Search

In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n = 2x = 24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of 5 interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding program or following transformation techniques.

Root-knot nematodes (Meloidogyne spp.) are major pests attacking carrots (Daucus carota) worldwide, causing galling and forking of the storage roots, rendering them unacceptable for market. Genetic resistance could significantly reduce the need for broad-spectrum soil fumigants in carrot production. In this study, genetic resistance to Meloidogyne incognita was mapped. Three diverse sources of resistance, from Syria (HM), Europe (SFF) and South America (Br1091), were identified. Two F2 mapping populations were developed using these parents, (Br1091 × HM1) and (SFF × HM2), as well as a segregating population derived from the self-pollination of a HM plant (HM3). Analysis revealed four QTLs conditioning resistance in Br1091 × HM1, three in SFF × HM2, and three in HM3. A consensus genetic map of the three populations revealed five non-overlapping QTLs for M. incognita resistance, one each on carrot chromosomes 1, 2, 4, 8, and 9. One QTL was present in all three populations, in the same region of chromosome 8 as Mj-1 which imparts resistance to M. javanica.

Plants have evolved strategies and mechanisms to detect and respond to pathogen attack. Different organs of the same plant may be subjected to different environments (e.g., aboveground versus belowground) and pathogens with different lifestyles. Accordingly, plants commonly need to tailor defense strategies in an organ-specific manner. Phytophthora infestans, causal agent of potato late blight disease, infects both aboveground foliage and belowground tubers. We examined the efficacy of transgene RB (known for conferring foliar late blight resistance) in defending against tuber late blight disease. Our results indicate that the presence of the transgene has a positive yet only marginally significant effect on tuber disease resistance on average. However, a significant association between transgene transcript levels and tuber resistance was established for specific transformed lines in an age-dependent manner, with higher transcript levels indicating enhanced tuber resistance. Thus, RB has potential to function in both foliage and tuber to impart late blight resistance. Our data suggest that organ-specific resistance might result directly from transcriptional regulation of the resistance gene itself.

Aims: To contribute to the understanding of phenomena related to different intensity electric current treatments on the growth and metabolism of selected micro-organisms using laboratory samples of pure and co-cultures (Saccharomyces cerevisiae strain 404 and Hanseniaspora guilliermondii strain 465). Methods and Results: Low electric current (10, 30, 50 and 100 mA) was applied to prepared samples. Parameters, such as polarity, treatment duration (18–48 h) and type of inoculum yeast, were varied one at a time to highlight their cause–effect relationships. The effects on cell activity as well as microflora viability were assessed. Bioindicators capable of describing the phenomena caused by the electric current on the microflora were identified. Conclusions: Results demonstrated that a low voltage treatment using graphite electrodes had a greater effect on the viable S. cerevisiae strain 404 microflora. There was less bactericidal activity in the S. cerevisiae strain 404 than in the H. guilliermondii strain 465. Significance and Impact of the Study: These results may be of significant importance in the development of new technological processes in the fields of agriculture and food, particularly new fermenting process controls.

Background Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. It belongs to a taxonomic group of wild potato species sexually isolated from cultivated potato. Consistent with genetic isolation, previous studies suggested that the genome of S. bulbocastanum (B genome) is structurally distinct from that of cultivated potato (A genome). However, the genome architecture of the species remains largely uncharacterized. The current study employed Diversity Arrays Technology (DArT) to generate a linkage map for S. bulbocastanum and compare its genome architecture with those of potato and tomato. Results Two S. bulbocastanum parental linkage maps comprising 458 and 138 DArT markers were constructed. The integrated map comprises 401 non-redundant markers distributed across 12 linkage groups for a total length of 645 cM. Sequencing and alignment of DArT clones to reference physical maps from tomato and cultivated potato allowed direct comparison of marker orders between species. A total of nine genomic segments informative in comparative genomic studies were identified. Seven genome rearrangements correspond to previously-reported structural changes that have occurred since the speciation of tomato and potato. We also identified two S. bulbocastanum genomic regions that differ from cultivated potato, suggesting possible chromosome divergence between Solanum A and B genomes. Conclusions The linkage map developed here is the first medium density map of S. bulbocastanum and will assist mapping of agronomical genes and QTLs. The structural comparison with potato and tomato physical maps is the first genome wide comparison between Solanum A and B genomes and establishes a foundation for further investigation of B genome-specific structural chromosome rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0123-6) contains supplementary material, which is available to authorized users.

