Genetic architecture of the circadian clock and flowering time in Brassica rapa
- 1.1k Downloads
The circadian clock serves to coordinate physiology and behavior with the diurnal cycles derived from the daily rotation of the earth. In plants, circadian rhythms contribute to growth and yield and, hence, to both agricultural productivity and evolutionary fitness. Arabidopsis thaliana has served as a tractable model species in which to dissect clock mechanism and function, but it now becomes important to define the extent to which the Arabidopsis model can be extrapolated to other species, including crops. Accordingly, we have extended our studies to the close Arabidopsis relative and crop species, Brassica rapa. We have investigated natural variation in circadian function and flowering time among multiple B. rapa collections. There is wide variation in clock function, based on a robust rhythm in cotyledon movement, within a collection of B. rapa accessions, wild populations and recombinant inbred lines (RILs) derived from a cross between parents from two distinct subspecies, a rapid cycling Chinese cabbage (ssp. pekinensis) and a Yellow Sarson oilseed (ssp. trilocularis). We further analyzed the RILs to identify the quantitative trait loci (QTL) responsible for this natural variation in clock period and temperature compensation, as well as for flowering time under different temperature and day length settings. Most clock and flowering-time QTL mapped to overlapping chromosomal loci. We have exploited micro-synteny between the Arabidopsis and B. rapa genomes to identify candidate genes for these QTL.
KeywordsQuantitative Trait Locus Circadian Clock Quantitative Trait Locus Analysis Clock Gene Period Length
This study was supported by a National Science Foundation grant (IOS 0605736) to C.R.M., C.W. and R.M. Amasino. We thank Fede Iñiguez-Luy (Temuco, Chile) for Brassica rapa IRRI RILs and linkage maps and the Centre for Genetic Resources, the Netherlands (CGN), for Brassica rapa accessions.
- Buckler ES, Holland JB, Bradbury P, Acharya C, Brown P, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz J, Goodman M, Harjes C, Guill K, Kroon D, Larsson S, Lepak N, Li H, Mitchell S, Pressoir G, Peiffer J, Rosas M, Rocheford T, Romay M, Romero S, Salvo S, Villeda H, da Silva H, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen M (2009) The genetic architecture of maize flowering time. Science 325:714–718PubMedCrossRefGoogle Scholar
- Cheung F, Trick M, Drou N, Lim YP, Park JY, Kwon SJ, Kim JA, Scott R, Pires JC, Paterson AH, Town C, Bancroft I (2009) Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell 21:1912–1928PubMedCrossRefGoogle Scholar
- Johnson CH, Elliott J, Foster R, Honma K-I, Kronauer R (2004) Fundamental properties of circadian rhythms. In: Dunlap JC, Loros JJ, DeCoursey P (eds) Chronobiology: biological timekeeping. Sinauer, Sunderland, pp 67–105Google Scholar
- Mun J-H, Kwon S-J, Yang T-J, Seol Y-J, Jin M, Kim J-A, Lim M-H, Kim JS, Baek S, Choi B-S, Yu H-J, Kim D-S, Kim N, Lim K-B, Lee S-I, Hahn J-H, Lim YP, Bancroft I, Park B-S (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111PubMedCrossRefGoogle Scholar
- Nakamichi N, Kita M, Niinuma K, Ito S, Yamashino T, Mizoguchi T, Mizuno T (2007) Arabidopsis clock-associated Pseudo-Response Regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway. Plant Cell Physiol 48:822–832PubMedCrossRefGoogle Scholar
- Park JY, Koo DH, Hong CP, Lee SJ, Jeon JW, Lee SH, Yun PY, Park BS, Kim HR, Bang JW (2005) Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol Gen Genomics 274:579–588CrossRefGoogle Scholar
- R Development Core Team (2009) R: A language and environment for statistical computing. Vienna, AustriaGoogle Scholar
- Trick M, Kwon SJ, Choi SR, Fraser F, Soumpourou E, Drou N, Wang Z, Lee SY, Yang TJ, Mun JH, Paterson AH, Town CD, Pires JC, Lim YP, Park BS, Bancroft I (2009) Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis. BMC Genomics 10:539PubMedCrossRefGoogle Scholar
- Wang S, Basten CJ, Zeng Z (2007) Windows Qtl Cartographer 2.5. N.C. State University, Bioinformatics Research Center, USAGoogle Scholar
- Wilczek AM, Roe JL, Knapp MC, Cooper MD, Lopez-Gallego C, Martin LJ, Muir CD, Sim S, Walker A, Anderson J, Egan JF, Moyers BT, Petipas R, Giakountis A, Charbit E, Coupland G, Welch SM, Schmitt J (2009) Effects of genetic perturbation on seasonal life history plasticity. Science 323:930–934PubMedCrossRefGoogle Scholar