Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice

Cytogenetic maps of sorghum chromosomes 3-7, 9, and 10 were constructed on the basis of the fluorescence in situ hybridization (FISH) of ~18-30 BAC probes mapped across each of these chromosomes. Distal regions of euchromatin and pericentromeric regions of heterochromatin were delimited for all 10 sorghum chromosomes and their DNA content quantified. Euchromatic DNA spans ~50% of the sorghum genome, ranging from ~60% of chromosome 1 (SBI-01) to ~33% of chromosome 7 (SBI-07). This portion of the sorghum genome is predicted to encode ~70% of the sorghum genes (~1 gene model/12.3 kbp), assuming that rice and sorghum encode a similar number of genes. Heterochromafin spans ~411 Mbp of the sorghum genome, a region characterized by a ~34-fold lower rate of recombination and ~3-fold lower gene density compared to euchromatic DNA. The sorghum and rice genomes exhibit a high degree of macrocolinearity; however, the sorghum genome is ~2-fold larger than the rice genome. The distal euchromatic regions of sorghum chromosomes 3-7 and 10 are ~1.8-fold larger overall and exhibit an ~1.5-fold lower average rate of recombination than the colinear regions of the homeologous rice chromosomes. By contrast, the pericentromeric heterochromatic regions of these chromosomes are on average ~3.6-fold larger in sorghum and recombination is suppressed ~15-fold compared to the colinear regions of rice chromosomes.