Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome

Abstract

We used quantitative real-time PCR analysis to measure the copy number of the BARE-1 retrotransposon in 5 cultivars of barley (Hordeum vulgare), as well as in samples from its wild relative, Hordeum spontaneum. Two sets of PCR primers were used to amplify regions within the long terminal repeat (LTR) and the reverse transcriptase (RT) gene of BARE-1 (GenBank accession Z17327). The LTR primers detected an average of 2.148 x 105 +/- 0.012 x 105 copies per haploid genome among barley samples, whereas the RT primers detected an average of 1.588 x 104 +/- 0.085 x 104 copies. The average ratio of LTR:RT was estimated to be 13.5:1. This finding indicates that more than 7% of the barley genome is occupied by BARE-1 elements in the form of solo LTRs and another 2.6% of the genome is occupied by the full-length element. Taken together, BARE-1 sequences represent approximately 9.6% of the barley genome among the barley plants used in this study. For the above estimation, a genome size of 5.44 x 103 Mb for H. vulgare and 5.39 x 103 Mb for H. spontaneum were assumed. Our study on quantification results of the BARE-1 for a small group of barley cultivars showed that there are significant differences among cultivars in terms of BARE-1 copy number, providing further evidence that BARE-1 is active and has a major role in shaping the barley genome as a result of breeding and selection. Quantification results also showed that most of the elements (> 90%) are present as truncated copies (solo LTRs). These results show that there is a high level of recombination leading to the formation of truncated elements and a subsequent DNA loss from the genome. Taken together, our study provides a glimpse into a dynamic micro-evolutionary process that is the by-product of genome reshuffling and directional selection in barley breeding programs.

Analysis of genetic diversity among tropical and subtropical maize inbred lines using SSR markers

“…Sun et al, (2001), the discrepancy between pedigree and molecular markersbased genetic diversity estimates may be caused by selection pressure for different breeding objectives. The results also revealed that pattern of grouping did not match well with available pedigree information which is in accordance with the results reported in oats (O'Donoughue et al, 1994), bread wheat (Barrett et al, 1998;Almanza-Pinzon et al, 2003, Soleimani et al, 2002. This analysis led to detection of 107 alleles (Table 2), with a mean of 2.55 alleles per locus.…”

Genome Size and the Role of Transposable Elements

“…One member of the family, the Bd2_RLC_14 element, is 20,769 years old and has 35 related solo LTRs. This is consistent with the high turnover seen for BARE elements in the Hordeum genome (Soleimani et al 2006;Vicient et al 1999b). Although the retrotransposon population of the genome, in evolutionary terms, has been removed rapidly, they are nevertheless continuing to propagate.…”

“…At the other extreme, cultivated barley has seven solo LTRs for every fulllength BARE element and wild barley (Hordeum vulgare ssp. spontaneum) and some other Hordeum species even higher ratios (Soleimani et al 2006;Vicient et al 1999b). The ratios for Hordeum reflect a relatively high turnover rate at least for BARE through solo LTR formation, despite the overall abundance of retrotransposons in the barley genome.…”

“…In barley, 12 families of retrotransposons account for almost 50 % of the 5.5 Gb genome (Wicker et al 2009), and overall the superfamily Gypsy is 1.5-fold more abundant than that of Copia (International Barley Genome Sequencing Consortium et al 2012). Among the related tribe Triticeae genomes, the BARE, WIS, and Angela families of superfamily Copia comprise more than 10 % of the genome (Kalendar et al 2000;Soleimani et al 2006;Vicient et al 1999a;Wicker et al 2009). Variation in the abundance of the BARE retrotransposon family is, moreover, sufficient to explain most of the difference in genome size between two Hordeum species (Vicient et al 1999b).…”

Analysis of plant diversity with retrotransposon-based molecular markers

“…In plants, the first time real-time PCR method was successfully used by Soleimani et al (2006) for quantification of BARE1 in five cultivars of barley (Hordeum vulgare) and two accessions of its wild relative, Hordeum spontaneum. Examining the LTR and reverse transcriptase domains revealed significant differences in BARE1 copy number among cultivars, providing further evidence that BARE1 is active and has a major role in shaping the barley genome as a result of breeding and selection.…”