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Exploring genomic diversity in wild and cultivated barley using high throughput DNA sequencing technology

Tan, Cong (2018) Exploring genomic diversity in wild and cultivated barley using high throughput DNA sequencing technology. PhD thesis, Murdoch University.

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Abstract

Barley (Hordeum vulgare L.) was domesticated from wild barley (Hordeum spontaneum L.) around 10,000 years ago in the Fertile Crescent. It has been widely used as a model organism to research plant adaptive evolutionary processes as well as a vital genetic repository to explore plant abiotic and biotic stress tolerance. This thesis used the recent barley genome sequence as a reference to characterise the genomic evolution of wild barley, explore genomic diversity, and created a database of barley genomic variation.

Wild barley accessions from oppos ite slopes of the ‘Evolution Canyon’ in Israel, separated by only 250 m but with drastically different microclimates, were sequenced at the transcriptome and whole-genome levels. Sympatric speciation was identified between the wild barleys from the two slopes, and the distance between them was even greater than that between cultivated barley and Tibetan wild barley. About 243 Mb genomic regions were identified under environmental selection. The number of upregulated genes from the south-facing slope wild barley was about eight times that of the north-facing slope under drought stress.

To explore genomic diversity in cultivated barley germplasm from Australia , wholegenome sequencing was conducted on eleven cultivated barley varieties. In total, 29,550,641 single nucleotide polymorphisms (SNPs) and 1,592,034 short insertions and deletions (InDels) were identified. These SNPs and InDels can be used to develop Kompetitive Allele Specific PCR (KASP) and InDel markers for genome-assisted breeding.

To facilitate access to and use of the genomic resources exploited in this study, a database of barley genomic variations, BarleyVarDB, was created. This database provides three main sets of information: (1) SNPs and InDels, (2) barley genome reference and its annotation, and (3) 522,212 whole genome-wide simple sequence repeats (SSRs).

Using the resources developed in this study, I characterised the mutation pattern of a barley mutant derived from gamma radiation. The results indicate that mutations induced by gamma radiation are not evenly distributed in the whole genome but occur in several concentrated regions in chromosomes. Besides, I narrowed down the candidate genes for high-tillering mutant phenotype from 139 to 15 by comparing the sequence difference in the 10 Mb target region between a pair of near isogenic lines using transcriptome sequencing.

Publication Type: Thesis (PhD)
Murdoch Affiliation: School of Veterinary and Life Sciences
Supervisor: Li, Chengdao
URI: http://researchrepository.murdoch.edu.au/id/eprint/41577
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