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

Abstract

BackgroundWild 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.ResultsTwo 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-995) contains supplementary material, which is available to authorized users.

Genomics of crop wild relatives: expanding the gene pool for crop improvement

“…A number of unique transcripts were identified in the wild barley, and of the SNPs identified, the desert ecotype had a higher proportion of nonsynonymous SNPs. These data are a valuable genomic resource for barley genomics and barley breeding (Bedada et al ., ).…”

Thermal plasticity of the circadian clock is under nuclear and cytoplasmic control in wild barley

“…spontaneum) populations sampled from a wide adaptive niche across Israel (Hubner et al, 2009). Since its establishment, it has become a foundational resource for studying plant adaptation and evolution, including the investigation of populations' behaviour under different environments (Bedada et al, 2014;Galkin et al, 2018;Hübner et al, 2012;Hübner et al, 2013). The period length and amplitude of the circadian rhythms are two traits that were found to be correlated with temperature and soil organic matter at the collection sites, respectively (Dakhiya et al, 2017).…”

Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance

“…Transcriptomic analysis is an effective approach to identify drought stress related genes, pathways, and processes. The studies on molecular mechanisms of drought tolerance using transcriptomic analysis have been reported extensively in many plants [ 15 – 20 ], including wheat [ 21 ], wild emmer wheat [ 22 , 23 ] and wild barley [ 24 , 25 ]; however, little is known about the Tibetan hulless barley. Recently, Zeng et al demonstrated changes in the gene expression patterns of well-watered, water deficit, and final water recovery stages in hulless barley.…”