The Northern Wheat Improvement Program (NWIP) of Australia has a major interest in the use of molecular marker-assisted selection of genetically superior cultivars. Molecular Marker Assisted Selection (MAS) has the potential to improve the efficiency of many aspects of the NWIP. The use of molecular markers enables gains in efficiency in breeding programs that previously required a lot of technical input, time, and effort to obtain the goals. Molecular MAS has the potential to reduce the number of years in breeding programs, maintain genetic diversity in recurrent selection programs, and improve the efficiency of backcrossing.
Previous work began the process of developing a framework molecular marker map for the Hartog/Seri RI population relevant to the Germplasm Enhancement Program (GEP) component of the NWIP (Nadella, 1999). Hartog is a selection from an introduction from Mexico, a high quality Australian wheat
cultivar widely grown in the north-eastern region of the Australian wheat belt. Seri M 82 (known to posses the IBL/IRS translocation) was developed by CIMMYT and is a high yielding line in the north-eastern region.
The original map was developed predominantly with AFLP markers. This AFLP map needs to be expanded and developed into a better saturated map to enable (I) analysis of the genetic architecture of traits segregating in the mapping population, and (2) evaluation of the efficiency of MAS for quantitative traits in the GEP and other components of the NWIP. In addition, the use of Simple Sequence Repeat (SSR) markers previously mapped to specific chromosomes would enable specific wheat chromosomes of many AFLP markers to be identified.
This thesis aimed to detect the efficiency and the feasibility of using Marker Assisted Selection before applying this method to assist the genetic improvement oj yield and other traits in Germplasm
Enhancement Program of the Australian Northern Wheat Improvement Program (NWIP). The particular objectives of this thesis were: (i) to select molecular markers that are appropriate for wheat, (ii) to detect polymorphism in wheat lines being used in the NWIP, and to investigate the similarities and relatedness among them, (iii) to construct an integrated SSR-AFLP linkage map for Hartog/Seri inbred population by combining data collected in this study (SSR data) with AFLP data collected by Nadella (1999), and (iv) to perform QTL analysis for markers linked to yellow spot or tan spot (caused by fungus Pyrenophora tritici-repentis) resistance and four important agronomic traits: plant height; days to flowering; grain weight and grain yield.
SSRs have been used to characterize genetic diversity among the 13 wheat (Triticum aestivum) lines used to establish the Germplasm Enhancement Program base populations. This breeding program is focused on yield improvement by
recurrent selection as part of the NWIP. Twenty-three SSR primer pairs were used to detect polymorphisms among the 13 lines. In total, 92 SSR bands were detected, of which 86 were polymorphic among the 13 lines. The dendrogram, constructed using the JACCARD coefficient and UPGMA clustering method, suggested a high level of diversity among the base population, and was in a good agreement with their pedigree information.
The integrated SSR-AFLP linkage map consisting of 85 SSR and 104 AFLP loci and covering a distance of 1230 cM has been constructed. This map comprised 21 wheat chromosomes with the number of markers in each chromosome ranging from 2 (chromosome 6D) to 21 (chromosome IB). This linkage map was used to analyse a number of traits of interest segregating in this population.
Using the SSR-AFLP linkage map for the Hartog/Seri RI population, it was possible to detect three major QTL for yellow spot. Two of these major QTL for
yellow spot resistance were located on chromosome ID and 5B. The other locus was linked to an unmapped AFLP marker XH40M/60B. There was some general agreement and validation between the QTL for agronomic traits detected by the previous AFLP study. However, the SSR-AFLP map detected some extra QTL which were not previously detected on the AFLP map alone. Five extra QTLs were detected on this map. Two QTL, h3 and hA for plant height, were detected on chromosomes 3A and 4D, dtf2 for days to flowering mapped to ID, gwt3 and ^xAfor grain weight mapped to chromosomes IB and 5B, and yldl and yld4 mapped to chromosomes IB and 4D. The QTLs ht3, dtf2, and yldl were located using an irtterval mapping algorithm with the SSR markers.