Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts

BMC Genomics

Karl J Schmid²  Eyal Fridman¹  Menachem Moshelion¹  Eyal Bdolach¹  Eyal Galkin¹  Thomas Müller²  Anna Westerbergh³  Girma Bedada³ 

[1] Institute of Plant Science and Genetics, The Hebrew University of Jerusalem, Rehovot, Israel;Institute for Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, D-70599 Stuttgart, Germany;Department of Plant Biology, Uppsala BioCenter, Linnean Centre of Plant Biology in Uppsala, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden

关键词: Genetic diversity;    Drought tolerance;    Transcriptome;    Hordeum spontaneum;   

Others  :  1092198
DOI  :  10.1186/1471-2164-15-995

 received in 2014-06-09, accepted in 2014-11-04,  发布年份 2014

【 摘 要 】

Background

Wild barley is adapted to highly diverse environments throughout its geographical distribution range. Transcriptome sequencing of differentially adapted wild barley ecotypes from contrasting environments contributes to the identification of genes and genetic variation involved in abiotic stress tolerance and adaptation.

Results

Two differentially adapted wild barley ecotypes from desert (B1K2) and Mediterranean (B1K30) environments were analyzed for drought stress response under controlled conditions. The desert ecotype lost more water under both irrigation and drought, but exhibited higher relative water content (RWC) and better water use efficiency (WUE) than the coastal ecotype. We sequenced normalized cDNA libraries from drought-stressed leaves of both ecotypes with the 454 platform to identify drought-related transcripts. Over half million reads per ecotype were de novo assembled into 20,439 putative unique transcripts (PUTs) for B1K2, 21,494 for B1K30 and 28,720 for the joint assembly. Over 50% of PUTs of each ecotype were not shared with the other ecotype. Furthermore, 16% (3,245) of B1K2 and 17% (3,674) of B1K30 transcripts did not show orthologous sequence hits in the other wild barley ecotype and cultivated barley, and are candidates of ecotype-specific transcripts. Over 800 unique transcripts from each ecotype homologous to over 30 different stress-related genes were identified. We extracted 1,017 high quality SNPs that differentiated the two ecotypes. The genetic distance between the desert ecotype and cultivated barley was 1.9-fold higher than between the Mediterranean ecotype and cultivated barley. Moreover, the desert ecotype harbored a larger proportion of non-synonymous SNPs than the Mediterranean ecotype suggesting different demographic histories of these ecotypes.

Conclusions

The results indicate a strong physiological and genomic differentiation between the desert and Mediterranean wild barley ecotypes and a closer relationship of the Mediterranean to cultivated barley. A significant number of novel transcripts specific to wild barley were identified. The higher SNP density and larger proportion of SNPs with functional effects in the desert ecotype suggest different demographic histories and effects of natural selection in Mediterranean and desert wild barley. The data are a valuable genomic resource for an improved genome annotation, transcriptome studies of drought adaptation and a source of new genetic markers for future barley improvement.

【 授权许可】

   
2014 Bedada et al.; licensee BioMed Central Ltd.

【 图 表 】

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