Tintilia is an autochthonous grapevine of the Italian Molise region which risked to disappear. However, recently, the production of Tintilia red wines is resuming and in the year 2011 the protected designation origin ‘Tintilia del Molise’ was officially registered. In this work, an analytical characterization of representative red wines from Tintilia grape is reported. A total of 36 different physicochemical variables were determined and discussed, considering those with an estimated coefficient of variation

Campania region has always been considered one of the most appreciated Italian districts for wine production. Wine distinctiveness arises from their native grapevines. To better define the chemical profile of Campania autochthonous red grape varieties, we analysed the phenolic composition of Aglianico di Taurasi, Aglianico del Vulture, Aglianico del Taburno, Piedirosso wines, and a minor native variety, Lingua di Femmina in comparison with Merlot and Cabernet Sauvignon, as reference cultivars. A genetic profiling was also carried out using microsatellite molecular markers with high polymorphic and unambiguous profiles. Principal component analysis applied to 72 wines based on the 18 biochemical parameters, explained 77.6% of the total variance and highlighted important biological entities providing insightful patterns. Moreover, comparison of SSR-based data with phenylpropanoid molecules exhibited a statistically significant correlation. Our approach might be reasonably adopted for future characterisations and traceability of grapevines and corresponding wines.

Parmigiano Reggiano is a hard, cooked cheese produced in specific areas of Northern Italy. The raw material is obtained by mixing the partly skimmed evening milk and whole morning milk. The mixture is then heated to 22°C, and natural whey starter is added at 28–30 g/l after 1–2 min, bringing the pH of the mixture to 6·2–6·3. After coagulation, which takes ∼15 min and occurs at 32–33°C owing to the addition of calf rennet powder, the curd is broken up for 2–4 min, cut into fragments and cooked at a temperature raised gradually to 42–44°C and then more quickly to 55–56°C over 10–15 min. The curd is left undisturbed, covered by the whey, for 40–60 min, then removed and placed inside a circular wooden mould. The cheese is held at ∼20°C for 3 d during which it is turned at frequent intervals to facilitate complete whey drainage. The cheese, which now has its typical shape and size, is then salted by immersion in brine (260–280 g NaCl/l at 16–17°C) for 20–24 d. During this period the cheese absorbs 15–18 g NaCl/kg and its weight decreases by 4%. During the subsequent period of ripening (12–24 months) in store rooms at 16–18°C and 85% moisture, the cheese is frequently turned. At the end of ripening the cheese is cylindrical in shape, with a slightly convex side, 0·22–0·24 m high, 0·40–0·45 m diam. weighs 35–36 kg, has 320–330 g fat/kg dry matter and a minutely granulated internal structure with small holes formed by the activity of some heterofermentative lactic acid bacteria.

Carrot is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94 cultivated and 65 wild carrot accessions. The accessions were attributed to three separate groups: wild, Eastern cultivated and Western cultivated. Twenty-seven markers showing signatures for selection were identified. They showed a directional shift in frequency from the wild to the cultivated, likely reflecting diversifying selection imposed in the course of domestication. A genetic linkage map constructed using 188 F2 plants comprised 431 markers with an average distance of 1.1 cM, divided into nine linkage groups. Using previously anchored single nucleotide polymorphisms, the linkage groups were physically attributed to the nine carrot chromosomes. A cluster of markers mapping to chromosome 8 showed significant segregation distortion. Two of the 27 DArT markers with signatures for selection were segregating in the mapping population and were localized on chromosomes 2 and 6. Chromosome 2 was previously shown to carry the Vrn1 gene governing the biennial growth habit essential for cultivated carrot. The results reported here provide background for further research on the history of carrot domestication and identify genomic regions potentially important for modern carrot breeding. Electronic supplementary material The online version of this article (doi:10.1007/s11032-013-9979-9) contains supplementary material, which is available to authorized users.

