Genome sequence of the progenitor of wheat A subgenome Triticum urartu

Ling, Hong‐Qing; Ma, Bin; Shi, Xiaoli; Liu, Hui; Dong, Lingli; Sun, Hua; Cao, Yinghao; Gao, Qiang; Zheng, Shusong; Li, Ye; Yu, Ying; Du, Huilong; Qi, Ming; Li, Yan; Lu, Hongwei; Yu, Hua; Cui, Yan; Wang, Ning; Chen, Chunlin; Wu, Huilan; Zhao, Yan; Zhang, Juncheng; Li, Yiwen; Zhou, Wenjuan; Zhang, Bairu; Hu, Wenqing; Eijk, Michiel J. T. van; Tang, Jinyu; Witsenboer, H.; Zhao, Shancen; Li, Zhensheng; Zhang, Aimin; Wang, Daowen; Liang, Chengzhi

doi:10.1038/s41586-018-0108-0

Cited by 371 publications

(324 citation statements)

References 72 publications

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“…An important goal for future research projects will be to infer when during evolution the expansion of some wheat MADS‐box gene subfamilies occurred. The evolutionary history of bread wheat is relatively well understood and the genomes of many of the descendants of the wheat ancestors have been sequenced (Jia et al ., ; Ling et al ., , ; Luo et al ., ; G. Zhao et al ., ). The genome sequences of pasta wheat and the closely related wild emmer have also been determined (Avni et al ., ; Maccaferri et al ., ).…”

Section: Discussionmentioning

confidence: 98%

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

et al. 2019

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Summary Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine‐tuning important traits is of great importance. MADS‐box genes are prime candidates for this, as they are involved in virtually all aspects of plant development. Here, we present a detailed overview of phylogeny and expression of 201 wheat MIKC‐type MADS‐box genes. Homoeolog retention is significantly above the average genome‐wide retention rate for wheat genes, indicating that many MIKC‐type homoeologs are functionally important and not redundant. Gene expression is generally in agreement with the expected subfamily‐specific expression pattern, indicating broad conservation of function of MIKC‐type genes during wheat evolution. We also found extensive expansion of some MIKC‐type subfamilies, especially those potentially involved in adaptation to different environmental conditions like flowering time genes. Duplications are especially prominent in distal telomeric regions. A number of MIKC‐type genes show novel expression patterns and respond, for example, to biotic stress, pointing towards neofunctionalization. We speculate that conserved, duplicated and neofunctionalized MIKC‐type genes may have played an important role in the adaptation of wheat to a diversity of conditions, hence contributing to the importance of wheat as a global staple food.

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Section: Discussionmentioning

confidence: 98%

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

et al. 2019

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“…To identify the similar sequences in common wheat and its relatives, the 161‐bp insertion in Q t was used as the query in Blast (basic local alignment search tool) searches of the genome databases of T. aestivum cv ‘Chinese Spring’ (International Wheat Genome Sequencing Consortium, ), T. turgidum ssp. dicoccoides (Emmer_v5.scaffolds) (Avni et al ., ), T. urartu (Ling et al ., ), Ae . speltoides (International Wheat Genome Sequencing Consortium, ) and A. tauschii (Luo et al ., ).…”

Section: Methodsmentioning

confidence: 99%

Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

et al. 2019

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Summary De‐domestication is a unique evolutionary process during which crops re‐acquire wild‐like traits to survive and persist in agricultural fields without the need for human cultivation. The re‐acquisition of seed dispersal mechanisms is crucial for crop de‐domestication. Common wheat is an important cereal crop worldwide. Tibetan semi‐wild wheat is a potential de‐domesticated common wheat subspecies. However, the crucial genes responsible for its brittle rachis trait have not been identified. Genetic mapping, functional analyses and phylogenetic analyses were completed to identify the gene associated with Qbr.sau‐5A, which is a major locus for the brittle rachis trait of Tibetan semi‐wild wheat. The cloned Qbr.sau‐5A gene is a new Q allele (Qt) with a 161‐bp transposon insertion in exon 5. Although Qt is expressed normally, its encoded peptide lacks some key features of the APETALA2 family. The abnormal functions of Qt in developing wheat spikes result in brittle rachises. Phylogenetic and genotyping analyses confirmed that Qt originated from Q in common wheat and is naturally distributed only in Tibetan semi‐wild wheat populations. The identification of Qt provides new evidence regarding the origin of Tibetan semi‐wild wheat, and new insights into the re‐acquisition of wild traits during crop de‐domestication.

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“…Multiple different wheat and wheat relative genome sequences have been published, including the genomes of the wild progenitors of hexaploid bread wheat: T. urartu (Ling et al ; Ling et al ), Aegilops tauschii (Jia et al ; Luo et al ; Zhao et al ; Zimin et al ) and T. turgidum ssp. dicoccoides (Avni et al ).…”

Section: Genomic Resources and Reference Sequencementioning

confidence: 99%

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

Haas

Schreiber

Mascher

2019

JIPB

107

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Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre‐dates the era of next‐generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole‐genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.

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Genome sequence of the progenitor of wheat A subgenome Triticum urartu

Cited by 371 publications

References 72 publications

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

Re‐acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de‐domestication

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

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