An improved protocol for carrot haploid and doubled haploid plant production using induced parthenogenesis and ovule excision in vitro

In this work, we describe an improved protocol for induced parthenogenesis and ovule culture of carrot (Daucus carota L.). The effects of pollination with parsley pollen and/or 2,4-dichlorophenoxyacetic acid (2,4-D) treatment on the stimulation of parthenogenesis were studied using heterozygous donor plants of 30 varieties and breeding populations of carrots. Isolated ovules, cultured in vitro, enlarged and developed embryos or calli. The application of 2,4-D on pollinated flowers stimulated callus development but did not increase the frequency of embryo development from ovules and, thus, was not useful for increasing the frequency of haploid plant recovery. The efficiency of embryo development was accession-dependent and varied from 0 to 24.29%. In optimized conditions, most accessions responded by embryo development exclusively. The highest frequency of embryo development was observed from ovules excised from ovaries 20–22 d after pollination with parsley pollen. Among several media used for ovule culture, 1/2-strength Murashige and Skoog medium with 0.06 μM indole-3-acetic acid (IAA) was the best. It allowed the production of embryos at a similar frequency as on the media supplemented with kinetin, gibberellic acid, putrescine, or thidiazuron, but restricted callus development. Most plants obtained were haploids and diploids derived from parthenogenesis, as evidenced by homozygosity at three independent loci based on isozyme and PCR analyses. In total, considering haploids and embryo-derived homozygous diploids together, 72.6% of regenerated plants were of gametic origin

Comparison of haploid and doubled haploid sugar beet clones in their ability to micropropagate and regenerate

Background: Haploid plant material is considered as recalcitrant to organogenesis, propagation, and maintenance in vitro. However, sugar beet ( Beta vulgaris L.) breeders utilizing doubled haploid (DH) technology in their breeding programs indicate that sugar beet haploids may be cultured in vitro as well as diploids. Thus in this paper the in vitro performance of haploid and the doubled haploid sugar beet of various origin was evaluated. The DHs were derived from haploids by diploidization and twelve such haploid and corresponding DH clone pairs were obtained thus the comparison included haploid and DH clones that had identical allelic composition and differed only in their ploidy level. Results: The genotypes differed in shoot morphology and susceptibility to blackening during culture in vitro, but no significant differences were observed between the haploids and DHs. The micropropagation rate was, on average, higher for the haploids than DHs. Viability of the midrib and petiole explants after a 6-week culture was highly genotype dependent, but not affected by explant ploidy level. However, regeneration efficiency depended on both the genotype and ploidy level. The explants of several haploids regenerated more frequently and developed more adventitious shoots than the corresponding DHs thus overall efficiency was higher for haploids. Conclusions: The results obtained indicate that most of the haploids used in the comparison performed similar to or even better than DHs. This suggests that sugar beet haploid material can be successfully used not only for the production of DHs, but also maintained in vitro and utilized in projects requiring haploid tissues as the source material

Efficient CRISPR/Cas9-based genome editing in carrot cells

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas9) is a powerful genome editing tool that has been widely adopted in model organisms recently, but has not been used in carrot—a model species for in vitro culture studies and an important health-promoting crop grown worldwide. In this study, for the first time, we report application of the CRISPR/Cas9 system for efficient targeted mutagenesis of the carrot genome. Multiplexing CRISPR/Cas9 vectors expressing two single-guide RNA (gRNAs) targeting the carrot flavanone-3-hydroxylase (F3H) gene were tested for blockage of the anthocyanin biosynthesis in a model purple-colored callus using Agrobacterium-mediated genetic transformation. This approach allowed fast and visual comparison of three codon-optimized Cas9 genes and revealed that the most efficient one in generating F3H mutants was the Arabidopsis codon-optimized AteCas9 gene with up to 90% efficiency. Knockout of F3H gene resulted in the discoloration of calli, validating the functional role of this gene in the anthocyanin biosynthesis in carrot as well as providing a visual marker for screening successfully edited events. Most resulting mutations were small Indels, but long chromosome fragment deletions of 116–119 nt were also generated with simultaneous cleavage mediated by two gRNAs. The results demonstrate successful site-directed mutagenesis in carrot with CRISPR/Cas9 and the usefulness of a model callus culture to validate genome editing systems. Given that the carrot genome has been sequenced recently, our timely study sheds light on the promising application of genome editing tools for boosting basic and translational research in this important vegetable crop

Agrobacterium rhizogenes-mediated transformation of Hypericum sinaicum L. for the development of hairy roots containing hypericin

