Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus.

Zifeng Ouyang,Gisele Kanzana,Fan Wu,Yimeng Wang,Jiyu Zhang,Tiantian Ma

doi:10.3390/plants10050890

Abstract

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

Highlights

IntroductionTransposons, including retrotransposons or DNA transposons, are mobile genetic elements that are common in the genomes of eukaryotes [1]
The maximum Long terminal repeat (LTR)-reverse transcriptase (RT) was found on chromosome 2 (∼1.38%), and the minimum was observed on chromosome 4 (∼1.18%) (Figure S1)
We found that sequence of the LTR-RTs and the reverse primer located in the LTR regions of the flanking sequence by that is the main cause inserted of polymorphisms, is in LTR-RTs (Figure 2).inserted

Summary

Introduction

Transposons, including retrotransposons or DNA transposons, are mobile genetic elements that are common in the genomes of eukaryotes [1]. A single, open reading frame (ORF) in which Gag and Pol are fused is common to both Ty1-copia and Ty3-gypsy elements, many retroelements have an extra ORF with an unknown function [2]. Long terminal repeat (LTR) retrotransposons that possess two long terminal repeats are the most abundant group of transposons in plants [3], and they are abundant in species with large genomes [4]. LTR retrotransposons play key roles in plant phenotype variations and in the evolution of genome structure and function [5,6,7,8].

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