Premise of the study: Analyses of genetic structure and phylogenetic relationships illuminate the origin and domestication of modern crops. Despite being an important worldwide vegetable, the genetic structure and domestication of carrot ( Daucus carota ) is poorly understood. We provide the fi rst such study using a large data set of molecular markers and accessions that are widely dispersed around the world.• Methods: Sequencing data from the carrot transcriptome were used to develop 4000 single nucleotide polymorphisms (SNPs). Eighty-four genotypes, including a geographically well-distributed subset of wild and cultivated carrots, were genotyped using the KASPar assay.• Key results: Analysis of allelic diversity of SNP data revealed no reduction of genetic diversity in cultivated vs. wild accessions. Structure and phylogenetic analysis indicated a clear separation between wild and cultivated accessions as well as between eastern and western cultivated carrot. Among the wild carrots, those from Central Asia were genetically most similar to cultivated accessions. Furthermore, we found that wild carrots from North America were most closely related to European wild accessions.• Conclusions: Comparing the genetic diversity of wild and cultivated accessions suggested the absence of a genetic bottleneck during carrot domestication. In conjunction with historical documents, our results suggest an origin of domesticated carrot in Central Asia. Wild carrots from North America were likely introduced as weeds with European colonization. These results provide answers to long-debated questions of carrot evolution and domestication and inform germplasm curators and breeders on genetic substructure of carrot genetic resources. Fil: Iorizzo, Massimo. University of Wisconsin. Department of Horticulture; Estados Unidos Fil: Senalik, Douglas A.. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department Of Agriculture. Agriculture Research Service; Vegetable Crops Research Unit; Estados Unidos Fil: Ellison, Shelby L.. University of Wisconsin. Department of Horticulture; Estados Unidos Fil: Grzebelus, Dariusz. University of Agriculture in Krakow. Department of Genetics, Plant Breeding and Seed Science; Polonia Fil: Cavagnaro, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mendoza; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Cuyo Mendoza-San Juan. Estación Experimental Agropecuaria La Consulta; Argentina Fil: Allender, Charlotte. University of Warwick. Warwick Crop Centre; Reino Unido Fil: Brunet, Johanne. United States Department Of Agriculture. Agriculture Research Service; Vegetable Crops Research Unit; Estados Unidos. University of Wisconsin. Department of Entomology; Estados Unidos Fil: Spooner, David M.. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department Of Agriculture. Agriculture Research Service; Vegetable Crops Research Unit; Estados Unidos Fil: Van Deynze, Allen. University of California. Seed Biotechnology Center ; Estados Unidos Fil: Simon, Phillip W.. University of Wisconsin. Department of Horticulture; Estados Unidos. United States Department Of Agriculture. Agriculture Research Service; Vegetable Crops Research Unit; Estados Unidos

Background Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

Background Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms. Results A de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations. Conclusions This study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources.

Background: 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. Results: Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping 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 F2 populations 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 D. carota accessions revealed a high level of polymorphism for these selected loci, with an average of 19 alleles/locus and 0.84 expected heterozygosity. Conclusions: 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 Fil: Cavagnaro, Pablo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Cuyo Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina Fil: Chung, Sang Min. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Dongguk University. Department of Life Science; Estados Unidos Fil: Manin, Sylvie. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture, Department of Horticulture; Turquía Fil: Yildiz, Mehtap. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Yuzuncu Yil University. Faculty of Agriculture. Department. of Horticulture; Corea del Sur Fil: Ali, Aamir. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Sargodha. Department of Biological Sciences; Pakistán Fil: Alessandro, María Soledad. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Mendoza-san Juan. Estación Experimental Agropecuaria la Consulta; Argentina Fil: Iorizzo, Massimo. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos Fil: Senalik, Douglas A.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados Unidos Fil: Simon, Philipp W.. University of Wisconsin-Madison. Department. of Horticulture; Estados Unidos. University of Wisconsin-Madison. Department of Horticulture. USDA-ARS. Vegetable Crops Unit; Estados Unidos

The effect of some phenolic compounds recurrent in wines on technological features of Oenococcus oeni was studied in order to individuate those strains to be utilized as starter in the deacidification of aged red wines. For this purpose, the growth and the L-malic acid metabolism of 100 O. oeni strains, previously isolated from different wines, was assayed in a synthetic medium added with ethanol, malic acid and phenol carboxylic (gallic, caffeic, p-coumaric and ferulic) acids or flavonoids (catechin and quercetin) at different concentrations. Results evidenced a different sensitivity of strains to each assayed compound. All the compounds restrained or stimulated the growth of 57 and 11 strains respectively, while no effect was detected on 6 strains. The remaining 26 strains showed a different behaviour: all were restrained by ferulic acid and stimulated by gallic acid and catechin. As for caffeic acid, 17 out of 26 strains were restrained, while 9 strains were stimulated. The main result obtained in this study was the establishment of a relationship between the effect of phenolic compounds on the O. oeni growth and the behaviour of the malolactic fermentation. This study may enrich the selection criteria of strains for the deacidification of aged red wines.

