Genomics-assisted dissection of barley morphology and development (ERA-PG 046)
Final Report Abstract
Barley is a large genome crop plant that has been a model plant for genetic research for over a century. Because of its simple genetics, it was one of the first plant species to be subjected to artificial mutagenesis. Plants containing mutations that affect the morphology or development of the plant are exceptionally important in biology because they allow researchers to identify the specific genes that control the affected processes. Mutations also have a role in crop improvement. For over 80 years, barley mutants have been generated and studied, and in some cases (for example plant stature and disease resistance) the responsible mutations have been incorporated into varieties that have been widely grown in European agriculture. This project is all about identifying the position in the genome of the specific genes that have been mutated in diverse collection of barley mutants. We then want to develop the information and resources to allow us to actually identify and characterise these mutated genes. This is particularly important as the barley genome is very large, about twice that of the human genome. Finally, as proof of principle, we plan isolate and study the genes that are mutated in a small set of mutant lines. We have chosen genes that affect the morphology of the barley spike (the inflorescence) and individual spikelets (the developing grain). During the project we located more than 500 barley mutants to specific regions of the barley genome, generated over 600,000 DNA sequences from the ends of large fragments of the barley genome that we maintain in bacterial cells, and have isolated one of the targeted three morphological mutant loci, while being very close to isolating the other two.
Publications
- 2009. International Barley Sequencing Consortium - at the threshold of efficient access to the barley genome. Plant Physiology 149, 142-147
Schulte, D., Close, T.J., Graner, A., Langridge, P., Matsumoto, T., Muehlbauer, G.J., Sato, K., Schulman, A.H., Waugh, R., Wise, R.P. & Stein, N.
- (2010) Genome-wide association mapping of morphological traits to candidate gene resolution in the un-sequenced barley genome. Proc. Natl. Acad. Sci. USA 107: 21611-21616
Cockram, J; White, J; Zuluaga, DL; Smith, D; Comadran, J; Macaulay, M; Luo, ZW; Kearsey, MJ; Werner, P; Harrap, D; Tapsell, C; Liu, H; Hedley, PE; Stein, N; Schulte, D; Steuernagel, B; Marshall, DF; Thomas, WTB; Ramsay, L; Mackay, I; Balding, DJ; Waugh, R; O'Sullivan, DM. AGOUEB Consortium
- 2010. Exploiting induced variation to dissect quantitative traits in barley. Biochemical Society Transactions 38, 683-688
Druka, A., Franckowiak, J.D., Lundqvist, U., Bonar, N., Alexander, J., Guzy-Wrobelskas, J., Ramsay, L., Druka, I., Grant, I., Macaulay, M., Vendramin, V., Shahinnia, F., Radovic, S., Houston, K., Harrap, D., Cardle, L., Marshall, D.F., Morgante, M., Stein, N. & Waugh, R.
- (2011) Analysis of the barley bract suppression gene TRD1. Theoretical and Applied Genetics 125, 33-45
Kelly Houston, Arnis Druka, Nicky Bonar, Malcolm Macaulay, Udda Lundqvist, Jerome Franckowiak, Michele Morgante, Nils Stein and Robbie Waugh
- (2011) Genetic dissection of barley morphology and development. Plant Physiology 155: 617-627
Druka, A; Franckowiak, J; Lundqvist, U; Bonar, N; Alexander, J; Houston, K; Radovic, S; Shahinnia, F; Vendramin, V; Morgante, M; Stein, N; Waugh, R
- 2011. Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. Proceedings of the National Academy of Sciences, USA 109, 4326-4331
Zakhrabekova, S., Gough, S.P., Braumann, I., Muller, A.H., Lundqvist, J., Ahmann, K., Dockter, C., Matyszczak, I., Kurowska, M., Druka, A., Waugh, R., Graner, A., Stein, N., Steuernagel, B., Lundqvist, U. & Hansson, M.
- 2011. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nature Genetics 43: 169-U125
Ramsay, L., Comadran, J., Druka, A., Marshall, D.F., Thomas, W.T.B., Macaulay, M., MacKenzie, K., Simpson, C.G., Fuller, J., Hayes, P.M., Lundqvist, U., Franckowiak, J.D., Close, T.J., Muehlbauer, G. & Waugh, R.
- (2012). A physical, genetical and functional sequence assembly of the barley genome. Nature (Lond) 491, 711-716
The International Barley Genome Sequencing Consortium (IBSC), Mayer, K.F.X., Waugh, R., Langridge, P., Close, T.J., Wise, R.P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbauer, G.J., and Stein, N.
(See online at https://doi.org/10.1038/nature11543) - (2012). High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theor Appl Genet 124, 373-384
Shahinnia, F., Druka, A., Frankowiak, J., Morgante, M., Waugh, R., and Stein, N.
(See online at https://doi.org/10.1007/s00122-011-1712-7) - 2012. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nature Genetics 44, 1388-1392
Comadran, J., Kilian, B., Russell, J.R., Ramsay, L., Stein, N., Ganal, M., Shaw, P., Bayer, M., Thomas, W.T.B., Marshall, D.F., Hedley, P.E., Tondelli, A., Pecchioni, N., Francia, E., Korzun, V., Walther, A. & Waugh, R.
(See online at https://doi.org/10.1038/ng.2447) - (2013) Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence. Proceedings of the National Academy of Sciences USA 110 (41), 16675-16680
Houston K, McKim SM, Comadran J, Bonar N, Druka I, Uzrek N, Cirillo E, Guzy-Wrobelska J, Collins NC, Halpin C, Hansson M, Dockter C, Druka A, Waugh R.
- (2014) A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms. Plant physiology 164 (1), 412-423
Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N.
(See online at https://doi.org/10.1104/pp.113.228213)
