Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

Abstract

Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs. A total of 193 retrotransposon-derived genetic markers, mainly iPBS, were used to obtain a genetic linkage map from 94 F7 inbred recombinant lines derived from the cross between the cultivar Lupa and the wild ancestor L. culinaris subsp. orientalis. The genetic map included 136 markers located in eight linkage groups. Clusters of tightly linked retrotransposon-derived markers were detected in linkage groups LG1, LG2, and LG6, hence denoting a non-random genomic distribution. Phylogenetic analyses identified the LTR-RT families in which internal and LTR sequences are included. Ty3-gypsy elements were more frequent than Ty1-copia, mainly due to the high Ogre element frequency in lentil, as also occurs in other species of the tribe Vicieae. LTR and internal sequences were used to analyze in silico their distribution among the contigs of the lentil draft genome. Up to 8.8% of the lentil contigs evidenced the presence of at least one LTR-RT similar sequence. A statistical analysis suggested a non-random distribution of these elements within of the lentil genome. In most cases (between 97% and 72%, depending on the LTR-RT type) none of the internal sequences flanked by the LTR sequence pair was detected, suggesting that defective and non-autonomous LTR-RTs are very frequent in lentil. Results support that LTR-RTs are abundant and widespread throughout of the lentil genome and that they are a suitable source of genetic markers useful to carry out further genetic analyses.

Analysis of genetic variability in F2 interspecific hybrids of mung bean (Vigna radiata) using inter-retrotransposon amplified polymorphism marker system

“…This marker system is commonly used in plant genotyping, including sunflower (Basirnia et al 2016), potato (Sharma and Nandineni 2014), papaya (Rashid et al 2014), date palm (Mirani et al 2020), bamboo (Li et al 2020), and Bletilla Chinese herb (Guo et al 2018). In addition, molecular marker based retrotransposon demonstrated an extensive application in plant genetic mapping (Liang et al 2016;Monden et al 2015;Rey-Baños et al 2017), genetic diversity (Mirani et al 2020;Sormin et al 2021;Vuorinen et al 2018), cultivar identification (Kim et al 2012), and the evolutionary studies (Konovalov et al 2010).…”

Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species

“…Most of the gypsy elements are Ogre or Tekay and the copia types are of the SIRE lineage. Ogre elements are large (up to 25 kb) and abundant in legumes, especially those of the Vicieae tribe 18 . These repeats constitute a large portion of the missing 1.1 Gb in our original, predominantly short-read, CDC Redberry genome assembly (https://knowpulse.usask.ca/genome-assembly/Lc1.2).…”

Widening the genetic base of cultivated gene pool following introgression from wild Lens taxa

“…The candidate genes were associated with boron toxicity tolerance and flowering time to develop gene‐based markers for these traits. Among recent advances, 193 retrotransposon‐derived genetic markers were generated to obtain a linkage map from 94 RILs of cultivated and wild lentil cross (Rey‐Baños, de Miera, García, & de la Vega, ). Tightly linked markers from LG1, LG2 and LG6 of eight linkage groups were obtained.…”