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. 2020 Mar;18(3):732-742.
doi: 10.1111/pbi.13240. Epub 2019 Sep 18.

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Kewei Feng  1 , Licao Cui  1   2 , Le Wang  3 , Dai Shan  4 , Wei Tong  1 , Pingchuan Deng  1 , Zhaogui Yan  5 , Mengxing Wang  1 , Haoshuang Zhan  1 , Xiaotong Wu  1 , Weiming He  4 , Xianqiang Zhou  4 , Jingjing Ji  4 , Guiping Zhang  4 , Long Mao  6 , Miroslava Karafiátová  7 , Hana Šimková  7 , Jaroslav Doležel  7 , Xianghong Du  1 , Shancen Zhao  8 , Ming-Cheng Luo  3 , Dejun Han  1 , Chi Zhang  4 , Zhensheng Kang  9 , Rudi Appels  10 , David Edwards  11 , Xiaojun Nie  1 , Song Weining  1
Affiliations

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Kewei Feng et al. Plant Biotechnol J. 2020 Mar.

Abstract

Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication-related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.

Keywords: 7DL chromosome arm; BAC by BAC; domestication; gene loss; physical mapping; wheat.

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Conflict of interest statement

The authors declare that there is no conflict of interests.

Figures

Figure 1
Figure 1
Genomic features of 7DL pseudomolecule. (a) Distribution of ncRNAs. (b) Density of Gypsy. (c) Density of Copia. (d) Density of high‐confidence genes in 7DL. (e): Distribution of genetic markers.
Figure 2
Figure 2
Comparison of gene families of wheat 7DL and homologous regions of related species of the grass family. Green: Oryza sativa; Brown: Brachypodium distachyum; Yellow: Hordeum vulgare; Blue: wheat 7DL.
Figure 3
Figure 3
Dot plot of genome comparison between Ta7DL (horizontal axis) and Ae7D (vertical axis) chromosome.
Figure 4
Figure 4
KEGG enrichment of lost genes of 7DL in Ae. tauschii.
Figure 5
Figure 5
Location of putative QTLs and their close linked positively selective genes in 7DL pseudomolecule.
See this image and copyright information in PMC

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