Genetic diversity structure of western-type carrots

BACKGROUND

Carrot is a crop with a wide range of phenotypic and molecular diversity. Within cultivated carrots, the western gene pool comprises types characterized by different storage root morphology. First western carrot cultivars originated from broad-based populations. It was followed by intercrosses among plants representing early open-pollinated cultivars, combined with mass phenotypic selection for traits of interest. Selective breeding improved root uniformity and led to the development of a range of cultivars differing in root shape and size. Based on the root shape and the market use of cultivars, a dozen of market types have been distinguished. Despite their apparent phenotypic variability, several studies have suggested that western cultivated carrot germplasm was genetically non-structured.

RESULTS

Ninety-three DcS-ILP markers and 2354 SNP markers were used to evaluate the structure of genetic diversity in the collection of 78 western type open-pollinated carrot cultivars, each represented by five plants. The mean percentage of polymorphic loci segregating within a cultivar varied from 31.18 to 89.25% for DcS-ILP markers and from 45.11 to 91.29% for SNP markers, revealing high levels of intra-cultivar heterogeneity, in contrast to its apparent phenotypic stability. Average inbreeding coefficient for all cultivars was negative for both DcS-ILP and SNP, whereas the overall genetic differentiation across all market classes, as measured by F_ST, was comparable for both marker systems. For DcS-ILPs 90-92% of total genetic variation could be attributed to the differences within the inferred clusters, whereas for SNPs the values ranged between 91 to 93%. Discriminant Analysis of Principal Components enabled the separation of eight groups cultivars depending mostly on their market type affiliation. Three groups of cultivars, i.e. Amsterdam, Chantenay and Imperator, were characterized by high homogeneity regardless of the marker system used for genotyping.

CONCLUSIONS

Both marker systems used in the study enabled detection of substantial variation among carrot plants of different market types, therefore can be used in germplasm characterization and analysis of genome relationships. The presented results likely reveal the actual genetic diversity structure within the western carrot gene pool and point at possible discrepancies within the cultivars' passport data.

Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

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.

Genetic structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae)

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 first 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.

Microfabricated silicon microneedles for nonviral cutaneous gene delivery

BACKGROUND

The skin represents an accessible somatic tissue for therapeutic gene transfer. The superficial lipophilic layer of the skin, the stratum corneum, however, constitutes a major obstacle to the cutaneous delivery of charged macromolecules such as DNA.

OBJECTIVES

To determine whether silicon-based microneedles, microfabricated via a novel isotropic etching/BOSCH reaction process, could generate microchannels in the skin of sufficient dimensions to facilitate access of lipid : polycation : pDNA (LPD) nonviral gene therapy vectors.

METHODS

Scanning electron microscopy was used to visualize the microconduits created in heat-separated human epidermal sheets after application of the microneedles. Following confirmation of particle size and particle surface charge by photon correlation spectrocopy and microelectrophoresis, respectively, the diffusion of fluorescent polystyrene nanospheres and LPD complexes through heat-separated human epidermal sheets was determined in vitro using a Franz-type diffusion cell. In-vitro cell culture with quantification by flow cytometry was used to determine gene expression in human keratinocytes (HaCaT cells).

RESULTS

The diffusion of 100 nm diameter fluorescent polystyrene nanospheres, used as a readily quantifiable predictive model for LPD complexes, through epidermal sheets was significantly enhanced following membrane treatment with microneedles. The delivery of LPD complexes either into or through the membrane microchannels was also demonstrated. In both cases considerable interaction between the particles and the epidermal sheet was observed. In-vitro cell culture was used to confirm that LPD complexes mediated efficient reporter gene expression in human keratinocytes in culture when formulated at the appropriate surface charge.

CONCLUSIONS

These studies demonstrate the utility of silicon microneedles in cutaneous gene delivery. Further studies are required to elucidate fully the influence of the physicochemical characteristics of gene therapy vectors, e.g. particle diameter and surface charge, on their diffusion through microchannels and to quantify gene expression in vivo.