Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley

Molina-Cano, José Luis; Russell, Joanne; Moralejo, Marian; Escacena, José-Luis; Arias, G.; Powell, W.

doi:10.1007/s00122-004-1878-3

Cited by 72 publications

(55 citation statements)

References 25 publications

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“…An interesting corollary of this possibility is that each human expansion out of the range may have resulted in a domestication, leaving phylogeographic evidence. Evidence for independent expansions has been found for emmer (41,42) and could perhaps explain the distinctiveness of Ethiopian crops from European counterparts, such as in the case of barley (19). Alternatively, traits may have become fixed within the wild progenitor range, all in one location or in a piecemeal fashion throughout the range.…”

Section: Genetic Expectations In a Protractedmentioning

confidence: 98%

“…The third genetic approach has been phylogenetic. According to gene phylogenies, some crops, such as flax, show evidence of monophyly (17), whereas others, such as rice and barley, are polyphyletic (18,19). Similarly, allozymes have also been used to establish polyphyly in crops such as lentils (20,21).…”

mentioning

confidence: 99%

“…Although the genome-wide evidence has been interpreted as supporting single origins and the rapid-transition model, it has conflicted frequently with gene phylogeny evidence. Perhaps the most notable conflict is in the case of barley, for which there is a large body of evidence that suggests at least a diphyletic origin (19,28). This conflict has been the source of some confusion, and its cause has yet to be identified.…”

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confidence: 99%

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

Allaby

Fuller

Brown³

2008

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

246

166

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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

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Section: Genetic Expectations In a Protractedmentioning

confidence: 98%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

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

Allaby

Fuller

Brown³

2008

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

246

166

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“…Domestication is likely to be a protracted process (Tanno and Willcox, 2006;Fuller, 2007;Allaby et al, 2008) that occurred in multiple locations (Molina-Cano et al, 2005;Ö zkan et al, 2005). This process of domestication can be seen as a gradual succession of selection steps leading to the 'elite' crop cultivated nowadays.…”

Section: Molecular Evolution Of Grape Colourmentioning

confidence: 99%

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

et al. 2009

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Polymorphisms in the grape transcription factor family VvMybA are responsible for variation in anthocyanin content in the berries of cultivated grapevine (Vitis vinifera L. subsp. sativa). Previous study has shown that white grapes arose through the mutation of two adjacent genes: a retroelement insertion in VvMybA1 and a single-nucleotide polymorphism mutation in VvMybA2. The purpose of this study was to understand how these mutations emerged and affected genetic diversity at neighbouring sites and how they structured the genetic diversity of cultivated grapevines. We sequenced a total of 3225 bp of these genes in a core collection of genetic resources, and carried out empirical selection tests, phylogenetic-and coalescence-based demographic analyses. The insertion in the VvMybA1 promoter was shown to have occurred recently, after the mutation of VvMybA2, both mutations followed by a selective sweep. The mutational pattern for these colour genes is consistent with progressively relaxed selection from constrained ancestral coloured haplotypes to light coloured and finally white haplotypes. Dynamics of population size in the VvMybA genes showed an initial exponential growth, followed by population size stabilization. Most ancestral haplotypes are found in cultivars from western region, whereas recent haplotypes are essentially present in table cultivars from eastern regions where intense breeding practices may have replaced the original diversity. Finally, the emergence of the white allele was followed by a recent strong exponential growth, showing a very fast diffusion of the initial white allele.

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“…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). Genotyping of chloroplast microsatellite markers has also suggested that barley has been domesticated more than once, on each occasion in a different geographical region (10). Unlike wheat and other founder crops, the natural distribution of wild barley scattered widely from the Near East to Central Asia and the Tibetan Plateau (5,11,12).…”

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.

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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

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Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley

Cited by 72 publications

References 25 publications

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

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

Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.)

Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley

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