Miniature Inverted Repeat Transposable Element Insertions Provide a Source of Intron Length Polymorphism Markers in the Carrot (Daucus carota L.)

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.

Mining for Candidate Genes Controlling Secondary Growth of the Carrot Storage Root

“…We set the number of assumed populations (K values) from 1 to 11 and the length of burn-in to 100,000 followed by 500,000 Monte Carlo iterations. The most likely number of clusters (K) was estimated as described by Stelmach et al [ 48 ]. To define the number of principal components needed to control population stratification, we performed Tracy–Widom statistics on PCA eigenvalues using ‘LEA‘ R package v.2.6.0 [ 49 ].…”

High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

“…Apart from SSRs, sequence-based markers developed in carrot can be exemplified with the works of Iorizzo et al [32] and Stelmach et al [33], where 4000 single nucleotide polymorphism (SNP) and 209 Intron Length Polymorphism (ILP) markers were developed, respectively. A hybridization-based genotyping strategy, DArT (Diversity Arrays Technology) genotyping, was also applied on carrot [34].…”

Comparative study of pine reference genomes reveals transposable element interconnected gene networks

“…Additionally, in the current study, MITE3321 insertions were found in both analyzed pine species, belonging to separate subgenera, suggesting similar distributions also in other pine species. Therefore, MITE3321 could be a useful molecular marker for genotyping of pine species, as shown for MITEs in other plant species [48,140,141].…”