Browsing by Author "McIntyre, L"

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An assessment of the application of DNA markers to studies of genetic diversity and marker assisted selection in sugarcane : SRDC Final report SD99001
(1999) Carroll, B; McIntyre, L; Berding, N
The project objectives were as follows:
Assessment of bulk segregant analysis and marker- assisted selection for economically important traits in sugarcane : SRDC final report BS138
(1998) Carroll, B; Berding, N; McIntyre, L
The main aim of this project was to assess the feasibility of bulk segregant analysis (BSA) and marker-assisted selection for important traits in sugarcane. The target trait for this feasibility study was rust resistance. Initially, crosses were successfully made between susceptible and resistant parents to produce two mapping populations. Unfortunately and surprisingly, we were not able to identify fully susceptible clones in four separate rust trials on the two populations. Poor rust development occurred in the first bench trial in 1996 at Meringa (including clones known to be susceptible), and the second trial in January 1997 was a total failure due to lack of rust development. The third rust resistance trial was conducted in Meringa in July 1997, but all of the clones in the mapping populations were resistant. The fourth rust trial on these two populations was completed at the start of 1998, and the results confirmed that all of the clones in these two initial mapping populations were resistant to common rust. Lack of segregation for rust resistance within progeny of sugarcane crosses had not been observed previously by sugarcane breeders in Meringa. This unexpected problem delayed the project as BSA could only proceed after a mapping population segregating for rust resistance had been identified.
Characterisation and maintenance of the Australian sugarcane mapping populations
(BSES, 2003) McIntyre, L
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.
Introgression of new genes from Saccharum officinarum
(SRDC, 2004) Jackson, P; Piperidis, G; Aitken, K; Li, J; Morgan, T; Foreman, J; Hewitt, M; McIntyre, L; Berding, N
Modern sugarcane cultivars are derived from two main ancestral species: Saccharum officinarum, which is the main source of high sucrose levels, and S. spontaneum. Only a small number of clones of either species have ever been incorporated into commercial cane breeding programs around the world. While incremental gains in cane yield and ratooning have been made by sugarcane breeders over the last 40 years sugarcane, there is concern that improvement in CCS has been very limited. One hypothesis for this is that because of the limited genetic base of sugarcane favourable alleles for high CCS in the breeding parent pool have already been fixed in current cultivars. If this hypothesis is correct then new genetic diversity will need to be introgressed from germplasm outside current breeding programs. Clones of S. officinarum, available in germplasm collections may provide a source of valuable high sucrose genes. However, introgression breeding using traditional breeding technologies is long term and high risk. The development of new DNA marker techniques has provided new opportunities for improving introgression breeding. These techniques provide a means to (i) characterise diversity within germplasm collections, (ii) identify genes or chromosomal regions, termed quantitative trait loci (QTL), from wild parents which cause positive or negative effects on important traits, which may then be selected for or against during breeding cycles. With this background in mind, this project had two concurrent aims: (i) To characterise a collection of S. officinarum clones for important phenotypic traits and for genetic diversity using DNA markers and identify a set of these for future breeding efforts; (ii) Using case study populations, to assess the value of using DNA marker assisted selection in introgression breeding in sugarcane. A range of candidate S. officinarum x commercial parent crosses were made at the start of the project using a random sample of S. officinarum clones not previously used in our breeding breeding program. From these a “case study” population was chosen for detailed investigation using DNA markers. Two of the progeny were subsequently chosen for “backcrossing” again to proven commercial parents to produce two other “backcross” populations. Concurrently, the collection of 282 S. officinarum clones in the Australian collection was also characterised using DNA markers, along with 147 parent clones in the Australian core breeding program. A subset of 158 S. officinarum clones, recently imported from overseas, was also evaluated in a field trial for CCS and cane yield across a plant and two ratoon crops.
