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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Abstract
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 | ||||||||||
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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: | 2014:108 | ||||||||||
Number of Pages: | 77 | ||||||||||
Papers/manuscripts: |
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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 | ||||||||||
ISSN: | 1652-6880 | ||||||||||
Language: | English | ||||||||||
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 | ||||||||||
URN:NBN: | urn:nbn:se:slu:epsilon-e-2240 | ||||||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2240 | ||||||||||
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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