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Structure–function analysis of the barley genome: the gene-rich region of chromosome 2HL

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Abstract

A major gene-rich region on the end of the long arm of Triticeae group 2 chromosomes exhibits high recombination frequencies, making it an attractive region for positional cloning. Traits known to be controlled by this region include chasmogamy/cleistogamy, frost tolerance at flowering, grain yield, head architecture, and resistance to Fusarium head blight and rusts. To assist these cloning efforts, we constructed detailed genetic maps of barley chromosome 2H, including 61 polymerase chain reaction markers. Colinearity with rice occurred in eight distinct blocks, including five blocks in the terminal gene-rich region. Alignment of rice sequences from the junctions of colinear chromosome segments provided no evidence for the involvement of long (>2.5 kb) inverted repeats in generating inversions. However, reuse of some junction sequences in two or three separate evolutionary breakage/fusion events was implicated, suggesting the presence of fragile sites. Sequencing across 91 gene fragments totaling 107 kb from four barley genotypes revealed the highest single nucleotide substitution and insertion–deletion polymorphism levels in the terminal regions of the chromosome arms. The maps will assist in the isolation of genes from the chromosome 2L gene-rich region in barley and wheat by providing markers and accelerating the identification of the corresponding points in the rice genome sequence.

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Acknowledgements

This work was funded by the GRDC, ARC, the University of Adelaide, and the South Australian government. We thank Paul Gooding for technical assistance, Kazahiro Sato for pedigree information, Tania Tabone and Matthew Hayden for assistance in developing the marker assays for NBP, OXO, and HYP29, Peter Langridge, Margaret Pallotta, and Stewart Coventry for seeds and marker data, and Geoffrey Fincher for critical reading of the manuscript.

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Authors and Affiliations

  1. Australian Centre for Plant Functional Genomics (ACPFG), School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia

    Andrew Chen, Ute Baumann & Nicholas C. Collins

  2. Department of Plant Science, University of Manitoba, 66 Dafoe Road, 222 Agriculture Building, Winnipeg, Manitoba, R3T 2N2, Canada

    Anita Brûlé-Babel

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  1. Andrew Chen
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  2. Anita Brûlé-Babel
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Correspondence to Nicholas C. Collins.

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Supplemental Table 1

Primers, PCR conditions, restriction enzymes, and sequences relating to polymorphism screen and markers (PDF 199 KB).

Supplemental Fig. 1

Rearrangements of chromosome segments 2, 3, and 4 involve reuse of junction intervals A, B, C, or D in multiple chromosome breakage/fusion events. The six possible scenarios in regard to the chronological sequence of inversions involving chromosome segments 2, 3, and 4 are illustrated. For each scenario, the number of inversions that each junction sequence is involved in is indicated in the table below (GIF 41.4 KB).

High resolution (TIF 432 KB).

Supplemental Fig. 2

Pedigrees of barley mapping parents Amagi Nijo, Haruna Nijo, WI2585, and Galleon. Dotted lines indicate derivation by selection alone. The extent of backcrossing is not shown (GIF 74.3 KB).

High resolution (TIF 962 KB).

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Chen, A., Brûlé-Babel, A., Baumann, U. et al. Structure–function analysis of the barley genome: the gene-rich region of chromosome 2HL. Funct Integr Genomics 9, 67–79 (2009). https://doi.org/10.1007/s10142-008-0099-2

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