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Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis

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Abstract

Crop wild relatives are considered as important genetic resources of allelic diversity for domesticated crop species. Their utilization in breeding programs, however, is often limited due to crossing barriers and genome incompatibilities. Wild relatives of barley possess attractive properties and hence allelic diversity for adapting barley better to changing environmental conditions. Therefore, gaining a better knowledge about genomic synteny between cultivated barley and wild relatives of the same genus is an important task. To visualize genomic collinearity in related species, 22 genomic single-copy and 14 complementary DNA (cDNA) chromosome 3H-specific probes were mapped to the chromosomes of Hordeum bulbosum, Hordeum marinum, Hordeum pubiflorum, Hordeum murinum, and Secale cereale by fluorescent in situ hybridization (FISH). Most probes showed reliable signals confirming homoeology between cultivated barley and related species. Differences in order and position of FISH markers demonstrated sequence movements or small-scale chromosomal rearrangements within genus Hordeum and confirmed interchromosomal rearrangements between barley and rye. Comparison between repeat-free genomic and cDNA probes showed that gene-containing single-copy genomic DNA (gDNA) probes are performing more reliably for FISH-based analysis of synteny.

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Abbreviations

Alexa 488:

Green-fluorescent dye

cDNA:

Complementary DNA

Cy3:

Cyanine dye

dUTP:

Deoxyuridine triphosphate

DAPI:

4′,6′-Diamidino-2-phenylindole

fl-cDNA:

Full-length complementary DNA

FISH:

Fluorescence in situ hybridization

FPcontig:

FingerPrinted Contig

gDNA:

Genomic DNA

NOR:

Nucleolus organizer region

rDNA:

Ribosomal DNA

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Acknowledgments

We would like to thank Katrin Kumke and Oda Weiss for the technical assistance and Karin Lipfert for the art work. We also thank Prof. Angeles Bermejo Cuadrado for supplying the probe pSc119.2, Prof. Yasunari Ogihara for supplied plasmids containing wheat cDNA (NBRP-WHEAT, http://www.shigen.nig.ac.jp/wheat/komugi/ests/tissueBrowse.jsp), and Prof. Kazuhiro Sato for the plasmids containing barley cDNA (Barley Gene Expression Database, http://barleyflc.dna.affrc.go.jp/hvdb/index.html). Special thanks to Dr. Frank Blattner for his support and suggestions on this work. This work was supported by the DFG (HO1779/21-1) to AH and NS.

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany

    Lala Aliyeva-Schnorr, Nils Stein & Andreas Houben

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  1. Lala Aliyeva-Schnorr
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  2. Nils Stein
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  3. Andreas Houben
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Corresponding author

Correspondence to Andreas Houben.

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Responsible Editor: Hans de Jong

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Fig. S1

S. cereale chromosomes after FISH with pSc119.2 (green). Chromosomes are counterstained by DAPI (grey). Differentiation of all chromosome pairs was described earlier by Cuadrado et al. (1995) using the repetitive families of 120-, 350-480-, and 610-bp DNA. (GIF 117 kb)

High Resolution Image (TIF 405 kb)

Fig. S2

Application of barley gDNA FISH probes and barley/wheat cDNA probes on H. bulbosum and S. cereale. (a) Single-copy FISH with 22 gDNA probes (red) on metaphase chromosomes of H. bulbosum were identified by pattern of microsatellite CTT (green). (b) FISH with gDNA probes (signals in red) on metaphase chromosomes of S. cereale were identified by pattern of tandem repeat pSc119.2. (c) Single-copy FISH with cDNA probes (red) on metaphase chromosomes of H. bulbosum identified by microsatellite CTT (green). (d) FISH with cDNA probes (red) on metaphase chromosomes of S. cereale identified by the tandem repeat probe pSc119.2. All chromosomes were counterstained with DAPI (grey). (GIF 187 kb)

High Resolution Image (TIF 16.4 mb)

Fig. S3

Application of barley single-copy gene-containing (gDNA) FISH probes on H. pubiflorum, H. marinum, and H. murinum. (a) Single-copy FISH with 18 gDNA probes (red) on metaphase chromosomes of H. pubiflorum were identified by pattern of microsatellite CTT (green). (b) Single-copy FISH with 18 gDNA probes (signals in red) on metaphase chromosomes of H. marinum were identified by pattern of microsatellite CTT (green). (c) Single-copy FISH with 18 gDNA probes ( red) on metaphase chromosomes of H. murinum were identified by pattern of microsatellite CTT (green). All chromosomes were counterstained with DAPI (grey). (GIF 143 kb)

High Resolution Image (TIF 3.60 mb)

Fig. S4

Comparative FISH mapping on metaphase chromosomes showing signals of selected cDNA probes (red) on H. vulgare and S. cereale. The insets show chromosome spreads and enlarged chromosomes with specific signals for three cDNA probes hybridized to barley (left) and rye (right). 5SrDNA (green) and pSc119.2 (green) were used as diagnostic probes for H. vulgare and for S. cereale, respectively. Chromosomes are counterstained with DAPI (grey). (GIF 198 kb)

High Resolution Image (TIF 4.27 mb)

Fig. S5

Comparison of intervals on the chromosome 3H of H. vulgare and homoeologous chromosome 3Hpub of H. pubiflorum indicated by the simultaneous hybridization of two boundary probes (1770 and 44666). The interval captures 58 % of the total physical length on H. vulgare and only 49.6 % of chromosome 3Hpub of H. pubiflorum. (GIF 107 kb)

High Resolution Image (TIF 1.21 mb)

Table S1

List of barley-specific contig derived probes with the determined cytogenetic position (CP) on (a) H. bulbosum, S. cereale (b) H. pubiflorum, H. marinum and H. murinum. Column 1 shows the first set of probes and column 2 the second set. Coding sequences are indicated in red, “na” - indicates that the corresponding probe was not tested on this species. (DOCX 22 kb)

Table S2

Subprobes and primer pairs designed for the generation of gDNA single-copy probes derived from FPcontigs (gDNA). (DOCX 29 kb)

Table S3

List of cDNAs with corresponding cytogenetic positions (CP) on chromosome 3H and its homoeologues on H. bulbosum and S. cereale. “nd” – signals were not detected on the species. (DOCX 16 kb)

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Aliyeva-Schnorr, L., Stein, N. & Houben, A. Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Res 24, 231–242 (2016). https://doi.org/10.1007/s10577-016-9518-8

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