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Genomic divergence in differentially adapted wild and domesticated barley

Bedada, Girma (2014). Genomic divergence in differentially adapted wild and domesticated barley. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis Agriculturae Sueciae, 1652-6880 ; 2014:108
ISBN 978-91-576-8164-5
eISBN 978-91-576-8165-2
[Doctoral thesis]

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Genomic divergence is responsible for plant differential adaptation to diverse and contrasting environments and different biotic stresses. This thesis focuses on the analyses of the adaptive genomic divergence in wild and domesticated barley and the driving evolutionary forces, and to identify genes and genetic variation with signature of adaptive selection.

By applying genome scanning, transcriptome sequencing and customized target-enriched pool sequencing approaches, we found strong adaptive patterns of genomic divergence in wild barley across environmental gradients in Israel, which is about two-thirds of the variation found in samples from the whole species range. Hence, high level of population structure driven by natural selection and neutral evolutionary forces was observed at large and small geographical scales. Strong phenotypic and genomic differentiation was detected between wild barley ecotypes from the desert and Mediterranean environments. The desert ecotype had better water use efficiency and higher leaf relative water content. The majority of the transcripts were non-shared between the ecotypes and hence novel transcripts were identified. The genomic divergence was about 2-fold higher in the desert ecotype and it harbored more deleterious mutations than the Mediterranean ecotype, which is genetically closer to cultivated barley. Novel transcripts from the desert ecotype and genes differentially expressed in another drought-tolerant ecotype showed higher genomic divergence than the average genes. Using the targeted captured pooled sequencing, we identified genes and genetic variation with signature of selection in wild and Ethiopian cultivated barley genotypes. Ethiopian barley had high genomic divergence similar to wild barley, retained large proportion of ancestral variation, and showed low genomic differentiation from the wild ancestor.

Using the targeted sequence capturing method, we were able to detect known BARE retroelement insertions and further identify genome-wide novel insertions from pooled sequencing of wild and Ethiopian barley genotypes.

Authors/Creators:Bedada, Girma
Title:Genomic divergence in differentially adapted wild and domesticated barley
Series Name/Journal:Acta Universitatis Agriculturae Sueciae
Year of publishing :November 2014
Depositing date:24 November 2014
Number of Pages:77
I.Girma Bedada, Anna Westerbergh, Eviatar Nevo, Abraham Korol and Karl J Schmid (2014). DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel. Heredity 112, 646-655.
II.Girma Bedada, Anna Westerbergh, Thomas Mueller, Eyal Galkin, Eyal Bdolach, Menachem Moshelion, Eyal Fridman and Karl J Schmid (2014). Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts. BMC Genomics 2014, 15:995. DOI:10.1186/1471-2164-15- 995.
III.Girma Bedada, Anna Westerbergh, Ivan Barilar and Karl J Schmid. Targeted capture sequencing of selected genes in wild and domesticated barley populations adapted to diverse environments. Manuscript.
IV.Girma Bedada, Anna Westerbergh and Karl J Schmid. TE-Capture: Genome-wide enrichment and pooled sequencing uncover novel BARE insertions in diverse wild and domesticated barley. Manuscript.
Place of Publication:Uppsala
Publisher:Department of Plant Biology, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8164-5
ISBN for electronic version:978-91-576-8165-2
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:F Plant production > F30 Plant genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Agrovoc terms:hordeum, barley, wild plants, genomes, genetic variation, drought tolerance, adaptation, gene expression
Keywords:wild barley, Hordeum, BARE, genomic divergence, transcriptome, population structure, drought tolerance, adaptation, Evolution Canyon, transposable element, targeted capture
Permanent URL:
ID Code:11666
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Plant Biology (from 140101)
External funders:FORMAS
Deposited By: Girma Bedada
Deposited On:25 Nov 2014 15:01
Metadata Last Modified:02 Dec 2014 11:09

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