Fine mapping of nematode resistance genes Rlnn1 and Cre8 in wheat (Triticum aestivum)

The root lesion nematode Pratylenchus neglectus and the cereal cyst nematode Heterodera avenae cause significant yield damage to wheat (Triticum aestivum L.) and crops that are grown in rotation with wheat. The focus of this thesis is on two loci in wheat, Rlnn1and Cre8, which confer resistance against P. neglectus and H. avenae, respectively, with an overall scientific goal of characterizing these two resistance loci as an initiative towards isolation of the causal gene(s) and identification of diagnostic molecular markers for the use in marker-assisted selection in wheat breeding programmes. The thesis presents improvements to an existing Excalibur/Kukri linkage map of chromosome 7A by adding Lr20 (a gene for resistance against leaf rust caused by Puccinia triticina), Sr15 (a gene for resistance against stem rust caused by P. graminis), Psy-A1 (a phytoene synthase gene), Cat3-A1 (a catalase gene) and 59 new molecular markers. The genomic location of the Rlnn1 quantitative trait locus (QTL) was confirmed as the distal end of long arm of chromosome 7A (7AL). It coincides with the position of Lr20/Sr15, Psy-A1, Cat3-A1 and 34 molecular markers. Based on the findings that 1) some markers that collocate with the resistance genes Lr20/Sr15 and Rlnn1 are widely separated in mapping populations that do not segregate for these genes; 2) when anchored to a chromosome 7A syntenic build, these markers spanned a 0.9-Mb region; and 3) no recombinants were found in a large population of recombinant inbred lines, it is suggested that the clustering of molecular markers/genes/QTL at the distal end of 7AL is due to suppressed recombination. The suppressed recombination in Excalibur may be a result of a translocation. This suggestion is based on 1) phylogenetic analysis of Psy-A1 alleles; 2) marker amplification patterns that suggested that sequences at the distal end of 7AL in Excalibur are very different from those in Kukri and Chinese Spring; 3) amplicons observed for a normally 7B-specific marker that collocates with Rlnn1 on 7AL, and 4) FISH images that revealed an unknown putative translocation in Excalibur that is absent in Kukri. It seems likely that the Rlnn1-containing segment of 7AL may have been translocated from a 7B-like chromosome arm with an unknown ancestry. Such a translocation could have pre-dated hexaploidisation and occurred in a tetraploid or diploid ancestor. The thesis also presents a high-resolution genetic linkage map for a Trident/Molineux population. This map was used to confirm the locations of three previously reported QTL for H. avenae, including the Cre8 locus mapped as a large-effect QTL at the distal end of the long arm of chromosome 6B (6BL), with an estimated position 0.9 cM from the closest markers. A cross was designed and made to develop a population for future use in fine mapping. With these materials and with the closely-linked molecular markers developed here, Cre8 seems amenable to positional cloning. In the research conducted for this thesis, the Rlnn1 and Cre8 resistance loci were mapped at the distal ends of 7AL and 6BL, respectively and diagnostic markers were identified for the use in marker-assisted selection. A suppressed recombination at the end of 7AL impedes the prospects of cloning Rlnn1, while the research reported here have identified suitable markers and genetic resources for cloning the Cre8 gene with a forward genetics approach.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 201