Aims: To better understand the outcome of employing low electric current (LEC) technology as a new preservation and alternative in wine technology, and to contribute to its development. It is used in industrial-scale winemaking with commercial yeast (Saccharomyces cerevisiae) during the grape must fermentation. Methods and Results: LEC (200 mA, time 16 days) was applied to fresh grape must as an alternative method to the usual sulfur dioxide addition used in the industrial process; two tanks, each 30 000 l, were employed for parallel fermentations. The results show that LEC decreased the survival time and increased the death rate of apiculate yeasts, whereas it did not affect the growth and survival of S. cerevisiae. A comparison was made of the main chemical and sensory parameters of the wines obtained. Conclusions: The results have demonstrated that the low-voltage treatment had a positive effect on the grape juice fermentation (yeast microflora) during the early stages of winemaking. Significance and Impact of the Study: These results could be of significant importance in developing, for ‘biological wine’, new winemaking technologies for an innovative control process of yeast fermentation.

Aims: To contribute to an understanding of the phenomena related to the effect of low electric current (LEC) in grape must fermentation during laboratory and pilot plant scale winemaking, with selected co-culture yeasts (Saccharomyces cerevisiae strain 404 and Hanseniaspora guilliermodii strain 465). Methods and Results: LEC (10, 30, 50 and 100 mA) was applied to fresh grape must as an alternative method to the usual addition of SO2. Parameters such as polarity, treatment duration (24–96 h) and type of inoculum yeast were varied one at a time. LEC decreased the survival time and increased the death rate of H. guilliermondii strain 465 in co-cultures, whereas it did not affect the growth and survival of S. cerevisiae strain 40. A final comparison was made of the main physico-chemical parameters on wine obtained after the different tests. Conclusions: The results have demonstrated that the low voltage treatment using a pair of graphite electrodes had a positive effect on grape juice fermentation (yeast microflora) during the early stages of winemaking, even with the potential of being an alternative method to the usual addition of SO2. Significance and Impact of the Study: These results could be of significant importance in developing new winemaking technologies for an innovative yeast fermentation control process for ‘biological wine’.

The aim of this work was to gain a comprehensive view of the microbiological char- acteristics of milk, natural whey starter, and cheese during the first months of ageing of Parmigiano Reggiano. A significant presence of different microbial groups in raw milk from the initial moments of production was rapidly substituted by various lactic acid bacteria. Natural whey starter contained a large number of thermophilic lactic acid bacteria ( Lactobacillus helveticus, L. delbrueckii ssp. lac- tis, L. delbrueckii ssp. bulgaricus) and some facultatively heterofermentative lactic acid bacteria belonging to L. rhamnosus. Thermophilic lactic acid bacteria disappeared within 30 d. Rod-shaped mesophilic facultatively heterofermentative lactic acid microflora, consisting of L. casei, L. paracasei ssp. paracasei, L. paracasei ssp. tolerans, L. rhamnosus and pediococci, progressively increased up to the fifth month of ageing. Results showed that thermophilic lactobacilli were derived from natural whey starter whereas Streptococcus thermophilusoriginated from raw milk. Further, natural whey starter was the source of L. rhamnosus which was present throughout the entire period of the cheese ageing. The other components of non-starter lactic acid microflora derived from raw milk.

Lactobacillus species (183 strains) isolated during the ripening of soppressata molisana, a typical fermented sausage from Molise, were characterized. Of these isolates the large majority (125 strains) was classified as Lactobacillus sake . Few strains were obligately heterofermentative and were identified as Lb. brevis . All strains were able to grow in the presence of 8% NaCl and a large majority was able to grow in the presence of 10% NaCl. No strains were able to hydrolyse pork fat at 18°C. Several isolates were H 2 O 2 and acetoin producers. Few strains were responsible for slime production. All the isolates also showed high resistance to nitrites.

One hundred and thirty-eight strains belonging toMicrococcusorStaphylococcusspecies isolated during the ripening of soppressata molisana, a traditional fermented sausage produced in Southern Italy, were characterized. Fifty-eight isolates belonged toMicrococcusspp. (with a predominance ofMicrococcus kristinae), 80 strains belonged toStaphylococcusspp. (with a predominance ofStaphylococcus xylosus). Nine percent of staphylococci were coagulase-positive and thermonuclease-negative. No strains ofStaphylococcus aureuswere isolated. All strains were able to grow in the presence of 10% NaCl; a large majority was able to reduce nitrates to nitrites both at 30 and 18°C. Forty-one percent of the micrococci and 16% of the staphylococci were able to hydrolyze pork fat at 30°C. In skim milk micrococci showed a higher proteolytic activity than staphylococci.

