The Experts below are selected from a list of 183 Experts worldwide ranked by ideXlab platform
Benjamin Kilian - One of the best experts on this subject based on the ideXlab platform.
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A tiered approach to genome-wide association analysis for the adherence of hulls to the caryopsis of Barley seeds reveals footprints of selection
BMC Plant Biology, 2019Co-Authors: Celestine Wabila, Benjamin Kilian, Volodymyr Radchuk, Kerstin Neumann, Andreas GranerAbstract:Seeds of Domesticated Barley are grouped into two distinct types, which differ in morphology. Caryopses covered by adaxial (palea) and abaxial (lemma) hulls that tightly adhere to the pericarp at maturity give rise to hulled seeds whereas caryopses without adhering hulls give rise to naked seeds. The naked caryopsis character is an essential trait regarding the end use of Barley. To uncover the genetic basis of the trait, a genome-wide association study (GWAS) has been performed in a panel comprising 222 2-rowed and 303 6-rowed spring Barley landrace accessions. In addition to the well-described Nud locus on chromosome 7H, three novel loci showed strong associations with the trait: the first locus on 2H was specifically detected in 6-rowed accessions, the second locus on 3H was found in 2-rowed accessions from Eurasia and the third locus on 6H was revealed in 6-rowed accessions from Ethiopia. PCR analysis of naked accessions also confirmed the absence of a 17 kb region harboring the Nud gene on chromosome 7H for all but one naked accession. The latter was characterized by a slightly variant phenotype of the caryopsis. Our findings provide evidence of the pervasiveness of the 17 kb deletion in spring Barley from different geographic regions and at the same time reveal genomic footprints of selection in naked Barley, which follow both geographic and morphological patterns.
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Barley Domestication, Adaptation and Population Genomics
Compendium of Plant Genomes, 2018Co-Authors: Karl J. Schmid, Benjamin Kilian, Joanne RussellAbstract:Wild and cultivated Barley are characterized by a high level of genetic diversity and a pronounced geographic population structure. Numerous studies using a diversity of markers showed that the centre of diversity of both wild and cultivated Barley is in the Western part of the Fertile Crescent where the species was presumably Domesticated. Comparisons of geographic diversity patterns suggested additional centres of domestication, of which the Eastern part of the Fertile Crescent (Iran or Himalaya), are most strongly supported. In wild Barley, the geographic distribution of genetic and phenotypic diversity largely follows a neutral isolation by distance pattern, but common-garden experiments and environmental association studies indicate that local adaptation by natural selection also had a significant influence on these patterns but, so far no strong candidate genes for local adaptation were identified. Cultivated Barley landraces and elite material have a significantly reduced level of genetic diversity compared to wild Barley which also shows significant geographic differentiation and evidence for local adaptation. Several major domestication genes have already been cloned and patterns of diversity largely confirm the hypotheses that these genes were exposed to strong domestication-related selection that caused a reduction of diversity in these genes. Ex situ genebank collections of wild and Domesticated Barley were used to define core collections that have been phenotyped and genotyped to facilitate allele mining and introgression into elite varieties. The future utilization of Barley genetic diversity will be facilitated by a good reference genome. The rapid progress of sequencing technologies and modern breeding methods like genomic selection and genome editing will contribute to an efficient utilization of Barley genetic diversity.
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On the Origin of the Non-brittle Rachis Trait of Domesticated Einkorn Wheat.
Frontiers in Plant Science, 2018Co-Authors: Mohammad Pourkheirandish, Benjamin Kilian, Hiroyuki Kanamori, Shun Sakuma, Assaf Distelfeld, George Willcox, Taihachi Kawahara, Takashi Matsumoto, Takao KomatsudaAbstract:Einkorn and emmer wheat together with Barley were among the first cereals to be Domesticated by humans more than 10,000 years ago, long before durum or bread wheat originated. Domesticated einkorn wheat differs from its wild progenitor in basic morphological characters such as the grain dispersal system. Here, we identify the brittle rachis 1 (Btr1) and brittle rachis 2 (Btr2) in einkorn as homologous to Barley. We show that a single non-synonymous amino acid substitution (alanine to threonine) at position 119 at btr1, responsible for the non-brittle rachis trait in Domesticated einkorn. Tracing this haplotype variation back to wild einkorn samples provides further evidence that the einkorn progenitor came from the Northern Levant. We show that the geographical origin of Domesticated haplotype coincides with the non-brittle Domesticated Barley haplotypes which suggest the non-brittle rachis phenotypes of einkorn and Barley were fixed in same geographic area in today’s South-east Turkey.
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Natural diversity of inflorescence architecture traces cryptic domestication genes in Barley (Hordeum vulgare L.)
