Mapping-by-sequencing Identifies HvPHYTOCHROME C As a Candidate Gene for the Early Maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 2014 Jul 6

PMID 24996910

Citations 44

Authors

Artem Pankin

Chiara Campoli

Xue Dong

Benjamin Kilian

Rajiv Sharma

Axel Himmelbach

Reena Saini

Seth J Davis

Nils Stein

Korbinian Schneeberger

Maria von Korff

Affiliations

Soon will be listed here.

Abstract

Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering.

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References

Mascher M, Muehlbauer G, Rokhsar D, Chapman J, Schmutz J, Barry K . Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 2013; 76(4):718-27. PMC: 4298792. DOI: 10.1111/tpj.12319. View

Campoli C, Drosse B, Searle I, Coupland G, von Korff M . Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. Plant J. 2011; 69(5):868-80. DOI: 10.1111/j.1365-313X.2011.04839.x. View

Hubner S, Hoffken M, Oren E, Haseneyer G, Stein N, Graner A . Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation. Mol Ecol. 2009; 18(7):1523-36. DOI: 10.1111/j.1365-294X.2009.04106.x. View

Mayer K, Waugh R, Brown J, Schulman A, Langridge P, Platzer M . A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012; 491(7426):711-6. DOI: 10.1038/nature11543. View

Turner A, Beales J, Faure S, Dunford R, Laurie D . The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley. Science. 2005; 310(5750):1031-4. DOI: 10.1126/science.1117619. View

von Korff M, Leon J, Pillen K . Detection of epistatic interactions between exotic alleles introgressed from wild barley (H. vulgare ssp. spontaneum). Theor Appl Genet. 2010; 121(8):1455-64. DOI: 10.1007/s00122-010-1401-y. View

Morrell P, Gonzales A, Meyer K, Clegg M . Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins. J Hered. 2013; 105(2):253-64. DOI: 10.1093/jhered/est083. View

Campoli C, Shtaya M, Davis S, von Korff M . 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 Biol. 2012; 12:97. PMC: 3478166. DOI: 10.1186/1471-2229-12-97. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

10.

Close T, Bhat P, Lonardi S, Wu Y, Rostoks N, Ramsay L . Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics. 2009; 10:582. PMC: 2797026. DOI: 10.1186/1471-2164-10-582. View

11.

Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K . Genetic dissection of barley morphology and development. Plant Physiol. 2010; 155(2):617-27. PMC: 3032454. DOI: 10.1104/pp.110.166249. View

12.

Habte E, Muller L, Shtaya M, Davis S, von Korff M . Osmotic stress at the barley root affects expression of circadian clock genes in the shoot. Plant Cell Environ. 2014; 37(6):1321-7. DOI: 10.1111/pce.12242. View

13.

Pokhilko A, Fernandez A, Edwards K, Southern M, Halliday K, Millar A . The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol. 2012; 8:574. PMC: 3321525. DOI: 10.1038/msb.2012.6. View

14.

von Korff M, Wang H, Leon J, Pillen K . AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp. spontaneum). Theor Appl Genet. 2006; 112(7):1221-31. DOI: 10.1007/s00122-006-0223-4. View

15.

Nagatani A . Phytochrome: structural basis for its functions. Curr Opin Plant Biol. 2010; 13(5):565-70. DOI: 10.1016/j.pbi.2010.07.002. View

16.

Balasubramanian S, Sureshkumar S, Agrawal M, Michael T, Wessinger C, Maloof J . The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet. 2006; 38(6):711-5. PMC: 1592229. DOI: 10.1038/ng1818. View

17.

Szucs P, Karsai I, von Zitzewitz J, Meszaros K, Cooper L, Gu Y . Positional relationships between photoperiod response QTL and photoreceptor and vernalization genes in barley. Theor Appl Genet. 2006; 112(7):1277-85. DOI: 10.1007/s00122-006-0229-y. View

18.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

19.

Liu X, Covington M, Fankhauser C, Chory J, Wagner D . ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell. 2001; 13(6):1293-304. PMC: 135570. DOI: 10.1105/tpc.13.6.1293. View

20.

Kilian B, Ozkan H, Kohl J, von Haeseler A, Barale F, Deusch O . Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genomics. 2006; 276(3):230-41. DOI: 10.1007/s00438-006-0136-6. View