SPP 1530: Flowering Time Control - from Natural Variation to Crop Improvement

PP-11: Schneeberger, von Korff

Development and implementation of advanced methods for the identification of barley flowering time genes using next generation sequencing

Variation in flowering time has always been a major target in breeding programs to adapt crops to a wide range of environments. Deciphering the genetic basis of flowering time variation is thus important for knowledge based breeding of new varieties. Temperate crops like barley and wheat are characterized by large genomes mostly comprising of repeats. Even though these complex genomes are an extreme challenge to all genetic attempts, new technologies allow accessing the gene spaces of these large genomes in a fast and cost-efficient way. Albeit the first reports on simultaneous genetic mapping and mutation identification by next generation sequencing found their way into scientific literature, the continuing bottleneck for high throughput identification of causal mutations remains the appropriate methods and genetic material. Like conventional map-based cloning efforts, such high-speed mapping methods require segregating populations as their primary material. Here we propose to establish two new strategies for mutant identification in barley, which carry the promise to tremendously speed up the generation of mapping populations. First, we propose generation of isogenic mapping populations through self-fertilization of heterozygous mutants as recently proposed for rice. As such mutant plants can be identified within the M2 families of the original screens, it does require one a single generation to establish the segregating population. Second, sequencing of allelic mutants carries the promise to reveal causative genes without any linkage-based analysis, as it is usually only one gene or a very small number of genes that feature severe changes within all allelic mutants. Using nine different allelic series with two to six alleles in each group will unravel the power of this approach. Once established, both of these methods will allow for exploiting the extensive genetic resources of barley mutant populations generated over the last decades.

Project-related publications

Mulki MA and von Korff M (2015). CONSTANS controls floral repression by upregulating VERNALIZATION 2 (Vrn-H2) in barley. Plant Physiology, doi: 10.1104/pp.15.01350.

Digel B, Pankin A, von Korff M (2015). Global Transcriptome Profiling of Developing Leaf and Shoot Apices Reveals Distinct Genetic and Environmental Control of Floral Transition and Inflorescence Development in Barley. Plant Cell, DOI: dx.doi.org/10.1105/tpc

Nordström KJV*, Albani MC*, James GV, Gutjahr C, Hartwig B, Turck F, Paszkowski U, Coupland G and Schneeberger K (2013). Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers", Nature Biotechnology. doi:10.1038/nbt.2515. *These authors contributed equally to this manuscript

Bergonzi S*, Albani MC*,  Ver Loren van Themaat E, Nordstrom KJ , Wang R, Schneeberger K, Moerland PD, and  Coupland G (2013): Mechanisms of age-dependent response to winter temperature in perennial flowering of Arabis alpina. Science 340, 1094-7, doi: 10.1126/science.1234116.*These authors contributed equally to this manuscript

Mueller LM, von Korff M, Davis SJ (2014). Connections between circadian clocks and carbon metabolism reveal species-specific effects on growth control. J Exp Bot, doi: 10.1093/jxb/eru117

Rollins JA, Drosse B, Mulki MA, Grando S, Baum M, Singh M, Ceccarelli S, von Korff M (2013). Variation at the vernalisation genes Vrn‑H1 and Vrn‑H2 determines growth and yield stability in barley (Hordeum vulgare) grown under dryland conditions in Syria. Theor. Appl. Genet., doi: 10.1007/s00122-013-2173-y

Campoli C, Pankin A, Drosse B, Casao CM, Davis SJ, and von Korff M (2013): HvLUX1 is a candidate gene underlying the early maturity 10 locus in barley: phylogeny, diversity, and interactions with the circadian clock and photoperiodic pathways. New Phytol., n/a-n/a, doi: 10.1111/nph.12346.

Faure S, Turner AS, Gruszka D, Christodoulou V, Davis SJ, von Korff M, Laurie DA (2012). Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) to short growing seasons. Proceedings of the National Academy of Sciences of the United States of America 109(21): 8328-33

Campoli C, Drosse B, Searle I, Coupland G, von Korff M (2012). Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. Plant J. 69 (5): 868-880

Campoli C, Shtaya M, Davis SJ, von Korff M (2012). Expression conservation within the circadian clock of a monocot: natural variation at barley Ppd-H1 affects circadian expression of flowering time genes, but not clock orthologs. BMC Plant Biology 12:97, doi: 10.1186/1471-2229-12-97

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