TY - JOUR
T1 - Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species
AU - Ubi, Benjamin Ewa
AU - Gorafi, Yasir Serag Alnor
AU - Yaakov, Beery
AU - Monden, Yuki
AU - Kashkush, Khalil
AU - Tsujimoto, Hisashi
N1 - Publisher Copyright:
Copyright © 2022 Ubi, Gorafi, Yaakov, Monden, Kashkush and Tsujimoto.
PY - 2022/9/2
Y1 - 2022/9/2
N2 - Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of “full site” insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 “full sites,” respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.
AB - Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of “full site” insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 “full sites,” respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.
KW - DNA markers
KW - Dryland
KW - genome analysis
KW - mite
KW - transposable elements
KW - wheat
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U2 - 10.3389/fpls.2022.995586
DO - 10.3389/fpls.2022.995586
M3 - Article
AN - SCOPUS:85138158337
SN - 1664-462X
VL - 13
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 995586
ER -