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Transcriptome sequencing of wild and cultivated Cicer species

Identifiers: SRA: SRP136396
BioProject: PRJNA436616
Study Type: 
Other
Abstract: Drought is the single most important factor limiting crop production globally. While climate change is predicted to increase aridity indices, current increases in temperature accompanied by reduced and variable rainfall impose penalties on crop yield, rendering many communities vulnerable to famine. A reduction in genetic variation is a known consequence of early crop domestication, subsequent methodical selection and modern crop improvement. This is observed in chickpea, Cicer arietinum, an important grain legume predominantly cultivated under rain fed conditions in Southern Asia and Sub Saharan Africa. Elite chickpea cultivars are depauperate of genetic variation, limiting the extent of further genetic improvement for drought tolerance via conventional breeding. Conversely, the crop's wild progenitor, Cicer reticulatum has over 100-fold genetic variation with its ecogeography and genomics recently well characterized by Cook lab. The major goal of is to characterize drought adaptive strategies in wild Cicer and associated functional divergence at transcriptional level, if any, in drought responses between chickpea and its wild progenitor.Towards this end, two C. reticulatum genotypes (Savur 063 and Kalkan 064) and two chickpea cultivars (drought susceptible and tolerant) will be assessed to characterize and rank the wild relatives in water use efficiency. Various drought scenarios will be imposed and a range of drought-related traits, including transpiration rates, water use efficiency, nitrogen fixation rates, total yield and diagnostic biomarkers, will be quantified. In a parallel set of experiments, drought-related transcriptional response will be characterized by comparing transcripts at different stress levels, over time and among host genotypes using RNAseq. To gain a better understanding of the impact of chickpea domestication on responses to drought stress, allele specific expression will be determined using F1 hybrids of C. reticulatum x C. arietinum to characterize the divergence within the proximal cis-regulatory elements that potentially underlie differences in drought tolerance.

Related SRA data

Experiments:
48 ( 12 samples )
Runs:
48 (145.1Gbp; 49.5Gb)
Additional objects:
File type count
fastq 48