Cultivated carrot and its wild ancestor co-occur in most temperate regions of the world and can easily hybridize. The genetic basis of the process of domestication in carrot is not well understood. Recent results of an investigation on genetic diversity structure of cultivated and wild carrot and signatures for domestication using Diversity Arrays Technology (DArT) allowed identification of polymorphisms differentiating wild and cultivated accessions. We selected one of these polymorphisms, showing the strongest evidence for directional selection in the course of domestication, and converted it into a co-dominant cleaved amplified polymorphic site (CAPS) marker named cult. To achieve that, we designed site-specific primers anchored in sequences flanking the original DArT clone, amplified and sequenced the PCR products derived from cultivated and wild carrot. A PstI restriction site present in the 'cultivated' variant and absent in the 'wild' was subsequently used for routine differentiation the two variants. We validated the cult marker on 88 accessions of cultivated and wild carrot, each represented by five individuals. The allelic variant associated with the wild phenotype was only rarely observed in cultivated carrot, mostly in purple-rooted accessions originating Turkey and Iran, possibly indicating that the physical association between the diagnostic polymorphism and the putative 'domestication gene' has been broken in a group of Eastern carrots.

The microbiology of raw milk, traditionally-made Caciocavallo cheese from Molise was studied throughout ripening. Three different media (MRS agar, MRS agar at pH 5.4 and LBS) and four different incubation temperatures (15, 22, 28 and 45degreesC) were used for lactobacilli, and M17 agar and Slanetz & Bartley medium were used for cocci with the aim of obtaining a complete view of the evolution of these microbial groups. The overall microbiological quality of the product was quite satisfactory; enterobacteria were already absent at 36 h following shaping. High counts of lactic acid bacteria were found in the cheese through the 3 months of ripening. The microbial population present from day 1 of ripening consisted essentially of mesophilic lactic acid bacteria, predominantly lactobacilli, which gradually obtained the advantage over the thermophilic strains. The predominant species were as follows: Lactobacillus paracasei subsp. paracasei, Lb. pentosus, Lb. coryneformis subsp. torquens, Lb. plantarum and Lb. brevis together with Lb. casei, Lb. mali, Lb. rhamnosus, Lb. sakei and Lb. coryneformis subsp. coryneformis. The thermophilic lactic acid bacteria could be ascribed to Lactobacillus helveticus, Lb. delbrueckii subsp. bulgaricus, Lb. delbrueckii subsp. lactis and Lb. delbrueckii subsp. delbrueckii. Lactococci were either Lc. lactis subsp. lactis or Lc. plantarum and enterococci were E. faecalis or E. faecium.

Background Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Results Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color. All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped. Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin pigmentation is controlled by at least three genes, in contrast to monogenic control reported previously. Conclusions This study generated the first high resolution gene-derived SNP-based linkage map in the Apiaceae. Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for RTPE, largely condition anthocyanin accumulation in carrot roots and leaves. Loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1118) contains supplementary material, which is available to authorized users.

International audience; Carrot (Daucus carota ssp. sativus) production can be affected by a wide range of pests and pathogens. At least five diseases of carrot are caused by bacterial pathogens, 36 by fungal and oomycete pathogens, two by phytoplasmas, and 13 by viruses; and seven genera of nematodes and two genera of parasitic plants affect carrot. In addition, numerous insect and mite pests can cause losses. There have been extensive efforts to select carrot cultivars with partial or complete resistance to many of these pathogens and pests, and to identify wild species with resistance to specific biotic stresses for introgression into breeding populations and commercial cultivars. For some pathogens and pests, significant advances have been made at identifying resistance and mapping that resistance to the carrot genome. For others, resistance has been identified, but the genetic basis is yet to be determined. For a majority of these diverse stresses, however, there has been little success at identifying highly effective resistance and understanding the genetic basis of resistance. The diversity of stresses as well as interactions among these pests and pathogens can complicate efforts to develop cultivars with resistance to all key biotic stresses in a region that also meet market and consumer expectations. New approaches to identifying resistant material and speeding traditional breeding are being developed with molecular breeding tools, including simple sequence repeat markers and deep-coverage libraries of the carrot genome. These valuable genomic resources will enhance efforts to identify and breed for resistance to carrot pests and pathogens.