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

Dariusz Grzebelus,Shelby Ellison,Thomas Nothnagel,Massimo Iorizzo,Rafal Baranski,Philipp W Simon,Kasia Heller-Uszynska,Alicja Macko-Podgorni,Charlotte Allender,Andrzej Kilian,Douglas Senalik,Pablo Cavagnaro

doi:10.1007/s11032-013-9979-9

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.

Highlights

Carrot is one of the most important root vegetable crops grown worldwide, on more than one million hectares (FAOSTAT 2011)
As Diversity Arrays Technology (DArT) markers are dominant, two allelic states are distinguished but the effective number of alleles depending on the ratio of the signal presence and absence was Ae = 1.667
We developed and validated the first DArT genotyping platform for carrot comprising more than 7,000 DArT clones, of which ca. 1,000 produced high-quality nonredundant polymorphic signals in the diversity and/or mapping populations

Summary

Introduction

Carrot is one of the most important root vegetable crops grown worldwide, on more than one million hectares (FAOSTAT 2011). Recently has a more systematic approach towards developing such tools been carried out, resulting in a set of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers identified through sequencing of carrot bacterial artificial chromosome (BAC) ends (Cavagnaro et al 2009) and comparative analysis of three carrot transcriptomes (Iorizzo et al 2011). Both marker systems were subsequently used for analysis of genetic diversity of D. carota, corroborating an earlier hypothesis on carrot evolution formulated on the basis of morphological observations by Small (1978). A recent study based on D. carota plants of different origin genotyped with more than 3,300 SNP markers suggested that Central Asia is the center of origin of cultivated carrot, and that orange-rooted carrots of the Western type were selected from the yellow domesticated carrots (Iorizzo et al 2013a)

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Conclusion