BACKGROUND: Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited. RESULTS: Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively. CONCLUSIONS: We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.
- MeSH
- celogenomová asociační studie * MeSH
- domestikace * MeSH
- Fagopyrum genetika metabolismus MeSH
- flavonoidy metabolismus MeSH
- genetická variace MeSH
- genetické techniky MeSH
- jednonukleotidový polymorfismus MeSH
- regulace genové exprese u rostlin MeSH
- šlechtění rostlin MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Čína MeSH
BACKGROUND: One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood. RESULTS: Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes. CONCLUSIONS: We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.
- MeSH
- CRISPR-Cas systémy MeSH
- DNA vazebné proteiny genetika MeSH
- domestikace * MeSH
- fylogeneze MeSH
- jaderné proteiny genetika MeSH
- lidé MeSH
- molekulární evoluce MeSH
- mozek MeSH
- multigenová rodina * MeSH
- myši inbrední C57BL MeSH
- myši knockoutované MeSH
- myši MeSH
- neurovývojové poruchy genetika MeSH
- placenta MeSH
- placentálové genetika MeSH
- poruchy autistického spektra genetika MeSH
- proteiny nervové tkáně genetika MeSH
- proteiny regulující apoptózu genetika MeSH
- těhotenství MeSH
- TOR serin-threoninkinasy genetika MeSH
- transkripční faktory genetika MeSH
- transpozibilní elementy DNA * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
- MeSH
- anotace sekvence MeSH
- Digitaria klasifikace genetika MeSH
- domestikace MeSH
- druhová specificita MeSH
- genetická variace MeSH
- genom rostlinný MeSH
- jedlá semena klasifikace genetika MeSH
- klimatické změny MeSH
- molekulární evoluce MeSH
- selekce (genetika) MeSH
- zemědělství metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Afrika MeSH
Broomcorn millet (Panicum miliaceum L.) is not one of the founder crops domesticated in Southwest Asia in the early Holocene, but was domesticated in northeast China by 6000 BC. In Europe, millet was reported in Early Neolithic contexts formed by 6000 BC, but recent radiocarbon dating of a dozen 'early' grains cast doubt on these claims. Archaeobotanical evidence reveals that millet was common in Europe from the 2nd millennium BC, when major societal and economic transformations took place in the Bronze Age. We conducted an extensive programme of AMS-dating of charred broomcorn millet grains from 75 prehistoric sites in Europe. Our Bayesian model reveals that millet cultivation began in Europe at the earliest during the sixteenth century BC, and spread rapidly during the fifteenth/fourteenth centuries BC. Broomcorn millet succeeds in exceptionally wide range of growing conditions and completes its lifecycle in less than three summer months. Offering an additional harvest and thus surplus food/fodder, it likely was a transformative innovation in European prehistoric agriculture previously based mainly on (winter) cropping of wheat and barley. We provide a new, high-resolution chronological framework for this key agricultural development that likely contributed to far-reaching changes in lifestyle in late 2nd millennium BC Europe.
- MeSH
- archeologie MeSH
- dějiny starověku MeSH
- domestikace MeSH
- proso růst a vývoj MeSH
- radioaktivní datování MeSH
- zemědělské plodiny růst a vývoj dějiny MeSH
- zemědělství dějiny MeSH
- Check Tag
- dějiny starověku MeSH
- Publikační typ
- časopisecké články MeSH
- historické články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
BACKGROUND: In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. RESULTS: We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed [Formula: see text] profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds. CONCLUSIONS: Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.
- MeSH
- chov metody MeSH
- domestikace MeSH
- fylogeneze MeSH
- fylogeografie metody MeSH
- genetická variace genetika MeSH
- genetické testování metody MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus genetika MeSH
- ovce genetika MeSH
- populační genetika metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Balkánský poloostrov MeSH
To elucidate the role of domestication, we used the impossible task paradigm to test Czechoslovakian Wolfdogs with a known proportion of 'wolfblood' in their DNA and, as a control group for our subjects, we used German shepherd dogs. We hypothesized that the difference between wolves and domestic dogs is based on genetics and modified by obedience; if so, the looking back performance of the subject should be linked to its proportion of wolf-genes. To prove that, we observed 73 Czechoslovakian Wolfdogs, and 27 German shepherd dogs, and analysed their human-directed gazing behaviour during our test. Our apparatus consisted of a glass container placed upside down over a small amount of food. The test proceeded with three solvable trials, in which the subject could obtain the food by manipulating the container, followed by an unsolvable one in which the container was fixed onto the board. Our results suggest that there is no significant correlation between the probability of looking back in Czechoslovakian Wolfdogs and their proportion of 'wolf blood'. However, the probability of looking back was higher in German Shepherd dogs than in Czechoslovakian Wolfdogs (odds ratio = 9.1). German Shepherd dogs showed not only a higher frequency of looking back, but also the duration of their looks was longer.
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisumsativum, P.abyssinicum) and wild (P.fulvum and P.elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P.sativum and P.elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
- MeSH
- acetyl-CoA-karboxylasa genetika MeSH
- alely * MeSH
- buněčné jádro genetika metabolismus MeSH
- cytoplazma genetika metabolismus MeSH
- domestikace MeSH
- fylogeneze MeSH
- hrách setý genetika metabolismus MeSH
- plastidy genetika metabolismus MeSH
- reprodukční izolace MeSH
- rostlinné proteiny genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
There is growing interest in the conservation and utilization of crop wild relatives (CWR) in international food security policy and research. Legumes play an important role in human health, sustainable food production, global food security, and the resilience of current agricultural systems. Pea belongs to the ancient set of cultivated plants of the Near East domestication center and remains an important crop today. Based on genome-wide analysis, P. fulvum was identified as a well-supported species, while the diversity of wild P. sativum subsp. elatius was structured into 5 partly geographically positioned clusters. We explored the spatial and environmental patterns of two progenitor species of domesticated pea in the Mediterranean Basin and in the Fertile Crescent in relation to the past and current climate. This study revealed that isolation by distance does not explain the genetic structure of P. sativum subsp. elatius in its westward expansion from its center of origin. The genetic diversity of wild pea may be driven by Miocene-Pliocene events, while the phylogenetic diversity centers may reflect Pleisto-Holocene climatic changes. These findings help set research and discussion priorities and provide geographical and ecological information for germplasm-collecting missions, as well as for the preservation of extant diversity in ex-situ collections.
- MeSH
- domestikace * MeSH
- fylogeneze MeSH
- fylogeografie * MeSH
- genetická variace * MeSH
- genomika MeSH
- hrách setý genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Střední východ MeSH
