14 Works

Georeferenced phylogenetic analysis of a global collection of wild and cultivated Citrullus species

Enoch Gbenato Achigan-Dako, Herve Degbey, Iago Hale & Frank Blattner
The geographical origin of watermelon (Citrullus lanatus) remains debated. While a first hypothesis suggests the center of origin to be west Africa, where a sister endemic species C. mucosospermus thrives, a second hypothesis suggests north-eastern Africa where the white-fleshed Sudanese Kordophan melon is cultivated. In this study, we infer biogeographical and haplotype genealogy for C. lanatus, C. mucosospermus, C. amarus, and C. colocynthis using non-coding cpDNA sequences (trnT-trnL and ndhF-rpl32 regions) from a global collection...

Data from: Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation

Marco Pellino, Diego Hojsgaard, Thomas Schmutzer, Uwe Scholz, Elvira Hörandl, Heiko Vogel & Timothy F. Sharbel
Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here we analyze genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of 5 genotypes of the Ranunculus auricomus complex, representing 3 sexual and 2 apomictic reproductive biotypes. The 5 sequence libraries were pooled and de novo assembly performed, and...

Data from: Relatedness severely impacts accuracy of marker- assisted selection for disease resistance in hybrid wheat

Jochen C. Reif, Yusheng Zhao, Manje Gowda, Tobias Würschum, C. Friedrich H. Longin, Thomas Miedaner, Erhard Ebmeyer, Ralf Schachschneider, Johannes Schacht, Jean-Pierre Martinant, Michael F. Mette & Ebrahim Kazmann
The accuracy of genomic selection depends on the relatedness between the members of the set in which marker effects are estimated based on evaluation data and the types for which performance is predicted. Here, we investigate the impact of relatedness on the performance of marker-assisted selection for fungal disease resistance in hybrid wheat. A large and diverse mapping population of 1,739 elite European winter wheat inbred lines and hybrids was evaluated for powdery mildew, leaf...

Haplotype-based genome-wide association increases the predictability of leaf rust (Puccinia triticina) resistance in wheat

Fang Liu, Yong Jiang, Yusheng Zhao, Albert W Schulthess & Jochen C Reif
Resistance breeding is crucial for a sustainable control of wheat leaf rust and SNP-based genome-wide association studies (GWAS) are widely used to dissect leaf rust resistance. Unfortunately, GWAS based on SNPs explained often only a small proportion of the genetic variation. We compared SNP-based GWAS with a method based on functional haplotypes (FH) considering epistasis in a comprehensive hybrid wheat mapping population composed of 133 parents plus their 1,574 hybrids and characterized with 626,245 high-quality...

Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci

Jonathan Brassac & Frank R. Blattner
Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger...

Data from: Islands and streams: clusters and gene flow in wild barley populations from the Levant

Sariel Hübner, Torsten Günther, Andrew Flavell, Eyal Fridman, Andreas Graner, Abraham Korol & Karl J. Schmid
The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter-mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analyzing a collection of 896...

Data from: Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis

Dijun Chen, Kerstin Neumann, Swetlana Friedel, Benjamin Kilian, Ming Chen, Thomas Altmann & Christian Klukas
Significantly improved crop varieties are urgently needed to feed the rapidly growing human population under changing climates. While genome sequence information and excellent genomic tools are in place for major crop species, the systematic quantification of phenotypic traits or components thereof in a high-throughput fashion remains an enormous challenge. In order to help bridge the genotype to phenotype gap, we developed a comprehensive framework for high-throughput phenotype data analysis in plants, which enables the extraction...

Cellular plasticity in response to suppression of storage proteins in the Brassica napus embryo

Hardy Rolletschek, Jörg Schwender, Christina König, Kent D. Chapman, Trevor Romsdahl, Christin Lorenz, Hans-Peter Braun, Peter Denolf, Katrien Van Audenhove, Eberhard Munz, Nicolas Heinzel, Stefan Ortleb, Twan Rutten, Sean McCorkle, Taras Borysyuk, André Guendel, Hai Shi, Michiel Vander Auwermeulen, Stephane Bourot & Ljudmilla Borisjuk
The trade-off between protein and oil storage in oilseed crops has been tested here in oilseed rape (Brassica napus) by analyzing the effect of suppressing key genes encoding protein storage products (napin, cruciferin). The phenotypic outcomes were assessed using nuclear magnetic resonance and mass spectrometry imaging, microscopy, transcriptomics, proteomics, metabolomics, lipidomics, immunological assays as well as by flux balance analysis. Surprisingly, the profile of storage products was only moderately changed in RNAi transgenics. However, embryonic...

Data from: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

José L. Blanco-Pastor, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar-Gutiérrez, Anna Maria Roschanski, Evelyn Willner, Klaus Dehmer, Matthew Hegarty, Hilde Muylle, Elisabeth Veeckman, Klaas Vandepoele, Tom Ruttink, Isabel Roldán-Ruiz, Stéphanie Manel & Jean-Paul Sampoux
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS...

Raw data for: Modes of grain number determination differentiate barely row-types

Venkatasubbbu Thirulogachandar, Ravi Koppolu & Thorsten Schnurbusch
Gaining knowledge on intrinsic interactions of various yield components is crucial to improve the yield potential in small grain cereals. It is well known in barley that increasing the grain number (GN) preponderantly improves their yield potential; however, the yield components determining GN and their association in barley row-types are less explored. In this study, we assessed different yield components like potential spikelet number (PSN), spikelet survival (SSL), spikelet number (SN), grain set (GS), and...

Data from: Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Nadine Bernhardt, Jonathan Brassac, Benjamin Kilian & Frank R. Blattner
Background: Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe’s evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. Results: The read data was used...

Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)

Nicolai M. Nürk, Simon Uribe-Convers, Berit Gehrke, David C. Tank & Frank R. Blattner
Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus...

Data from: A pre-Miocene Irano-Turanian cradle: origin and diversification of the species-rich monocot genus Gagea (Liliaceae)

Angela Peterson, Dörte Harpke, Jens Peterson, Alexander Harpke & Lorenzo Peruzzi
The Irano‐Turanian (IT) floristic region is considered an important centre of origin for many taxa. However, there is a lack of studies dealing with typical IT genera that also occur in neighbouring areas. The species-rich monocot genus Gagea Salisb. shows a centre of diversity in IT region and a distribution in adjacent regions, therefore representing a good study object to investigate spatial and temporal relationships among IT region and its neighbouring areas (East-Asia, Euro-Siberia, Himalaya,...

Data from: Mating system and environmental variation drive patterns of adaptation in Boechera spatifolia (Brassicaceae)

Kelsi A. Grogan, Timothy F. Sharbel, John K. McKay, John T. Lovell & Kelsi Grogan
Determining the relative contribution of population genetic processes to the distribution of natural variation is a major goal of evolutionary biology. Here, we take advantage of variation in mating system to test the hypothesis that local adaptation is constrained by asexual reproduction. We explored patterns of variation in ecological traits and genome-wide molecular markers in Boechera spatifolia (Brassicaceae), a species that contains both apomictic (asexual) and sexual individuals. Using a combination of quantitative genetics, neutral...

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