Reference genome-directed resolution of homologous and homeologous relationships within and between different oat linkage maps

Authors: Gutierrezgonzalez, Juan; Garvin, David

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2011
Publication Date: 8/19/2011
Citation: Gutierrez-Gonzalez, J.J., Garvin, D.F. 2011. Reference genome-directed resolution of homologous and homeologous relationships within and between different oat linkage maps. The Plant Genome. 4(3):178-190.

Interpretive Summary: Oats are an important crop for both humans and animals. However, their 21 chromosomes have a complex structure that poses challenges to genetic research, and this had slowed oat crop improvement. We completed a comparison between the chromosome structure of oat to that of Brachypodium, a small grass that is related to oat, but has just five simple chromosomes and whose genetic code has been completely deciphered. We were able to determine that the chromosomes of oat are comprised of rearranged combinations of blocks of Brachypodium chromosomes. In contrast, a wild relative of oat shows less shuffling of chromosome sections. By using different regions of the Brachypodium chromosomes as reference points and then relating oat chromosomes to the reference points, we were able to postulate how oat chromosomes evolved over the last 35 million years. Further, using information from our chromosome comparisons, we are able to suggest how oat scientists might combine oat genetic information obtained by various groups. By improving our understanding of oat chromosome structure, oat scientists will be able to accelerate oat genetics research, leading to new improved oat varieties.

Technical Abstract: Genome research on oat (Avena sativa) has received less attention than wheat and barley because it is a less prominent component of the food chain. To assess the potential of the model grass Brachypodium as a surrogate for oat genome research, the whole genome sequence (WGS) of Brachypodium was employed for comparative analysis with oat genetic linkage maps. Sequences of mapped molecular markers from one diploid Avena and two oat maps were aligned to the Brachypodium WGS to infer syntenic relationships. Diploid Avena and Brachypodium exhibit a high degree of synteny with 18 syntenic blocks covering 87% of the oat genome, which permitted postulation of an ancestral Aveneae chromosome structure. Synteny between oat and Brachypodium was also prevalent, with 50 syntenic blocks covering 76.6% of the Kanota x Ogle linkage map. Co-alignment of diploid and hexaploid maps to Brachypodium helped resolve homoeologous relationships between different oat linkage groups, as well as revealing many major rearrangements in oat subgenomes. Extending the analysis to a second oat linkage map (Ogle x TAM) identified several putative homologous linkage groups across the two oat populations. These results indicate that the Brachypodium genome sequence will be a useful resource to assist genetics and genomics research in oat. The analytical strategy employed here should be applicable for genome research in other cool season grass crops with modest amounts of genomic data.