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

Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

<p>Abstract</p> <p>Background</p> <p>The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs), will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels.</p> <p>Results</p> <p>Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F₂mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1%) were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F₂populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F₂, allowing the genetic mapping of 55 SSRs (38 codominant) onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs), with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 <it>D. carota </it>accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity.</p> <p>Conclusions</p> <p>The addition of 55 SSRs to the carrot map, together with marker characterizations in six other mapping populations, will facilitate future comparative mapping studies and integration of carrot maps. The markers developed herein will be a valuable resource for assisting breeding, genetic, diversity, and genomic studies of carrot and other Apiaceae.</p

Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber.</p> <p>Results</p> <p>A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The <it>in silico </it>PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.</p> <p>Conclusions</p> <p>The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.</p

High Temperature Alters Anthocyanin Concentration and Composition in Grape Berries of Malbec, Merlot, and Pinot Noir in a Cultivar-Dependent Manner

Climate is determinant for grapevine geographical distribution, berry attributes, and wine quality. Due to climate change, a 2&ndash;4 &deg;C increase in mean diurnal temperature is predicted by the end of the century for the most important Argentine viticulture region. We hypothesize that such temperature increase will affect color intensity and other quality attributes of red grapes and wines. The present study investigated the effect of high temperature (HT) on anthocyanin concentration and composition, pH, and resveratrol and solids content in berries of three major wine-producing varieties during fruit ripening in two seasons. To this end, a structure that increased mean diurnal temperature by 1.5&ndash;2.0 &deg;C at berry sites, compared to Control (C) plants grown without such structure, was implemented in field grown vineyards of Malbec, Merlot, and Pinot Noir. Results revealed a cultivar-dependent response to HT conditions, with Malbec and Pinot Noir berries exhibiting significant decreases in total anthocyanin concentration (TAC) at veraison and harvest, respectively, while Merlot maintained an unaffected pigment content under HT. The decrease in TAC was associated with reduced levels of delphinidin, cyanidin, petunidin, peonidin, and malvidin glycosides, and increased ratios of acylated (AA)/non-acylated anthocyanins (NAA), suggesting pigment acylation as a possible stress-response mechanism for attenuating HT negative effects. Under HT, Pinot Noir, which does not produce AA, was the only cultivar with lower TAC at harvest (p &lt; 0.05). pH, resveratrol, and solids content were not affected by HT. Our results predict high, medium, and low plasticity with regard to color quality attributes for Malbec, Merlot, and Pinot Noir, respectively, in the context of climate change

Dataset on absorption spectra and bulb concentration of phenolic compounds that may interfere with onion pyruvate determinations

We present data on absorption spectra (400–540 nm) and concentration of phenolic compounds quercetin, myricetin, kaempferol, rutin, catechin, epicatechin gallate (ECG) and epigallocatechin gallate (EGCG), in yellow, red and white onions. These data are related to the article entitled “Variability in spectrophotometric pyruvate analyses for predicting onion pungency and nutraceutical value” (Beretta et al., 2017) [1]. Given the relevance of pyruvate determinations for estimating onion pungency and functional value, it is important to identify compounds that can interfere with pyruvate determinations when using two previously published analytical procedures, namely Schwimmer and Weston (1961) (SW) [2] and Anthon and Barret (2002) (AB) [3], which are based on spectrophotometry and light-absorbance at 420 nm and 515 nm, respectively. The data presented in this article are absorption spectra for 7 onion phenolic compounds in the range 400–540 nm, which include wavelengths used by the two pyruvate analytical methods (Schwimmer and Weston, 1961; Anthon and Barret, 2002) [2,3] that were compared in our reference article (Beretta et al., 2017) [1]. Additionally, bulb content data for these 7 phenolic compounds in onion cultivars and F2 progenies with different bulb color were included to allow further analyses

Diversidad genética para contenido de antocianos, carotenoides, fenoles y capacidad antioxidante en zanahorias de diferentes colores

Existen variedades de zanahorias de distintos colores que acumulan en sus raíces antocianos (ANT), dando lugar a tonalidades moradas, y diferentes pigmentos carotenoides, responsables de los colores naranja, amarillo y rojo. Estos pigmentos confieren -además del color de raíz- propiedades benéficas para la salud, siendo la capacidad antioxidante (CAOX) uno de los principales efectos nutracéuticos de esta hortaliza. Las zanahorias también acumulan en sus raíces otros compuestos fenólicos (CF) antioxidantes (diferentes a los ANT). A los fines del mejoramiento genético, es importante conocer la contribución relativa de estos fitoquímicos en la CAOX de zanahorias, para definir prioridades de selección en los caracteres implicados en la CAOX. En este trabajo se caracterizaron 28 genotipos de zanahoria de diferente color de raíz (incluidas zanahorias de raíz blanca sin acumulación de pigmentos) para contenido de ANT y carotenoides (por HPLC), CF (por espectrofotometría) y CAOX (por ABTS, DPPH, FRAP y ORAC) en dos años de cultivo, y se investigaron correlaciones entre el contenido de los fitoquímicos y la CAOX. Se encontró variabilidad significativa (p<0.05) y substancial para todas las variables analizadas. Los valores más altos de CAOX se observaron en zanahorias moradas con alto contenido de ANT y CF, y los más bajos en zanahorias blancas. Estos resultados, sumados a valores altos de correlación (r=0.70-0.94, p<0.001) obtenidos entre el contenido de ANT y CF con la CAOX, sugieren que los antocianos y otros fenoles serían los principales aportantes a la CAOX de zanahorias.Fil: Carvajal, Sofia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Mauricci, M.. Universidad de Buenos Aires. Facultad de Agronomía; ArgentinaFil: Pérez, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Bannoud, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Agronomía; ArgentinaFil: Perez, F.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Cavagnaro, Fernando Pablo. 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; ArgentinaXLVIII Congreso Argentino de GenéticaCiudad Autónoma de Buenos AiresArgentinaSociedad Argentina de Genétic