Map-based chromosome and trait tagging in sugarcane using cytological and RFLP markers
(1999) McIntyre, L
Sugarcane is a complex aneuploid, polyploid, interspecific hybrid. At the time that this project began, molecular mapping in sugarcane was in its infancy and was only being attempted in interspecific crosses or within the selfed progeny of a variety. Two objectives of this project were, therefore, to demonstrate that markers could be used in variety by variety crosses in sugarcane and that molecular marker maps could be constructed in such crosses. Using a variety of marker types, these objectives have been met as described below. The major aim of the project was to enable the Australian sugar industry to access overseas information on traits, markers and genome organisation in sugarcane and other grasses. This was to be achieved using two strategies. Firstly, other groups nationally and overseas have begun searching for markers linked to agronomic traits of interest and relevance to sugarcane. These markers, identified in sugarcane and related grasses such as sorghum and maize, might provide a more rapid means of identifying useful markers for the Australian sugarcane industry, as compared to searching for markers de novo, as had been done in all other sugarcane populations to date. The second strategy was to develop a framework map in an Australian sugarcane cross using these and other markers. This map could then be used as a means of both identifying new markers linked to traits of interest in sugarcane and of aligning Australian co-segregation groups with linkage groups, and the information contained within, identified in other maps of sugarcane and related grasses in other laboratories.
Perfect markers for sugarcane mapping
(2001) McIntyre, L
Sugarcane is a complex aneuploid, polyploid, interspecific hybrid. Most breeding traits are complex and molecular markers associated with these traits are a tool that may assist breeders to more efficiently identify sugarcane clones containing these desirable traits. At the start of this project, molecular mapping in sugarcane was relatively new with maps being developed in interspecific crosses or within the selfed progeny of a variety. These maps relied heavily on the use of two major marker types, namely restriction fragment length polymorphisms (RFLPs) and randomly amplified polymorphic DNA (RAPDs), both of which had major disadvantages in their ease and reliability of use. The area of genomics was also very new, and genomics studies of sugarcane were being initiated in Australia, the USA, Brazil and South Africa, generating large amounts of gene information and potential markers for mapping in many traits of interest. The major objectives of this project were, therefore, to compare genomic regions associated with traits in Australian and French sugarcane populations, to demonstrate whether “candidate genes”, derived from partial gene sequences (termed expressed sequence tags, ESTs), were a useful strategy for the identification of closely linked markers for traits of interest, and to develop methods other than the RFLP approach to enable more rapid screening of ESTs in mapping populations. Using a variety of approaches, these objectives have been met as described below. Australian sugarcane maps have now been generated from two crosses involving Australian sugarcane varieties or elite material. Each cross has been used to generate two maps, one for the male and female parent of the cross. The Q1 population is derived from a cross between Q117 and 74C42, while the Q3 population is derived from a cross between Q117 and MQ77-340. The four maps now have approximately 300-450 markers each, using mainly PCRbased markers, namely simple sequence repeat (SSRs) and amplified fragment length polymorphisms (AFLPs). Our policy of using SSRs that have been mapped in the French variety R570, currently the largest published map with approximately 1000 markers, has assisted our comparative mapping attempts between the Australian and French maps. Many of the cosegregation groups identified in the Q1 and Q3 population maps have been tentatively aligned with Linkage Groups in R570 on the basis of shared SSRs. Using this approach, we have shown that the same SSRs are linked to sugar and fibre-related traits in both R570 and Q3 populations. This observation provides additional support to the usefulness of these SSRs in markerassisted selection. In addition, novel associations were also identified for both Q3 and R570 populations. These marker-trait associations could be due to different parts of the genome being mapped in the two populations, to novel alleles in the two populations, or to fixation of this region in one of the populations. The alignment between the R570 and Q3 population maps was more difficult than anticipated because most markers on the R570 map were AFLPs and because marker sizes had not been recorded for either map. AFLPs are plentiful but are more difficult to score accurately and comparatively. In addition, the low level of genome coverage in both maps (~33% for R570 and <20% for Q3) meant that genome comparisons could 3 only be made at the homology group level as it was likely that different linkage groups within a homology group had been mapped in the two populations.