Genetic Resources and Crop Evolution, 2017Co-Authors: Helmy M. Youssef, Martin Mascher, Benjamin Kilian, Nils Stein, Mohammad A. Ayoub, Thorsten SchnurbuschAbstract:Many-grained mutants occurring spontaneously among their less well-endowed field mates may have appeared to early farmers as fortunate twists of fate foreboding wealth and abundance. In Domesticated Barley, the number of kernel rows in spike can be tripled by recessive mutant alleles at the Six - rowed spike 1 ( vrs1 ) locus that abolish the suppression of lateral spikelet fertility. In another Barley row-type, so called intermedium-spike ( int ), lateral floret size is often intermediate between six-and two-rowed types. Phenotypic and sequence analyses of our intermedium-spike collection revealed that other genes can increase the size of florets and even stimulate occasional grain setting in lateral spikelets. Here, we show that a complete six-rowed phenotype occurs in a diverse panel of intermedium-spike Barley carrying wildtype Vrs1 in the presence of the Int - c.a allele of the intermedium spike - c ( int - c ) gene, previously considered only as a modifier of lateral spikelet fertility. Int - c.a -type alleles had arisen before domestication and are associated with the enlargement of lateral florets in wild Barley, suggesting that natural selection/evolution acts towards reduced lateral floret size. Since Int - c.a cannot overcome the suppression of lateral florets in the genomic background of wild Barleys, we infer the existence of other gene loci, at which novel alleles or allelic combinations were selected for after domestication, to increase grain number of Barley independently of Vrs1 .
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Sequence diversification in recessive alleles of two host factor genes suggests adaptive selection for bymovirus resistance in cultivated Barley from East Asia
Theoretical and Applied Genetics, 2017Co-Authors: Ping Yang, Benjamin Kilian, Antje Habekuß, Bernhard J. Hofinger, Kostya Kanyuka, Andreas Graner, Frank Ordon, Nils SteinAbstract:Key message Two distinct patterns of sequence diversity for the recessive alleles of two host factors HvPDIL5 - 1 and HvEIF4E indicated the adaptive selection for bymovirus resistance in cultivated Barley from East Asia. Abstract Plant pathogens are constantly challenging plant fitness and driving resistance gene evolution in host species. Little is known about the evolution of sequence diversity in host recessive resistance genes that interact with plant viruses. Here, by combining previously published and newly generated targeted re-sequencing information, we systematically analyzed natural variation in a broad collection of wild ( Hordeum spontaneum ; Hs ) and Domesticated Barleys ( Hordeum vulgare ; Hv ) using the full-length coding sequence of the two host factor genes, HvPDIL5 - 1 and HvEIF4E , conferring recessive resistance to the agriculturally important Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV). Interestingly, two types of gene evolution conferred by sequence variation in Domesticated Barley, but not in wild Barley were observed. Whereas resistance-conferring alleles of HvEIF4E exclusively contained non-synonymous amino acid substitutions (including in-frame sequence deletions and insertions), loss-of-function alleles were predominantly responsible for the HvPDIL5 - 1 conferred bymovirus resistance. A strong correlation between the geographic origin and the frequency of Barley accessions carrying resistance-conferring alleles was evident for each of the two host factor genes, indicating adaptive selection for bymovirus resistance in cultivated Barley from East Asia.
Martin Mascher - One of the best experts on this subject based on the ideXlab platform.
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the contribution of cis and trans acting variants to gene regulation in wild and Domesticated Barley under cold stress and control conditions
Journal of Experimental Botany, 2020Co-Authors: Matthew Haas, Axel Himmelbach, Martin MascherAbstract:: Barley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans, termed the domestication syndrome. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changes resulting from domestication in Barley. We used RNA sequencing to examine allele-specific expression in hybrids between wild and Domesticated Barley. Our results show that most genes have conserved regulation. In contrast to studies of allele-specific expression in interspecific hybrids, we find almost a complete absence of trans effects. We also find that cis regulation is largely stable in response to short-term cold stress. Our study has practical implications for crop improvement using wild relatives. Genes regulated in cis are more likely to be expressed in a new genetic background at the same level as in their native background.
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Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley.
Molecular Biology and Evolution, 2019Co-Authors: Steven Dreissig, Martin Mascher, Stefan HeckmannAbstract:: Meiotic recombination generates genetic diversity upon which selection can act. Recombination rates are highly variable between species, populations, individuals, sexes, chromosomes, and chromosomal regions. The underlying mechanisms are controlled at the genetic and epigenetic level and show plasticity toward the environment. Environmental plasticity may be divided into short- and long-term responses. We estimated recombination rates in natural populations of wild Barley and Domesticated landraces using a population genetics approach. We analyzed recombination landscapes in wild Barley and Domesticated landraces at high resolution. In wild Barley, high recombination rates are found in more interstitial chromosome regions in contrast to distal chromosome regions in Domesticated Barley. Among subpopulations of wild Barley, natural variation in effective recombination rate is correlated with temperature, isothermality, and solar radiation in a nonlinear manner. A positive linear correlation was found between effective recombination rate and annual precipitation. We discuss our findings with respect to how the environment might shape effective recombination rates in natural populations. Higher recombination rates in wild Barley populations subjected to specific environmental conditions could be a means to maintain fitness in a strictly inbreeding species.
