New cis-regulatory elements in the Rht-D1b locus region of wheat

Duan, Jialei; Wu, Jiajie; Liu, Yue; Xiao, Jianhui; Zhao, Guangyao; Gu, Yong–Qiang; Jia, Jizeng; Kong, Xiuying

doi:10.1007/s10142-012-0283-2

Cited by 13 publications

(4 citation statements)

References 49 publications

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“…The majority of the predicted amino acid sequences such as the C-terminal domain were highly conserved among these species with slightly variable lengths. Furthermore, we detected a CNS shared by all the surveyed grasses, which is in accordance with previous report [35]. …”

Section: Resultssupporting

confidence: 93%

“…The conservation of different CNSs could vary among plant species. The CNSs conserved among all the plant species, can be named as inter plant genome CNSs, while the CNSs conserved among the grass species can be regarded as inter grass genome CNSs [35,39]. The three CNSs reported in present study were conserved only among the three wheat subgenomes, so they were named as inter subgenome CNSs.…”

Section: Discussionmentioning

confidence: 80%

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Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

Kong

Shi

et al. 2013

PLoS ONE

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Hexaploid bread wheat contains A, B, and D three subgenomes with its well-characterized ancestral genomes existed at diploid and tetraploid levels, making the wheat act as a good model species for studying evolutionary genomic dynamics. Here, we performed intra- and inter-species comparative analyses of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known “green revolution” gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheat. The divergence of D genome between diploid and hexaploid is lower than those of A genome, suggesting that D genome diverged latter than others. The divergence among the A, B and D subgenomes was larger than that among different ploidy levels for each subgenome which mainly resulted from genomic structural variation of insertions and, perhaps deletions, of the repetitive sequences. Meanwhile, the repetitive sequences caused genome expansion further after the divergence of the three subgenomes. However, several conserved non-coding sequences were identified to be shared among the three subgenomes of wheat, suggesting that they may have played an important role to maintain the homolog of three subgenomes. This is a pilot study on evolutionary dynamics across the wheat ploids, subgenomes and differently related grasses. Our results gained new insights into evolutionary dynamics of Rht-1 region at sequence level as well as the evolution of wheat during the plolyploidization process.

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Section: Resultssupporting

confidence: 93%

Section: Discussionmentioning

confidence: 80%

Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

Kong

Shi

et al. 2013

PLoS ONE

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“…Our capture assay does not include repetitive regions so we could not precisely establish the borders of the deleted region. However, we were able to determine that this deletion occurs in a chromosomal region that is highly conserved among several Poaceae species (Duan et al 2012 ; Wilhelm et al 2013a ) and harbors at least nine annotated genes including wheat orthologs of TEOSINTE BRANCHED1 ( TB1 , TraesCS4B01G042700), a C3HC4-Type RING Finger (TraesCS4B01G042900) and Rht-B1 (TraesCS4B01G043100, Table 2 ). To identify which of these genes is causative for the increased height phenotype, it will be necessary to characterize independent knockout mutants for each of the deleted genes.…”

Section: Discussionmentioning

confidence: 99%

Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study

Howell

Vasquez-Gross

et al. 2017

Mol Genet Genomics

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Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.Electronic supplementary materialThe online version of this article (10.1007/s00438-017-1401-6) contains supplementary material, which is available to authorized users.

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“…A comparison to variants in Lolium perenne (Asp et al 2011) showed that INDELS in several different locations within intron 1 could modify Vrn1 expression. Additional examples include the identification of the bract suppression gene Trd1 , a GATA transcription factor, on barley 1H through fine mapping and anchoring of the phenotype to a syntenic region in rice (Houston et al 2012), the boron toxicity tolerance gene on barley 4H (Sutton et al 2007), the Rht-D1 gene region on 4D (Duan et al 2012), and the NAC transcription factor on wheat 6B (Distelfeld et al 2004, 2012). In the case of the NAC transcription factor, the functional attributes appeared to be quite different in rice and wheat (Distelfeld et al 2012) and indicated extrapolating function based on shared DNA sequence structure may not always be possible.…”

Section: Comparative Genomics Reveals Unique Features Of the Triticeamentioning

confidence: 99%

Integrating cereal genomics to support innovation in the Triticeae

Feuillet

Stein

Rossini

et al. 2012

Funct Integr Genomics

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The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.

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New cis-regulatory elements in the Rht-D1b locus region of wheat

Cited by 13 publications

References 49 publications

Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

Dynamic Evolution of Rht-1 Homologous Regions in Grass Genomes

Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study

Integrating cereal genomics to support innovation in the Triticeae

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