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Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0002-2017-4177
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Nordiska museet, Swedish Museum of Cultural History, Stockholm, Sweden; 3The Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.ORCID iD: 0000-0002-4654-5722
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0002-9850-5546
2017 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 18, article id 118Article in journal (Refereed) Published
Abstract [en]

Background

The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene.

Results

Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb.

Conclusions

The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.

Place, publisher, year, edition, pages
BioMed Central, 2017. Vol. 18, article id 118
Keywords [en]
Selective sweep, Grain protein content (GPC), Emmer, Durum, Domestication gene
National Category
Genetics Evolutionary Biology
Identifiers
URN: urn:nbn:se:liu:diva-144103DOI: 10.1186/s12863-017-0566-7ISI: 000418687000001OAI: oai:DiVA.org:liu-144103DiVA, id: diva2:1170914
Available from: 2018-01-05 Created: 2018-01-05 Last updated: 2019-08-02Bibliographically approved
In thesis
1. Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials
Open this publication in new window or tab >>Exploring Fennoscandian agricultural history through genetic analysis of aged crop materials
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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 17-19th 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 17th 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 previous study. By studying extant landrace materials of Mediterranean tetraploid wheat, it was found that the non-functional allele showed signs indicative of a selective sweep. This selection did not, however, appear to have occurred during domestication.

In conclusion, aged plant specimens from both museum and archaeological contexts could contribute greatly to our knowledge about historical cultivation, extending the investigated period into the mid 17th century. Subfossil and waterlogged archaeobotanical materials do contain endogenous DNA, suggesting that they are better suited for genetic analysis than charred ones, at least as far as cereals are concerned. There is potential for classifying archaeological Brassica remains using NGS, even though further optimisation of sample and library preparation may be necessary. And finally, despite NAM-B1 showing signs of selection it should not be considered a domestication gene in tetraploid wheat.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2018. p. 52
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1959
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:liu:diva-152569 (URN)10.3384/diss.diva-152569 (DOI)9789176851944 (ISBN)
Public defence
2018-12-19, Planck, Fysikhuset, Campus Valla, Linköping, 09:15 (English)
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Supervisors
Available from: 2018-11-07 Created: 2018-11-07 Last updated: 2019-08-02Bibliographically approved

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Lundström, MariaLeino, Matti W.Hagenblad, Jenny

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