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Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides).
BMC Plant Biol. 2017 Oct 27; 17(1):175.BP

Abstract

BACKGROUND

Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes.

RESULTS

We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat.

CONCLUSIONS

For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.

Authors+Show Affiliations

Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel.Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel.Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel.Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel.Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel. kashkush@bgu.ac.il.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29078757

Citation

Domb, Katherine, et al. "Transposable Elements Generate Population-specific Insertional Patterns and Allelic Variation in Genes of Wild Emmer Wheat (Triticum Turgidum Ssp. Dicoccoides)." BMC Plant Biology, vol. 17, no. 1, 2017, p. 175.
Domb K, Keidar D, Yaakov B, et al. Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides). BMC Plant Biol. 2017;17(1):175.
Domb, K., Keidar, D., Yaakov, B., Khasdan, V., & Kashkush, K. (2017). Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides). BMC Plant Biology, 17(1), 175. https://doi.org/10.1186/s12870-017-1134-z
Domb K, et al. Transposable Elements Generate Population-specific Insertional Patterns and Allelic Variation in Genes of Wild Emmer Wheat (Triticum Turgidum Ssp. Dicoccoides). BMC Plant Biol. 2017 Oct 27;17(1):175. PubMed PMID: 29078757.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides). AU - Domb,Katherine, AU - Keidar,Danielle, AU - Yaakov,Beery, AU - Khasdan,Vadim, AU - Kashkush,Khalil, Y1 - 2017/10/27/ PY - 2016/12/04/received PY - 2017/10/17/accepted PY - 2017/10/29/entrez PY - 2017/10/29/pubmed PY - 2018/6/6/medline KW - Copy number variation KW - Dicoccoides KW - Emmer wheat KW - Genetic variation KW - TE dynamics KW - Transposable elements SP - 175 EP - 175 JF - BMC plant biology JO - BMC Plant Biol. VL - 17 IS - 1 N2 - BACKGROUND: Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes. RESULTS: We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. CONCLUSIONS: For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/29078757/Transposable_elements_generate_population_specific_insertional_patterns_and_allelic_variation_in_genes_of_wild_emmer_wheat__Triticum_turgidum_ssp__dicoccoides__ L2 - https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1134-z DB - PRIME DP - Unbound Medicine ER -