KS Aitken1, N Piperidis2, Y Sun2, N Hewage Don2, G Piperidis3 and X Wei3
1Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, QLD 4072, Australia; karen.aitken@uq.edu.au
2Sugar Research Australia, 17 Iris Place, Acacia Ridge, QLD 4110, Australia
3Sugar Research Australia, Level 10, 300 Queen Street, Brisbane, QLD, 4000 Australia
Comparative mapping in sugarcane has had limited application due to initially markers such as AFLPs being used to generate maps for the large genome with no sequence information attached. With the advent of SNP markers generated from sequence data and the release of the R570 genome sequence, there is now the ability to compare genetic maps generated among different varieties. An ability to compare map positions allows the location of genes or quantitative trait loci to be compared confirming their location and providing validation of marker information for breeders to use for marker-assisted selection. Two bi-parental crosses were screened with the 58K sugarcane Axiom array and the genome structure of the parental maps were compared. A total of 597 progeny were genotyped from two crosses. The first cross was between two cultivars Q208 x Q209 and the other a cross between a cultivar, Q241, and QC90-289 an important high-sugar parental clone with high combining ability. The SNP genotyping data were generated from 7432 to 9870 single dose markers. The genetic maps were created using JoinMap V4. The number of linkage groups (LG) for each parent varied from 143 to 200, with total map lengths from 12,486 cM to 14,776 cM generating amongst the highest coverage genetic maps published to date. Comparing linkage groups among the genetic maps showed that 12% to 30% were in common between the parents. Of the LGs in common, the average distance covered was 80 cM. For all parents, large interspecific recombinant linkage groups were identified that involved sugarcane chromosomes Ch5/Ch9/Ch6 and Ch7/Ch10/Ch8 inherited from Saccharum spontaneum. In addition to these, three of the parents had inter-chromosome translocations, all of which involved different chromosomes. These results verify the large diversity in sugarcane genome structure and indicate that sequencing of additional cultivars is required to understand this diverse genome.