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Swedish University of Agricultural Sciences (2014)

Genomic divergence in differentially adapted wild and domesticated barley

Bedada, Girma

Titre : Genomic divergence in differentially adapted wild and domesticated barley.

Auteur : Bedada, Girma

Université de soutenance : Swedish University of Agricultural Sciences

Grade : Doctor of Philosophy (PhD) 2014

Résumé
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.

Mots clés : hordeum ; barley ; wild plants ; genomes ; genetic variation ; drought tolerance ; adaptation ; gene expression ; wild barley ; Hordeum ; BARE ; genomic divergence ; transcriptome ; population structure ; drought tolerance ; adaptation ; Evolution Canyon ; transposable element ; targeted capture

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Page publiée le 6 novembre 2015, mise à jour le 17 juin 2017