Characterisation and maintenance of the Australian sugarcane mapping populations
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There were two major aims to this project. The first was to identify markers linked to major diseases of sugarcane that were difficult and expensive to select for. The second objective was to determine the cross-transferability of markers by testing the association between markers and traits in other germplasm. Both of these aims have been successfully addressed. Fiji Disease virus (FDV) and Pachymetra are two major diseases of sugarcane. Both require laborious and expensive screening in the field or glasshouse and consequently, only limited numbers of clones can be screened. Thus, both of these traits are candidates for molecular markers. Successful identification of molecular markers associated with these diseases could enable indirect selection for resistance to be undertaken, in the absence of screening, or with reduced screening, for the diseases themselves. Two populations, Q117 x 74C42 and Q96 x Q178, were developed by Dr Nils Berding (BSS038) and each contained more than 200 progeny. Both populations had been previously scored for numerous sugar-related and agronomic traits and marker-trait associations (QTLs) identified for all traits in the Q117 x 74C42 population. One objective in this project was to see if QTLs identified in Q117 x 74C42 would detect the same traits in the Q96 x Q178 population. Unfortunately, in the process of mapping in this second population, it was discovered that the population was a mixture of several very small, different populations. This project objective could not be completed as planned, but was modified, as discussed below. In addition to the approximately 300 markers already scored on the Q117 x 74C42 population (CTA024), a further 1100 amplified fragment length polymorphism markers (AFLPs), simple sequence repeat (SSR) markers and resistance gene analogue (RGAs) were scored. The first two types were used as they are PCR-based, reliable, easy to generate, and the type of markers currently being used in other sugarcane maps. RGAs are potential candidate genes for disease resistance. Unfortunately, during the amalgamation of the marker information, it became apparent that the replanted progeny clones had become “renumbered” in the field. It was thus not possible to combine the two data sets, and consequently, new maps were developed for the Q117 x 74C42 population using just the AFLP, RGA and SSR data. The 1100 markers were used to develop two parental maps. The Q117 map contains 407 markers in 75 linkage groups, while the 74C42 map contains 447 markers in 84 linkage groups.