygenase (sulfo-SMO) pathway in Agrobacterium tumefaciens features a periplasmic sulfoquinovosyl glycerol binding protein, SmoF, and an ATP-binding cassette (ABC) transporter. Here, we use X-ray crystallography, differential scanning fluorimetry and isothermal titration calorimetry to study SQ glycoside recognition by SmoF. This work reveals that in addition to SQGro, SmoF can also bind SQ, a simple methyl glycoside and even a short-chain SQDG analogue. Molecular recognition of these substrates is achieved through conserved interactions with the SQ-headgroup together with more plastic interactions with the aglycones. This suggests that the solute binding protein of A. tumefaciens, and related SQ-binding proteins from other sulfoglycolytic pathways, can provide their host organisms direct access to most of the SQ metabolites known to be produced by phototrophs