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Brewing genomes

Australia produces high quality barley, with annual production averaging over 9 million tonnes/year. It is a widely grown crop (second in size only to wheat) and occupies a large geographic area – around 4 million hectares – and it is dispersed from southern Queensland through to Western Australia.

Australia has an enviable reputation for producing a reliable supply of high-quality barley in a contaminant-free climate. Australian barley is highly sought after by the malting, brewing, distilling, Shochu (Japanese distilled spirit) and feed industries and is well known for its low moisture content and low foreign material.

Since its domestication in the Fertile Crescent about 10 000 years ago, barley accompanied the spread of agriculture into Europe during the 5th and 6th millennia BC. It was subsequently introduced to North America and Australia by European settlers in the 17th and 18th centuries.

The Australian growing season is different from that in many European and North American countries, and the breeding activities are expected to have shaped the genomes of Australian barley cultivars and led to significant phenotypic and genetic divergence from the counterparts grown in other agroclimatic regions. Of special interest is selection for gene variants associated with fast development, that is early flowering, allowing the crops to escape terminal heat during the maturation stage.

To better understand the gentic basis for adaptation of Australian barley cultivars we sequenced and de novo assembled the genomes of two early Australian barley varieties, namely “Clipper” and “Stirling” in collaboration with Prof. Chengdao Li, Director of the Western Crop Genetics Alliance at Murdoch University.

A collage of the two historical barley varieties sequenced, Stirling (upper left) and Clipper (lower right). Photos by Rex Rowles (Mortlock Malt) and Thomas Ryan (Barossa Valley Craft Malt), used with permission.

The genomes were assembled using HiFi+Hi-C sequencing strategy. The assembly length of the Clipper and Stirling genomes are 4.28 Gb and 4.26 Gb with a contig N50 of 39.4 Mb and 36.9 Mb, respectively. In-situ Hi-C sequencing anchored 97% of sequences to seven chromosomes in both assemblies. The interactive contact map of the chromosomes is included below. Visit the assembly pages for Hordeum vulgare cv. Stirling and Hordeum vulgare cv. Clipper for more details!

Funding was provided by the Grain Research and Development Corporation Australia. E.L.A. was supported by the Welch Foundation (Q-1866), a McNair Medical Institute Scholar Award, an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375), a US-Israel Binational Science Foundation Award (2019276), the Behavioural Plasticity Research Institute (NSF DBI-2021795), NSF Physics Frontiers Center Award (NSF PHY-2019745), and an NIH CEGS (RM1HG011016-01A1). For more details read our paper:

Hu, H., Wang, P., Angessa, T.T., Zhang, X.-Q., Chalmers, K.J., Zhou, G., Hill, C.B., Jia, Y., Simpson, C., Fuller, J., Saxena, A., Al Shamaileh, H., Iqbal, M., Chapman, B., Kaur, P., Dudchenko, O., Aiden, E.L., Keeble-Gagnere, G., Westcott, S., Leah, D., Tibbits, J.F., Waugh, R., Langridge, P., Varshney, R., He, T. and Li, C. (2023), Genomic signatures of barley breeding for environmental adaptation to the new continents. Plant Biotechnol. J.
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