Abstract
The prevalence of non-autonomous class II transposable elements (TEs) in plant genomes may serve as a tool for relatively rapid and low-cost development of gene-associated molecular markers. Miniature inverted-repeat transposable element (MITE) copies inserted within introns can be exploited as potential intron length polymorphism (ILP) markers. ILPs can be detected by PCR with primers anchored in exon sequences flanking the target introns. Here, we designed primers for 209 DcSto (Daucus carota Stowaway-like) MITE insertion sites within introns along the carrot genome and validated them as candidate ILP markers in order to develop a set of markers for genotyping the carrot. As a proof of concept, 90 biallelic DcS-ILP markers were selected and used to assess genetic diversity of 27 accessions comprising wild Daucus carota and cultivated carrot of different root shape. The number of effective alleles was 1.56, mean polymorphism informative content was 0.27, while the average observed and expected heterozygosity was 0.24 and 0.34, respectively. Sixty-seven loci showed positive values of Wright's fixation index. Using Bayesian approach, two clusters comprising four wild and 23 cultivated accessions, respectively, were distinguished. Within the cultivated carrot gene pool, four subclusters representing accessions from Chantenay, Danvers, Imperator, and Paris Market types were revealed. It is the first molecular evidence for root-type associated diversity structure in western cultivated carrot. DcS-ILPs detected substantial genetic diversity among the studied accessions and, showing considerable discrimination power, may be exploited as a tool for germplasm characterization and analysis of genome relationships. The developed set of DcS-ILP markers is an easily accessible molecular marker genotyping system based on TE insertion polymorphism.
Highlights
Transposable elements (TEs) are segments of DNA that can move themselves to new chromosomal location
Insertion sites of 209 DcSto Miniature inverted-repeat transposable element (MITE) within introns of annotated genes were chosen to develop Daucus carota Stowawaylike Intron Length Polymorphism (DcS-intron length polymorphism (ILP)) markers evenly distributed throughout the genome (Figure 1)
Of the remaining 109 sites, six did not amplify efficiently; 32 were monomorphic for all tested plants; 13 showed a complex pattern resulting from nonspecific amplification, whereas 58 yielded polymorphic products not associated with DcSto insertions
Summary
Transposable elements (TEs) are segments of DNA that can move themselves to new chromosomal location They are prevalent in the genomes of both prokaryotes and eukaryotes, and account for a great subsection of the genetic variation in plants and animals. Miniature inverted-repeat transposable elements (MITEs) are a special type of class II non-autonomous elements with a maximum of a few hundred base pairs in size (Hua-Van et al, 2005). They were first discovered in plant genomes (Bureau and Wessler, 1992, 1994), they have been identified in a wide range of animal, eubacteria and archea genomes (Brügger et al, 2002; Feschotte et al, 2002). MITEs are usually present in many thousand copies per genome. 22,000 identified Stowaway MITEs were classified into 34 families in the Oryza sativa genome (Feschotte et al, 2003), whereas 18,000 MITE insertions were classified into 18 families in the Triticum spp. genome (Yaakov et al, 2013)
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