Sizing the genetic and physical centromere of barley chromosomes as a prerequisite of understanding genome evolution in the genus Hordeum
Plant Genetics and Genomics
Final Report Abstract
Genetic maps are based on the frequency of recombination and often show different positions of molecular markers in comparison to physical maps, particularly in the centromere that is generally poor in meiotic re-combinations. To decipher the position and order of DNA sequences genetically mapped to the centromere of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization (FISH) with mitotic metaphase and meiotic pachytene chromosomes was performed with 70 genomic single-copy probes derived from 65 fingerprinted BAC contigs genetically assigned to this recombination cold spot. The total physical distribution of the centromeric 5.5 cM bin of 3H comprises 58% of the mitotic metaphase chromosome length. Long genetic distances at subterminal regions translated into short physical distances, confirming that recombination events occur more often at distal regions of chromosome 3H. Non-overlapping FISH signals were frequently obtained for probes with a physical distance of at least 30 - 60 Kb. Only 8% of analyzed chromosomes showed a symmetric order of FISH signals on both sister chromatids. Due to the dynamic packing of metaphase chromatin the order of two adjacent single-copy signals along the chromosome arms outside the (peri)centromeric regions can only reliably be determined if the cytological distance is ~3%, corresponding to 21.6 Mb. Mitotic and meiotic chromatin of this recombination poor region is preferentially marked by a heterochromatin-typical histone mark (H3K9me2), while recombination enriched subterminal chromosome regions are enriched in euchromatin-typical histone marks (H3K4me2, H3K4me3, H3K27me3) suggesting that the meiotic recombination rate could be influenced by the chromatin landscape. To visualize genomic collinearity in related barely species, 22 genomic single-copy and 14 cDNA chromosome 3H-specific probes were mapped to the chromosomes of Hordeum bulbosum, H. marinum, H. pubiflorum, H. murinum and Secale cereale by FISH. Most probes showed reliable signals confirming homoeology between barley and related species. Differences in order and position of FISH markers demonstrated gene movements within genus Hordeum and confirmed interchromosomal rearrangement between barley and rye. Comparison between repeat free genomic and cDNA probes showed that gene containing single copy gDNA probes are performing more reliably for FISH-based analysis of synteny.
Publications
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Barley gets physical: Physical mapping of barley BACs using fluorescent in situ hybridization. 02.09. – 06.09.2013, The 19th International Chromosome Conference, Bologna, Italy
Lala Aliyeva, Thomas Schmutzer, Nils Stein, Andreas Houben
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(2015) Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant Journal, 84, 385-394
Aliyeva-Schnorr, L., Beier, S., Karafiatova, M., Schmutzer, T., Scholz, U., Dolezel, J., Stein, N. and Houben, A.
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(2015b) A fast air-dry dropping chromosome preparation method suitable for FISH in plants. Journal of Visualized Experiments : JoVE, 106
Aliyeva-Schnorr, L., Ma, L. and Houben, A.
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(2016) Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Research 24, 231-242
Aliyeva-Schnorr, L., Stein, N. and Houben, A.
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(2016) Cytogenetic mapping of BAC contigs assigned to barley chromosome 3H and comparative subchromosomal analysis within the genus Hordeum, Martin-Luther-Universität Halle-Wittenberg
Lala Aliyeva-Schnorr
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Cytogenetics and genetic stocks for physical mapping and sequencing. In: Stein N., Muehlbauer G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham, S. 25-44
Houben, A, Aliyeva-Schnorr, L., Prasad Joshi, G. and Endo, T.
