ARS | Publication request: Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 8, 2011
Publication Date: May 19, 2011
Citation: Huo, N., Garvin, D.F., You, F., McMahon, S.A., Luo, M., Gu, Y.Q., Lazo, G.R., Vogel, J.P. 2011. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theoretical and Applied Genetics. 123(3):455-464.

Interpretive Summary: The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. The need for a model grass has become more urgent with the increased emphasis on developing grasses as biofuel crops. Many Brachypodium resources have been developed including whole genome sequence, highly efficient transformation and a large germplasm collection. Missing from this list is a high-density genetic linkage map. We developed a genetic linkage map using single nucleotide polymorphism (SNP) markers. This is essentially a genetic blueprint of the Brachypodium genome which will serve as a foundation for future genetic studies in this new model plant. By comparing this genetic map to the sequenced genome we observed that recombination rate was positively correlated with gene density and negatively correlated with repeat density, two findings that have been observed in numerous other organisms. By comparing adjacent regions with high and low recombination rates we showed that recombination rate was positively correlated with the degree of synteny between Brachypodium and rice.

Technical Abstract: The small annual grass Brachypodium distachyon (Brachypodium) is rapidly emerging as a powerful model system to study questions unique to the grasses. Many Brachypodium resources have been developed including whole genome sequence, highly efficient transformation and a large germplasm collection. Missing from this list is a high-density genetic linkage map. We developed a genetic linkage map using single nucleotide polymorphism (SNP) markers and an F2 mapping population of 476 individuals. SNPs were identified by targeted resequencing of single copy genomic sequences. Using the Illumina GoldenGate Genotyping platform we placed 558 markers into five linkage groups corresponding to the five chromosomes of Brachypodium. The unusually long total genetic map length, 1,598 centiMorgans (cM), indicates that the Brachypodium mapping population has a high recombination rate. By comparing the genetic map to genome features we showed that the recombination rate was positively correlated with gene density and negatively correlated with repetitive regions and the sites of ancestral chromosome fusions. By comparing adjacent regions with high and low recombination rates we showed that recombination rate was positively correlated with the degree of synteny between Brachypodium and rice. We created a robust genetic map that will serve as a foundation for future genetic studies in this new model plant. Recombination rate was positively correlated with gene density and negatively correlated with repeat density, two findings that have been observed in numerous other organisms. There was a surprising correlation between interspecific synteny and recombination rate.