Hypericum sinaicum L. is an endangered Egyptian medicinal plant of high importance due to the presence of naphthodianthrones (hypericins), which have photodynamic properties and pharmaceutical potential. We sought to assess H. sinaicum ability to develop hairy roots that could be cultured in contained conditions in vitro and used as a source for hypericin production. We used four A. rhizogenes strains differing in their plasmids and chromosomal backgrounds to inoculate excised H. sinaicum root, stem and leaf explants to induce hairy root development. Additionally, inoculum was applied to shoots held in Rockwool cubes supporting their stand after removal of the root system. All explant types were susceptible to A. rhizogenes although stem explants responded more frequently (over 90%) than other explant types. The A4 and A4T A. rhizogenes strains were highly, and equally effective in hairy root induction on 66-72% of explants while the LBA1334 strain was the most effective in transformation of shoots. Sonication applied to explants during inoculation enhanced the frequency of hairy root development, the most effective was 60 s treatment doubling the percentage of explants with hairy roots. However, shoot transformation was the most effective approach as shoots developed hairy roots within 10 days after inoculation. Molecular analyses confirmed that the established hairy root cultures in vitro were indeed obtained due to a horizontal gene transfer from bacteria. These cultures grew fast and the hypericin content in hairy roots was about two fold higher than in H. sinaicum plants as determined by HPLC

Effects of cultivation year and growing location on the phenolic profile of differently coloured carrot cultivars

Carrots (Daucus carota L.) are economically and nutritionally important crops that, apart from carotenoids, contain numerous phenolic compounds which are assumed to exert health beneficial effects. The total phenolic contents of fruits and vegetables are known to depend on cultivar and growing conditions; however, studies examining the variability of a collection of carrots comprising differently coloured cultivars are rare. Therefore, the objective of the present study was to investigate the phenolic compounds of ten differently coloured carrot cultivars considering the effects of three cultivation years at two growing locations. Although total phenolic contents varied in a wide range, both purple cultivars ‘Anthonina’ and ‘Deep Purple’ significantly exceeded those of yellow, orange, red, and uncoloured cultivars (P ≤ 0.05) with amounts from 4,113 to 11,737 mg [kg dry matter (DM)]-1. In contrast to the purple roots, the other generally were characterised by far lower polyphenol contents ranging from 33 to 1,369 mg (kg DM)-1. Interestingly, the values did not considerably vary within these cultivars. In the present study, contrary to cultivar specific effects, the infl uence of growing location was found to be rather weak, supposedly due to similar climatic conditions at both locations. Similarly, variation of phenolic contents from year-to-year was less pronounced. In conclusion, the selection of breeding material was found to be of utmost importance regarding the expression of polyphenols in differently coloured carrots

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

Intra-population genetic diversity of cultivated carrot (Daucus carota L.) assessed by analysis of microsatellite markers

Intra-population variation of 18 cultivated carrot (Daucus carota L. ssp. sativus) populations of diverse origins was evaluated using codominant microsatellite (SSR) markers. Using 27 genomic and EST-derived SSR markers, 253 alleles were identified with a mean 9.4 alleles per marker. Most of the alleles (60.5%) were rare i.e., with the frequency ≤ 0.05 while only 3.95% of alleles occurred with frequency > 0.6. EST-derived SSR markers were less polymorphic than genomic SSR markers. Differences in allele occurrence allowed 16 out of 18 populations to be assigned to either the Western or Asian carrot gene pools with high probability. Populations could be also discriminated due to the presence of private alleles (25.3% of all alleles). Most populations had excess of alleles in the homozygous state indicating their inbreeding, although heterozygous loci were common in F1 hybrids. Genetic diversity was due to allelic variation among plants within populations (62% of total variation) and between populations (38%). Accessions originating from continental Asia and Europe had more allelic variants and higher diversity than those from Japan and USA. Also, allelic richness and variability in landraces was higher than in F1 hybrids and open-pollinated cultivars

A protocol for sonication-assisted Agrobacterium rhizogenes-mediated transformation of haploid and diploid sugar beet (Beta vulgaris L.) explants

Hairy root cultures obtained after Agrobacterium rhizogenes-mediated genetic transformation can serve as a model system for studying plant metabolism and physiology, or can be utilized for the production of secondary metabolites. So far no efficient protocol of hairy root development in sugar beet has been publically released. In this work, two A. rhizogenes strains (A4T and LBA1334) carrying a binary vector pBIN-m-gfp5-ER or pCAMBIA1301 possessing gfp and uidA reporter genes were used to transform petiole explants of haploid and diploid sugar beet genotypes. Five treatment combinations of sonicated-assisted Agrobacterium-mediated transformation were compared. Hairy roots appeared on 0% to 54% of explants depending on the treatment combination used. The highest frequency was achieved when explants of a diploid genotype were sonicated for 15 s in the inoculum containing A. rhizogenes of OD600=0.5 and then co-cultured for three days. Using the same treatment combinations the explants of haploid genotypes developed hairy roots with the frequency ranging from 10% to 36%. Transformation efficiency was independent on the bacterial strain used. The results indicate that haploid sugar beet explants are amenable to transformation using A. rhizogenes, and that the efficiency of that process can be increased by applying short ultrasound treatment