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linear modeling reveals a predominance of cis over trans regulatory effects in wild and Domesticated Barley
bioRxiv, 2019Co-Authors: Matthew Haas, Axel Himmelbach, Martin MascherAbstract:Barley, like other crops, has experienced a series of genetic changes that have 12 impacted its architecture and growth habit to suit the needs of humans, termed 13 the domestication syndrome. Domestication also resulted in a concomitant 14 bottleneck that reduced sequence diversity in genes and regulatory regions. Little 15 is known about regulatory changes resulting from domestication in Barley. We 16 used RNA-seq to examine allele-specific expression (ASE) in hybrids between wild 17 and Domesticated Barley. Our results show that most genes have conserved 18 regulation. In contrast to studies of allele specific expression in interspecific 19 hybrids, we find almost a complete absence of trans effects. We also find that cis 20 regulation is largely stable in response to short-term cold stress. Our study has 21 practical implications for crop improvement using wild relatives. Genes regulated 22 in cis are more likely to be expressed in a new genetic background at the same 23 level as in their native background. 24 Introduction 25
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The highly divergent Jekyll genes, required for sexual reproduction, are lineage specific for the related grass tribes Triticeae and Bromeae
Plant Journal, 2019Co-Authors: Volodymyr Radchuk, Martin Mascher, Nils Stein, Rajiv Sharma, Elena Potokina, Ruslana Radchuk, Diana Weier, Eberhard Munz, Miriam Schreiber, Thomas WickerAbstract:: Phylogenetically related groups of species contain lineage-specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the Jekyll gene, required for sexual reproduction, exists in two much diverged allelic variants, Jek1 and Jek3. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. Jek3 has a similar expression as Jek1 and complements the Jek1 function in Jek1-deficient plants. Jek1 and Jek3 allelic variants were almost equally distributed in a collection of 485 wild and Domesticated Barley accessions. All Domesticated Barleys harboring the Jek1 allele belong to single haplotype J1-H1 indicating a genetic bottleneck during domestication. Domesticated Barleys harboring the Jek3 allele consisted of three haplotypes. Jekyll-like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non-invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the Jekyll function. The emergence of Jekyll suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the Jekyll genes as lineage-specific.
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Origin and evolution of qingke Barley in Tibet.
Nature Communications, 2018Co-Authors: Xingquan Zeng, Martin Mascher, Qijun Xu, Shuaicheng Li, Juhong ZhouAbstract:Tibetan Barley (Hordeum vulgare L., qingke) is the principal cereal cultivated on the Tibetan Plateau for at least 3,500 years, but its origin and domestication remain unclear. Here, based on deep-coverage whole-genome and published exome-capture resequencing data for a total of 437 accessions, we show that contemporary qingke is derived from eastern Domesticated Barley and it is introduced to southern Tibet most likely via north Pakistan, India, and Nepal between 4,500 and 3,500 years ago. The low genetic diversity of qingke suggests Tibet can be excluded as a center of origin or domestication for Barley. The rapid decrease in genetic diversity from eastern Domesticated Barley to qingke can be explained by a founder effect from 4,500 to 2,000 years ago. The haplotypes of the five key domestication genes of Barley support a feral or hybridization origin for Tibetan weedy Barley and reject the hypothesis of native Tibetan wild Barley.
Davide Bulgarelli - One of the best experts on this subject based on the ideXlab platform.
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structure and function of the bacterial root microbiota in wild and Domesticated Barley
Cell Host & Microbe, 2015Co-Authors: Davide Bulgarelli, Ruben Garridooter, Philipp C Munch, Aaron Weiman, Johannes Droge, Alice C Mchardy, Paul SchulzelefertAbstract:The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and Domesticated accessions of Barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the Barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of Barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the Barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.
Paul Schulzelefert - One of the best experts on this subject based on the ideXlab platform.
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structure and function of the bacterial root microbiota in wild and Domesticated Barley
Cell Host & Microbe, 2015Co-Authors: Davide Bulgarelli, Ruben Garridooter, Philipp C Munch, Aaron Weiman, Johannes Droge, Alice C Mchardy, Paul SchulzelefertAbstract:The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and Domesticated accessions of Barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the Barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of Barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the Barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.
Alice C Mchardy - One of the best experts on this subject based on the ideXlab platform.
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structure and function of the bacterial root microbiota in wild and Domesticated Barley
Cell Host & Microbe, 2015Co-Authors: Davide Bulgarelli, Ruben Garridooter, Philipp C Munch, Aaron Weiman, Johannes Droge, Alice C Mchardy, Paul SchulzelefertAbstract:The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and Domesticated accessions of Barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the Barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of Barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the Barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface.