A Phylogenetic Analysis Based on Nucleotide Sequence of a Marker Linked to the Brittle Rachis Locus Indicates a Diphyletic Origin of Barley

Azhaguvel, Perumal; Komatsuda, Takao

doi:10.1093/aob/mcm129

Cited by 73 publications

(59 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Extensive work has been devoted to establishing monophyly versus polyphyly with mixed results. Some gene phylogenies showed evidence of monophyly, such as in the case of flax (Allaby et al, 2005), while others indicated polyphyly as in the case of rice and barley (Londo et al, 2006, MolinaCano et al, 2005, Azguvel and Komatsuda 2007. However, the multiregionalism suggested by polyphyly still assumes a rapid process in which gene flow between nascent crop populations does not occur.…”

Section: Genetic Analysis Within the Rapid Transition Paradigmmentioning

confidence: 99%

“…In the case of the tough rachis mutation, most crops have a single underlying mutation responsible for the trait, with the notable exception of barley that has two (Takahashi 1972, Azguvel andKomatsuda 2007), seemingly supporting the rapid transition paradigm. However, the genetic expectation becomes quite different under the protracted transition paradigm, Fig.…”

Section: The Chronology Of Trait Fixationmentioning

confidence: 99%

See 1 more Smart Citation

Integrating the processes in the evolutionary system of domestication

Allaby

2010

Journal of Experimental Botany

View full text Add to dashboard Cite

Genetics has long been used as a source of evidence to understand domestication origins.A recent shift in the emphasis of archaeological evidence from a rapid transition paradigm of hunter-gatherers to agriculturalists to a protracted transition paradigm has highlighted how the scientific framework of interpretation of genetic data was quite dependent on archaeological evidence, resulting in a period of discord in which the two evidence types appeared to support different paradigms. Further examination showed that the discriminatory power of the approaches employed in genetics was low, and framed within the rapid paradigm rather than testing it. In order to interpret genetic data under the new protracted paradigm it must be taken into account how that paradigm changes our expectations of genetic diversity. Preliminary examination suggests that a number of features that constituted key evidences in the rapid paradigm are likely to be interpreted very differently in the protracted paradigm. Specifically, in the protracted transition the mode and mechanisms involved in the evolution of the domestication syndrome have become much more influential in the shape of genetic diversity. The result is that numerous factors interacting over several levels of organization in a domestication system need to be taken into account in order to understand the evolution of the process. This presents a complex problem of integration of different data types which is difficult to describe formally. One possible way forward is to use Bayesian Approximation approaches that allow complex systems to be measured in a way that does not require such formality.

show abstract

Section: Genetic Analysis Within the Rapid Transition Paradigmmentioning

confidence: 99%

Section: The Chronology Of Trait Fixationmentioning

confidence: 99%

Integrating the processes in the evolutionary system of domestication

Allaby

2010

Journal of Experimental Botany

View full text Add to dashboard Cite

show abstract

“…It is assumed that such mutations occur within cultivated crops because they would be rapidly removed through purifying selection from wild populations, and so independent domestications would select independent mutations. In many crops only one tough rachis mutant is known, supporting a single origin on this evidence, although barley is an unusual case in that two mutants are known (12,13). The second line of inquiry has considered the reduction in genetic diversity associated with the domestication bottleneck.…”

mentioning

confidence: 95%

The genetic expectations of a protracted model for the origins of domesticated crops

Allaby

Fuller

Brown³

2008

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

248

166

View full text Add to dashboard Cite

Until recently, domestication has been interpreted as a rapid process with little predomestication cultivation and a relatively rapid rise of the domestication syndrome. This interpretation has had a profound effect on the biological framework within which investigations into crop origins have been carried out. A major underlying assumption has been that artificial selection pressures were substantially stronger than natural selection pressures, resulting in genetic patterns of diversity that reflect genetic independence of geographic localities. Recent archaeobotanical evidence has overturned the notion of a rapid transition, resulting in a protracted model that undermines these assumptions. Conclusions of genome-wide multilocus studies remain problematic in their support of a rapid-transition model by indicating that domesticated crops appear to be associated by monophyly with only a single geographic locality. Simulations presented here resolve this conflict, indicating that the results observed in such studies are inevitable over time at a rate that is largely influenced by the long-term population size. Counterintuitively, multiple origin crops are shown to be more likely to produce monophyletic clades than crops of a single origin. Under the protracted transition, the importance of the rise of the domestication syndrome becomes paramount in producing the patterns of genetic diversity from which crop origins may be deduced. We identify four different interacting levels of organization that now need to be considered to track crop origins from modern genetic diversity, making crop origins a problem that could be addressed through system-based approaches.domestication ͉ phylogenetics ͉ protracted transition ͉ simulation

show abstract

“…Many reports indicate that cultivated barley was first domesticated about 10,000 y ago in the Near East Fertile Crescent (3,5). However, the debate on the monophyletic or polyphyletic origin of barley still remains contentious (1,(5)(6)(7)(8)(9). Morrell and Clegg, based on the resequencing data from 18 loci, proposed that barley has been domesticated at least twice, once in the Near East Fertile Crescent and then 1,500-3,000 km farther east (7).…”

mentioning

confidence: 99%

Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

Dai

Chen

Wang

et al. 2014

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

View full text Add to dashboard Cite

The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wildbarley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions.evolution | genetic diversity | genomic similarity | RNA-Seq | single nucleotide variants

show abstract

A Phylogenetic Analysis Based on Nucleotide Sequence of a Marker Linked to the Brittle Rachis Locus Indicates a Diphyletic Origin of Barley

Cited by 73 publications

References 23 publications

Integrating the processes in the evolutionary system of domestication

Integrating the processes in the evolutionary system of domestication

The genetic expectations of a protracted model for the origins of domesticated crops

Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

Contact Info

Product

Resources

About