Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

Background: The amphiploid species Brassica napus (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types), 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results: Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions: The distribution of chloroplast haplotypes eliminates any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast haplotypes in B. napus and B. rapa accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within B. napus can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to B. napus occurred on more than one occasion, and involved different maternal genotypes

Who is sowing our seeds? A systematic review of the use of plant genetic resources in research

Collections of plant genetic resources managed by genebanks function to conserve the range of genetic diversity present in crop genepools. They can facilitate access to valuable allelic variation for both plant breeders and researchers who are able to request germplasm for use in crop improvement and both basic and applied scientific research. The direct impact of genebank collections is often unclear as downstream uses of germplasm samples may not be reported back to the genebank of origin. This study aims to systematically review scientific use of germplasm using the UK Vegetable Genebank (UKVGB) as a model. Between the years of 1980–2016, a total of 271 publications were identified as using UKVGB material. The frequency of publications and the international nature of use increased significantly over the time period studied. Accessions directly sourced from the UKVGB made up the majority of material used by researchers, but material from research-derived resources such as differential sets and core collections or diversity sets have also been used. Resistance to pests and diseases and genetic diversity were the main topics of study although germplasm was used to address a wide range of other research questions. Genebanks such as UKVGB provide an essential resource of allelic diversity in crop genepools which supports a diverse range of research projects. The utilisation of these plant genetic resources has increased over time, contributing to a substantial number of publications. Developments in sequencing technologies have no doubt played a part as larger numbers of accessions can be utilized in a single experiment, but the increase also no doubt reflects a greater interest in the use of allelic diversity to overcome challenges in crop improvement and research

Spontaneous gene flow from rapeseed (Brassica napus) to wild Brassica oleracea

Research on the environmental risks of gene flow from genetically modified (GM) crops to wild relatives has traditionally emphasized recipients yielding most hybrids. For GM rapeseed (Brassica napus), interest has centred on the ‘frequently hybridizing’ Brassica rapa over relatives such as Brassica oleracea, where spontaneous hybrids are unreported in the wild. In two sites, where rapeseed and wild B. oleracea grow together, we used flow cytometry and crop-specific microsatellite markers to identify one triploid F(1) hybrid, together with nine diploid and two near triploid introgressants. Given the newly discovered capacity for spontaneous introgression into B. oleracea, we then surveyed associated flora and fauna to evaluate the capacity of both recipients to harm cohabitant species with acknowledged conservational importance. Only B. oleracea occupies rich communities containing species afforded legislative protection; these include one rare micromoth species that feeds on B. oleracea and warrants further assessment. We conclude that increased attention should now focus on B. oleracea and similar species that yield few crop-hybrids, but possess scope to affect rare or endangered associates

Genetic diversity structure of western-type carrots

Abstract: 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 FST, 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

CarrotDiverse : understanding variation in a wild relative of carrot

Genebanks and other ex situ collections have a significant role in the conservation, management and use of crop genetic diversity, including that of crop wild relatives. Efficient management and use depends on insight into the patterning and distribution of genetic diversity as well as obtaining baseline information on phenotypic characters and traits. Wild carrot (Daucus carota L.) is the closest wild relative of cultivated carrot (Daucus carota L. subsp. sativus (Hoffm.) Arcang.), and is a potential source of useful traits for crop improvement. There are over 900 accessions of D. carota described as wild in European genebanks, however associated phenotypic and genotypic characterization data are sparse. The influence of environment on phenotype is also not well understood in this taxon, meaning that it is difficult to ascertain how data collected at different locations can be compiled and collated. We present initial results of CarrotDiverse, a collaborative project in which wild D. carota accessions are undergoing detailed phenotypic and morphological characterization in parallel at three sites of varying latitude across Europe located in Portugal, France and Sweden. This will allow us to understand which traits are affected by environmental variables. Basic phenotypic information is being collected on a further 150 accessions. Furthermore, resistance screening to Alternaria species and polyacetylene profiling will be included in the evaluation. A Genotyping by Sequencing approach will be used to generate knowledge about genetic background and trait associations. The project will result in a significant data set which will facilitate the use of crop wild relatives in carrot breeding and improvement

Towards better tasting and more nutritious carrots: Carotenoid and sugar content variation in carrot genetic resources

The genetic diversity present in crop species is crucial for crop improvement and consequently enables development of new, nutritious agricultural products. Seed collections held in genebanks facilitate access to this diversity and in the case of carrot (Daucus carota), they consist of material collected from across the world, permitting access to the diversity present in the whole genepool. However to date, no systematic evaluation of chemical composition has been made on this material. This study aimed to determine the available variation in carotenoid and sugar content in the roots of 118 carrot accessions in order to understand how the levels of these nutritious compounds vary across the global carrot genepool. The carotenoid and sugar content in root tissue was assessed. The total carotenoid content was related to root colour and ranged from 0 to 40 mg per 100 g fresh weight. Orange rooted European accessions were more carotenoid-rich than Asian accessions, and advanced cultivars contained on average 20% more carotenoids than older cultivated material (landraces). Sugar content varied from 5.1% to 13.6% and European and American materials contained on average 18% more total sugars than Asian accessions. Orange rooted advanced cultivars had a lower ratio of non-reducing to reducing sugars than landraces. The results obtained indicate that several accessions with elevated content of carotenoids and/or sugars exist in genebank collections. The results are of significance as they support more efficient utilisation of genebank material in breeding programmes which deliver novel cultivars with enhanced nutritional value. The occurrence of such a range of sugar and carotenoid contents supports the role of genebank collections as a source of diversity useful in the creation of novel and nutritionally improved cultivars

Farming Today

Charlotte Smith visits the Warwick Crop Centre to find out about work to increase vegetable yields, and quality, in the face of climate change and increasing pressures on food security. Currently the UK imports about 40% of the food consumed here, but a ComRes poll commissioned by Farming Today and BBC 1's Countryfile found that 88% of people said that the UK is too reliant on food from abroad