Identification of a functional transposon insertion in the maize domestication gene tb1

Studer, Anthony J.; Zhao, Qiong; Ross‐Ibarra, Jeffrey; Doebley, John

doi:10.1038/ng.942

Cited by 678 publications

(565 citation statements)

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“…Furthermore, the 11.0-kb insertion, which probably occurred after the ectopic recombination event, may have led to the creation of the functional black rice promoter of Kala4 (Figure 3). Several functional polymorphisms that cause regulatory alterations have been reported to produce domestication traits (Konishi et al, 2006;Studer et al, 2011;Meyer and Purugganan, 2013;Chakrabarti et al, 2013;Xu et al, 2015). In the case of teosinte branched 1 in maize, an insertion of a transposon called Hopscotch acts as an enhancer of gene expression and contributed to the change in apical dominance of maize upon domestication (Studer et al, 2011).…”

Section: The Structural Change In the Promoter Of Kala4 Confers The Bmentioning

confidence: 99%

The Birth of a Black Rice Gene and Its Local Spread by Introgression

et al. 2015

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The origin and spread of novel agronomic traits during crop domestication are complex events in plant evolution. Wild rice (Oryza rufipogon) has red grains due to the accumulation of proanthocyanidins, whereas most cultivated rice (Oryza sativa) varieties have white grains induced by a defective allele in the Rc basic helix-loop-helix (bHLH) gene. Although the events surrounding the origin and spread of black rice traits remain unknown, varieties with black grains due to anthocyanin accumulation are distributed in various locations throughout Asia. Here, we show that the black grain trait originated from ectopic expression of the Kala4 bHLH gene due to rearrangement in the promoter region. Both the Rc and Kala4 genes activate upstream flavonol biosynthesis genes, such as chalcone synthase and dihydroflavonol-4-reductase, and downstream genes, such as leucoanthocyanidin reductase and leucoanthocyanidin dioxygenase, to produce the respective specific pigments. Genome analysis of 21 black rice varieties as well as red-and white-grained landraces demonstrated that black rice arose in tropical japonica and its subsequent spread to the indica subspecies can be attributed to the causal alleles of Kala4. The relatively small size of genomic fragments of tropical japonica origin in some indica varieties indicates that refined introgression must have occurred by natural crossbreeding in the course of evolution of the black trait in rice.

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Section: The Structural Change In the Promoter Of Kala4 Confers The Bmentioning

confidence: 99%

The Birth of a Black Rice Gene and Its Local Spread by Introgression

et al. 2015

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“…Expression of the dominant maize Tb1 allele is about 2-fold greater than the recessive teosinte allele (Doebley et al, 1997;Hubbard et al, 2002, Studer et al, 2011. A critical regulatory region is located between 58.7 and 69.5 kb upstream of the Tb1 coding sequence (Clark et al, 2006).…”

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confidence: 99%

“…A critical regulatory region is located between 58.7 and 69.5 kb upstream of the Tb1 coding sequence (Clark et al, 2006). Recent evidence has shown that two transposable element insertions in this essential region of the Tb1 gene are responsible for elevated expression of the maize Tb1 allele (Studer et al, 2011;Zhou et al, 2011). In maize, plant architecture derives from two types of branches that affect its agronomic utility.…”

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confidence: 99%

“…the ear. The Tb1 gene is required for inhibiting outgrowth of both types of branches as well as initiating development of the female inflorescence (Doebley et al, 1997;Clark et al, 2006;Studer et al, 2011). Maize, which is a host of the parasitic plant, Striga spp., as well as an arbuscular mycorrhizae symbiont, produces at least two SLs (5-deoxy-strigol and sorghumol; Awad et al, 2006).…”

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Diverse Roles of Strigolactone Signaling in Maize Architecture and the Uncoupling of a Branching-Specific Subnetwork

et al. 2012

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Strigolactones (SLs) control lateral branching in diverse species by regulating transcription factors orthologous to Teosinte branched1 (Tb1). In maize (Zea mays), however, selection for a strong central stalk during domestication is attributed primarily to the Tb1 locus, leaving the architectural roles of SLs unclear. To determine how this signaling network is altered in maize, we first examined effects of a knockout mutation in an essential SL biosynthetic gene that encodes CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8), then tested interactions between SL signaling and Tb1. Comparative genome analysis revealed that maize depends on a single CCD8 gene (ZmCCD8), unlike other panicoid grasses that have multiple CCD8 paralogs. Function of ZmCCD8 was confirmed by transgenic complementation of Arabidopsis (Arabidopsis thaliana) max4 (ccd8) and by phenotypic rescue of the maize mutant (zmccd8::Ds) using a synthetic SL (GR24). Analysis of the zmccd8 mutant revealed a modest increase in branching that contrasted with prominent pleiotropic changes that include (1) marked reduction in stem diameter, (2) reduced elongation of internodes (independent of carbon supply), and (3) a pronounced delay in development of the centrally important, nodal system of adventitious roots. Analysis of the tb1 zmccd8 double mutant revealed that Tb1 functions in an SL-independent subnetwork that is not required for the other diverse roles of SL in development. Our findings indicate that in maize, uncoupling of the Tb1 subnetwork from SL signaling has profoundly altered the balance between conserved roles of SLs in branching and diverse aspects of plant architecture.

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“…mays) from its wild ancestor, teosinte (Z. mays L. subsp. parviglumis), and there has been strong selection at this locus during maize domestication (30). The tb1 locus, on chromosome 1, interacts with another locus on chromosome 3 to affect the sexuality of the inflorescences (31), and the allelic state of the chromosome 3 gene has a dramatic impact on tb1 effect size.…”

Section: Epistasis Affects Domestication and Crop Improvement Traitsmentioning

confidence: 99%

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

Doust

Lukens

Olsen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Domestication is a multifaceted evolutionary process, involving changes in individual genes, genetic interactions, and emergent phenotypes. There has been extensive discussion of the phenotypic characteristics of plant domestication, and recent research has started to identify the specific genes and mutational mechanisms that control domestication traits. However, there is an apparent disconnect between the simple genetic architecture described for many crop domestication traits, which should facilitate rapid phenotypic change under selection, and the slow rate of change reported from the archeobotanical record. A possible explanation involves the middle ground between individual genetic changes and their expression during development, where gene-by-gene (epistatic) and gene-by-environment interactions can modify the expression of phenotypes and opportunities for selection. These aspects of genetic architecture have the potential to significantly slow the speed of phenotypic evolution during crop domestication and improvement. Here we examine whether epistatic and gene-byenvironment interactions have shaped how domestication traits have evolved. We review available evidence from the literature, and we analyze two domestication-related traits, shattering and flowering time, in a mapping population derived from a cross between domesticated foxtail millet and its wild progenitor. We find that compared with wild progenitor alleles, those favored during domestication often have large phenotypic effects and are relatively insensitive to genetic background and environmental effects. Consistent selection should thus be able to rapidly change traits during domestication. We conclude that if phenotypic evolution was slow during crop domestication, this is more likely due to cultural or historical factors than epistatic or environmental constraints.QTL | genotype-by-environment interactions | G × E | Setaria | domestication syndrome

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Identification of a functional transposon insertion in the maize domestication gene tb1

Cited by 678 publications

References 33 publications

The Birth of a Black Rice Gene and Its Local Spread by Introgression

The Birth of a Black Rice Gene and Its Local Spread by Introgression

Diverse Roles of Strigolactone Signaling in Maize Architecture and the Uncoupling of a Branching-Specific Subnetwork

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

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