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Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa

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Abstract

Circadian clocks regulate plant growth and development in response to environmental factors. In this function, clocks influence the adaptation of species to changes in location or climate. Circadian-clock genes have been subject of intense study in models such as Arabidopsis thaliana but the results may not necessarily reflect clock functions in species with polyploid genomes, such as Brassica species, that include multiple copies of clock-related genes. The triplicate genome of Brassica rapa retains high sequence-level co-linearity with Arabidopsis genomes. In B. rapa we had previously identified five orthologs of the five known Arabidopsis pseudo-response regulator (PRR) genes that are key regulators of the circadian clock in this species. Three of these B. rapa genes, BrPRR1, BrPPR5, and BrPPR7, are present in two copies each in the B. rapa genome, for a total of eight B. rapa PRR (BrPRR) orthologs. We have now determined sequences and expression characteristics of the eight BrPRR genes and mapped their positions in the B. rapa genome. Although both members of each paralogous pair exhibited the same expression pattern, some variation in their gene structures was apparent. The BrPRR genes are tightly linked to several flowering genes. The knowledge about genome location, copy number variation and structural diversity of these B. rapa clock genes will improve our understanding of clock-related functions in this important crop. This will facilitate the development of Brassica crops for optimal growth in new environments and under changing conditions.

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Acknowledgments

This work was supported by grants from “Research Program for Agricultural Science & Technology Development (Project No. PJ907049)”, National Academy of Agricultural Science and BioGreen 21 Program (project No. PJ008025), the Rural Development Administration, Republic of Korea. We thank Dr. Hans J. Bohnert in University of Illinois for comment about comparison between paralogous genes and editing in English.

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  1. Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration, 224 Suinro Gwonseon-gu, Suwon, Gyeonggi-do, 441-707, Republic of Korea

    Jin A. Kim, Jung Sun Kim, Joon Ki Hong & Yeon-Hee Lee

  2. National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea

    Beom-Soon Choi

  3. Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul, 133-791, Republic of Korea

    Beom-Soon Choi

  4. Department of Genomics, National Academy of Agricultural Science, Rural Development Administration, 224 Suinro Gwonseon-gu, Suwon, Gyeonggi-do, 441-707, Republic of Korea

    Young-Joo Seol

  5. Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul, 151-744, Republic of Korea

    Chang Hoo Jeon

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  1. Jin A. Kim
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Communicated by A. Schnittger.

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Supplemental Fig. 1 The quantitative real-time RT-PCR of BrPRR genes mRNA in B. rapa plants grown under a 16-h day/8-h night photoperiod (A) or for 72 h in the light (B). Plant tissues were collected every 3 h and analyzed for the expression of BrPRR genes by quantitative RT–PCR using the gene-specific probes shown in Table 1. qRT-PCR reaction were performed with 3 technical replication using Bio-Rad system and the SYBR Green I master mix in a volume 20ul.

Supplemental Fig. 2 Comparison of the predicted amino acid sequences of all PRR genes in B. rapa using ClustalW2(http://www.ebi.ac.uk/Tools/msa/clustalw2/) in EMBL-EBI web site. The strictly conserved glutamate (E) and the CCT and PRR domains are indicated.

Supplemental Fig. 3 Comparison of the predicted amino acid sequences of PRR3 and its B. rapa ortholog BrPRR3. The strictly conserved glutamate (E) and the CCT and PRR domains are indicated.

Supplemental Fig. 4 Comparison of the predicted amino acid sequences of PRR5 and its two B. rapa orthologs BrPRR5a and BrPRR5b. The strictly conserved glutamate (E) and the CCT and PRR domains are indicated.

Supplemental Fig. 5 Comparison of the predicted amino acid sequences of PRR7 and its two B. rapa orthologs BrPRR7a and BrPRR7b. The strictly conserved glutamate (E) and the CCT and PRR domains are indicated.

Supplemental Fig. 6 Comparison of the predicted amino acid sequences of PRR9 and its B. rapa ortholog BrPRR9. The strictly conserved glutamate (E) and the CCT and PRR domains are indicated.

Supplemental Fig. 7 Comparison of exon–intron structures of PRR3 (A), PRR5 (B), PRR7 (C), and PRR9 (D) with those of orthologous genes in B. rapa. Lines and boxes indicate introns and exons, respectively. Numbers indicate the start positions of the first exon. Coding regions of PRR genes were respectively aligned with their genomic sequences

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Kim, J.A., Kim, J.S., Hong, J.K. et al. Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa . Mol Genet Genomics 287, 373–388 (2012). https://doi.org/10.1007/s00438-012-0682-z

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