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

Abstract

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 materialThe online version of this article (doi:10.1007/s11032-013-9979-9) contains supplementary material, which is available to authorized users.

DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland

“…The 906 DArT markers were also found to be useful in providing a complete picture of genetic diversity in the Miscanthus collection of 180 accessions. Overall, the average PIC (0.22) of the Miscanthus microarray DArT markers was found to be lower than that observed in other plant species where similar markers were developed, such as wheat (0.44) (Raman et al 2010), cassava (0.42) (Xia et al 2005), sorghum (0.41) (Mace et al 2008), and carrot (0.30) (Grzebelus et al 2014), but comparable to that observed in Asplenium fern (0.21) (James et al 2008), Lesquerella (0.21) (Von Mark et al 2013) and sugar beet (0.28) (Simko et al 2012). Around 25.5 % of the DArT markers exhibited a PIC value in the range of 0.40 and 0.50 and these markers might be considered particularly informative.…”

“…The DArT technology is very suitable for high-throughput work and has been determined to have clear advantages in time and cost aspects of genotyping, in that it allows simultaneously type hundreds or thousands loci in a single array without prior knowledge genome sequence. The DArT technology has been Simko et al 2012;Castillo et al 2013;Grzebelus et al 2014), but no information is available on Miscanthus till date. In the present study, the DArT platform for Miscanthus collection were found both acceptable and provided robust information about the genetic variation in this collection.…”

“…The distribution of these new developed DArT markers remains to be determined. However, we could speculate that these DArT markers will be distributed throughout the genome with marker density highly correlated with gene density, in light of the empirical data from many other organisms whose DArT system was applied more broadly including genetic mapping and/or sequence-based physical mapping Grzebelus et al 2014).…”

“…DArT provides means of simultaneous genotyping of hundreds to thousands of dominant DArT markers obtained from nucleotide polymorphisms within restriction enzyme recognition sites. Therefore, DArT can be applied to minor crops such as Miscanthus, due to its potential to accelerate gene discovery and initiate molecular breeding without prior sequence data information (Ovesná et al 2013;Grzebelus et al 2014).…”

Development and use of molecular markers: past and present

“…In recent years, DArT has assumed the status of highly reliable, robust and useful markers for analysis of genetic diversity, as well as genetic mapping using linkage or association studies both in a variety of model and non-model crops such as Eucalyptus Restriction digestion, ligation of adapters, end sequencing and sequence analysis Baird et al (2008) Specific-locus amplified fragment sequencing (SLAF-seq) Deep sequencing, Sequence alignment Sun et al (2013) pearl millet (Supriya et al, 2011), carrot (Grzebellus et al, 2014), barley (Lex et al, 2014), sugarcane (Aitken et al, 2014). Subtracted diversity array (SDA; Li et al, 2006) is an advancement over DArT incorporating the benefits of subtractive suppression hybridization (SSH) based microarray, in order to enrich the resulting data with polymorphic genomic DNA sequences.…”