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Isolation of Circadian-associated Genes in Brassica rapa by Comparative Genomics with Arabidopsis thaliana  

Kim, Jin A (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Yang, Tae-Jin (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Kim, Jung Sun (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Park, Jee Young (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Kwon, Soo-Jin (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Lim, Myung-Ho (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Jin, Mina (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Lee, Sang Choon (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Lee, Soo In (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Choi, Beom-Soon (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Um, Sang-Hee (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Kim, Ho-Il (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Chun, Changhoo (Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University)
Park, Beom-Seok (Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB))
Publication Information
Molecules and Cells / v.23, no.2, 2007 , pp. 145-153 More about this Journal
Abstract
Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose genome was triplicated after divergence from Arabidopsis, we identified B. rapa BAC clones containing these genes by BLAST analysis of B. rapa BAC end sequences against the five corresponding Arabidopsis regions. Subsequent fingerprinting, Southern hybridization, and PCR allowed identification of five BAC clones, one for each of the five circadian-related genes. By draft shotgun sequencing of the BAC clones, we identified the complete gene sequences and cloned the five expressed B. rapa circadian-associated gene members, BrPRRs 1, 3, 5, 7, and 9. Phylogenetic analysis revealed that each BrPRR was orthologous to the corresponding APRR at the sequence level. Northern hybridization revealed that the five genes were transcribed at distinct points in the 24 hour period, and Southern hybridization revealed that they are present in 2, 1, 2, 2, and 1 copies, respectively in the B. rapa genome, which was triplicated and then diploidized during the last 15 million years.
Keywords
Brassica rapa; BAC End Sequence; Circadian-associated Genes; Comparative Genomics;
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