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Characterization of four B-chromosome-specific RAPDs and the development of SCAR markers on the maize B-chromosome

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Abstract

Understanding the molecular organization of the maize B-chromosome is hindered by its high homology with A-chromosomes. Recently, various approaches have been employed to overcome this hindrance, and several B-chromosome-specific sequences have been identified. Here, we cloned and characterized four previously published B-chromosome-specific RAPD fragments in detail. The results of sequence analysis, Southern hybridization and fluorescence in situ hybridization revealed that the four RAPD fragments are repetitive and present on both the B- and A-chromosomes, which supports an A-chromosome origin of the B-chromosome. We further developed four sequence-characterized amplified region (SCAR) markers derived from the four B-chromosome-specific RAPDs. These markers amplified PCR products exclusively in plants with B-chromosomes and were further mapped to definite distal heterochromatic regions of the B-chromosome by 15 B–A translocations. Furthermore, reverse transcriptase-PCR revealed that two of the four B-chromosome-specific RAPD fragments are transcriptionally active. These results demonstrate the feasibility of using B-chromosome-specific RAPD sequences to generate SCAR markers specific to the B-chromosome and might apply to other sequences of the maize B-chromosome.

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Acknowledgments

This work was supported by the National Sciences Council Grant of Taiwan (NSC99-2311-B-005-003-MY3 and NSC102-2311-B-005-001-).

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Authors and Affiliations

  1. Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan

    Kuo-Wei Kao, Chien-Yu Lin & Ya-Ming Cheng

  2. Department of Biological Science and Technology, China Medical University, Taichung, Taiwan

    Shu-Fen Peng

Authors
  1. Kuo-Wei Kao
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  2. Chien-Yu Lin
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  3. Shu-Fen Peng
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  4. Ya-Ming Cheng
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Corresponding author

Correspondence to Ya-Ming Cheng.

Additional information

Communicated by S. Hohmann.

K.-W. Kao and C.-Y. Lin contributed equally to this work.

Electronic supplementary material

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438_2014_926_MOESM1_ESM.docx

Supplementary material 1 Supplementary Fig. 1 Breakpoints of 15 B–A translocations on the maize B-chromosome. The breakpoints of the TB-1La, TB-3Sb, TB-4Sa, TB-7Lb, and 11 B-10L translocations (TB-10L) are indicated by arrows. BS, B-chromosome short arm; CK, centromere and centromeric knob; PE, proximal euchromatin; DH1–DH4, four distal heterochromatins; DE, distal euchromatin (DOCX 15 kb)

438_2014_926_MOESM2_ESM.tif

Supplementary material 2 Supplementary Fig. 2 Binding sites of SCAR primers on the four B-chromosome-specific RAPDs. The hollow arrows indicate the SCAR primer-binding sites (TIFF 182 kb)

438_2014_926_MOESM3_ESM.tif

Supplementary material 3 Supplementary Fig. 3 Amplification of B-chromosome-specific fragments using four RAPD primers. Genomic DNA from L289+0B (0B) and L289+1B (1B) was used to amplify B-chromosome-specific DNA fragments (arrows) using four RAPD primers: UBC313 (a), UBC345 (b), UBC349 (c), and UBC426 (d). M, molecular weight marker (molecular weights shown at left) (TIFF 215 kb)

438_2014_926_MOESM4_ESM.tif

Supplementary material 4 Supplementary Fig. 4 Screening of B-chromosome-specific SCAR primer combinations. Genomic DNA from L289+0B (lane 1), L289+1B (lane 2), W23+0B (lane 3), and W23+1B (lane 4) was used to amplify B-chromosome-specific fragments (arrows) using the SCAR primer combinations 313-F1/313-R1 (a), 313-F2/313-R1 (b), 313-F3/313-R1 (c), 345-F1/345-R1 (d), 345-F1/345-R2 (e), 349-F1/349-R1 (f), 349-F2/349-R1 (g), 349-F2/349-R2 (h), 426-F1/426-R1 (i), 426-F1/426-R2 (j), 426-F1/426-R3 (k), 426-F2/426-R1 (l), 426-F2/426-R2 (m), and 426-F2/426-R3 (n). M, molecular weight marker (molecular weights are shown at left) (TIFF 1576 kb)

Supplementary material 5 (TIFF 706 kb)

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Kao, KW., Lin, CY., Peng, SF. et al. Characterization of four B-chromosome-specific RAPDs and the development of SCAR markers on the maize B-chromosome. Mol Genet Genomics 290, 431–441 (2015). https://doi.org/10.1007/s00438-014-0926-1

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