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. 2018 Dec;16(12):2077-2087.
doi: 10.1111/pbi.12940. Epub 2018 Jun 13.

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

Bala Ani Akpinar  1 , Sezgi Biyiklioglu  1 , Burcu Alptekin  1 , Miroslava Havránková  2 , Jan Vrána  2 , Jaroslav Doležel  2 , Assaf Distelfeld  3 , Pilar Hernandez  4 ; IWGSC  5 ; Hikmet Budak  1
Affiliations

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

Bala Ani Akpinar et al. Plant Biotechnol J. 2018 Dec.

Abstract

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.

Keywords: chromosome sorting; comparative genomics; hexaploid wheat; next-generation sequencing; wild emmer wheat.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1
Distribution of repetitive elements in the A and B subgenomes. Repeat annotations of three chromosomes belonging to each subgenome were combined to assess the repetitive landscape of the subgenomes. DNA: DNA transposons; En‐SPM/CACTA, Harbinger, MuDR/Mutator, Tc1/Mariner and hobo/Activator are DNA transposon subfamilies, while long terminal repeats (LTR) elements and long and short interspersed elements (LINEs, SINEs) are retroelements.
Figure 2
Figure 2
Syntenic relationships of homeologous group 5 chromosomes with the Brachypodium genome, rice chromosome 3 (Os3) and sorghum chromosome 1 (Sb1). For simplicity, only chromosomes of interest are shown for rice and sorghum. Chromosome lengths for Brachypodium are relative to each other, while for rice and sorghum, chromosome lengths are arbitrary. Red asterisks highlight syntenic regions observed for Tdic5A but not Tdic5B.
Figure 3
Figure 3
Expression pattern of Autophagy‐related genes from hexaploid wheat. (a) Tissue and time‐zone specific expression of ATG genes. (b) The expression pattern of ATG genes in grain tissue and grain tissue layers. (c) The ATG expression pattern under heat and drought stresses. The expression is normalized to control.
See this image and copyright information in PMC

References

    1. Akpinar, B.A. and Budak, H. (2016) Dissecting miRNAs in wheat D genome progenitor, Aegilops tauschii. Front. Plant Sci. 7, 1–17. - PMC - PubMed
    1. Akpinar, B.A. , Lucas, S.J. , Vr, J. , Dole, J. and Budak, H. (2014) Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum). Plant Biotechnol. J. 13, 740–752. - PubMed
    1. Akpinar, B.A. , Kantar, M. and Budak, H. (2015a) Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct. Integr. Genomics, 15, 587–598. - PubMed
    1. Akpinar, B.A. , Yuce, M. , Lucas, S. , Vrána, J. , Burešová, V. , Doležel, J. and Budak, H. (2015b) Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci. Rep. 5, 10763. - PMC - PubMed
    1. Akpinar, B.A. , Lucas, S. and Budak, H. (2016) A large‐scale chromosome‐specific SNP discovery guideline. Funct. Integr. Genomics, 17, 97–105. - PubMed

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