Molecular markers for the discrimination of Triticum turgidum L. subsp. dicoccum (Schrank ex Schübl.) Thell. and Triticum timopheevii (Zhuk.) Zhuk. subsp. timopheevii

Boscato, Paola; Carioni, Christian; Brandolini, Andrea; Sadori, Laura; Rottoli, Mauro

doi:10.1016/j.jas.2007.03.003

Cited by 14 publications

(9 citation statements)

References 29 publications

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“…Their prevalence in the archaeobotanical record in combination with them often being morphologically well-preserved has made them into attractive targets for genetic analyses. Genetic analyses of such materials have, however, produced mixed results (Boscato, et al, 2008;Bunning, et al, 2012;Oliveira, et al, 2012b;Bilgic, et al, 2016;Castillo, et al, 2016). Nistelberger, et al, (2016) evaluated charred materials of barley, grape, maize and rice using whole-genome sequencing with and without capture, which showed that the chances of successful analysis are exceptionally low and hardly worthwhile.…”

Section: Resultsmentioning

confidence: 99%

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Lundström

2018

Linköping Studies in Science and Technology. Dissertations

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Crop plants have undergone a multitude of genetic changes during and following their domestication. The spread of agriculture brought the crops to new geographic regions exposing them to new environments and selection pressures along the way. This gave rise to many local variants with traits favoured both by agricultural practices and the environment. Agriculture was introduced in Fennoscandia (Norway, Sweden, Finland and Denmark) around 4000 BC. The composition of the archaeobotanical record gives some clues as to which species were cultivated, but macroscale analyses rarely reach beyond that. Therefore, methods like genetic analysis are necessary to expand our knowledge about the history of crop cultivation. Under optimal conditions, DNA can survive in biological samples for several hundred thousand years. The preservation of plant specimens in the Fennoscandian climate has, however, rarely been explored. This thesis therefore attempts to dive deeper into the Fennoscandian cultivation history through genetic analyses of aged plant materials from both museum collections and archaeological sources. Cereal grains from a range of preservation conditions were evaluated to find which ones might be of interest for genetic investigations. Desiccated materials gave the highest success rates, in agreement with previous studies. Waterlogged materials appeared to contain small amounts of endogenous DNA, whereas genetic analysis of charred cereals failed completely in all samples. Population structure was investigated in 17-19 th century materials of both barley and rye from Sweden and Finland. Northern and southern populations of Finnish six-row barley were distinct from one another. In southern Sweden, genetic analysis suggested conserved population structure extending over 200 years. The genetic composition of rye also seemed mostly conserved, but rye did not show geographic population structure across the investigated region in Sweden and Finland. A long-standing question in Fennoscandian crop history has been the interpretation of historical written records mentioning Brassica (cole crops, turnips and mustards), as well as the species identity of archaeobotanical finds of Brassica seeds. Thus, Next Generation Sequencing (NGS) was applied to identify which Brassica types that were cultivated in 17 th century Kalmar, Sweden. The analysis corroborated morphological species classification in two of the investigated subfossil seeds, whereas no conclusions could be drawn from the remaining samples. The genome coverages were too low to allow subspecies identification. Wheat has been cultivated in Fennoscandia since the introduction of agriculture but has increased dramatically in importance over the last century. The functional allele of the wheat nutrition gene NAM-B1 was found to be particularly prominent in Fennoscandian wheats, likely associated with its effect on grain maturation time. Here the evolutionary history of NAM-B1 was investigated to see if it could truly be considered a domestication gene as suggested in a pr...

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Section: Resultsmentioning

confidence: 99%

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Lundström

2018

Linköping Studies in Science and Technology. Dissertations

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“…timopheevii , a marker must also give a null or diagnostic signal for the A genome, which diverged from the ancestor of the B and G genomes approximately 7 million years ago [9,10] and so also has extensive sequence similarity. Early studies indicated that the multicopy ribosomal DNA (rDNA) transcription units have features that enable the three genomes to be distinguished [11,12], and two polymerase chain reactions (PCRs) intended to be specific for the internal transcribed spacer of the G genome rDNA units were designed for identification of archaeological specimens [13]. However, one of these PCRs gave nonspecific amplification products with modern T .…”

Section: Introductionmentioning

confidence: 99%

A discriminatory test for the wheat B and G genomes reveals misclassified accessions of Triticum timopheevii and Triticum turgidum

2019

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The tetraploid wheat species Triticum turgidum and Triticum timopheevii are morphologically similar, and misidentification of material collected from the wild is possible. We compared published sequences for the Ppd-A1 , Ppd-B1 and Ppd-G1 genes from multiple accessions of T . turgidum and T . timopheevii and devised a set of four polymerase chain reactions (PCRs), two specific for Ppd-B1 and two for Ppd-G1 . We used these PCRs with 51 accessions of T . timopheevii and 20 of T . turgidum . Sixty of these accessions gave PCR products consistent with their taxon identifications, but the other eleven accessions gave anomalous results: ten accessions that were classified as T . turgidum were identified as T . timopheevii by the PCRs, and one T . timopheevii accession was typed as T . turgidum . We believe that these anomalies are not due to errors in the PCR tests because the results agree with a more comprehensive analysis of genome-wide single nucleotide polymorphisms, which similarly suggest that these eleven accessions have been misclassified. Our results therefore show that the accepted morphological tests for discrimination between T . turgidum and T . timopheevii might not be entirely robust, but that species identification can be made cheaply and quickly by PCRs directed at the Ppd-1 gene.

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“…Boscato et al (2008), in their quest to identify T. timopheevii from charred fossil remains, designed ribosomal internal transcribed spacer primers discriminating T. timopheevii and T. dicoccum but were unsuccessful in retrieving ancient DNA. We also applied this approach to modern timopheevii, but in vain.…”

Section: Introductionmentioning

confidence: 99%

Multiplex PCR effectively identifies tetraploid Triticum AABB – or AAGG-genome species

Tanno

Takeuchi

Akahori

et al. 2017

Plant Genet. Resour.

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We developed a multiplex PCR DNA marker for quick and easy identification of the AAGG-genome timopheevii lineage, including Triticum timopheevii, Triticum araraticum and hexaploid Triticum zhukovskyi (AAAmAmGG), and the AABB-genome emmer wheat lineage, including Triticum durum, Triticum dicoccum and Triticum dicoccoides. Distinguishing between tetraploid AAGG- and AABB-genome wheat species based on morphology is known to be difficult. This multiplex PCR system is based on the simultaneous PCR amplification of two chloroplast regions, matK and rbcL. The matK region molecularly distinguishes the two lineages, whereas the rbcL region is a positive control amplicon. We also examined whether the simple sequence repeat is a fixed mutation within species, using genetic resources in the collection of KOMUGI, Kyoto University, which comprises accessioned species collected across diverse geographical areas. The multiplex PCR marker distinguished AAGG from AABB species with complete accuracy.

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Molecular markers for the discrimination of Triticum turgidum L. subsp. dicoccum (Schrank ex Schübl.) Thell. and Triticum timopheevii (Zhuk.) Zhuk. subsp. timopheevii

Cited by 14 publications

References 29 publications

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials

A discriminatory test for the wheat B and G genomes reveals misclassified accessions of Triticum timopheevii and Triticum turgidum

Multiplex PCR effectively identifies tetraploid Triticum AABB – or AAGG-genome species

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