Genetic and biological analysis of root lesion nematode (Pratylenchus thornei) resistance loci in wheat

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dc.contributor.advisorCollins, Nicholas C.
dc.contributor.advisorOldach, Klaus H.
dc.contributor.advisorLinsell, Katherine J.
dc.contributor.authorRahman, Muhammad Shefatur
dc.contributor.schoolSchool of Agriculture, Food and Wineen
dc.date.issued2019
dc.descriptionIncludes Appendix 1 -- Appendix 2 -- Movie Clip 6.1
dc.description.abstractThe root lesion nematode Pratylenchus thornei feeds on roots of wheat (Triticum aestivum) plants, causing significant damage to the roots at the cellular level, resulting in yield reduction. In a previous study, P. thornei resistance QTL, QRlnt.sk-6D and QRlnt.sk-2B were identified in a Sokoll/Krichauff wheat DH population. The current project was undertaken with the aim to dissect the genetic and biological basis of this resistance. To better define the genetic basis of resistance, both resistance loci were fine mapped using the Sokoll/Krichauff DH population and six newly developed RIL populations. Bulked segregation analysis with the 90K Wheat SNP array identified linked SNPs, which were subsequently converted to KASP assays for mapping in the DH and RIL populations. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Ae. tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid-biosynthetic-pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker assisted breeding of P. thornei resistant wheat cultivars. To quantify P. thornei from wheat root, a qPCR-based assay was developed. A standard curve was produced to quantify P. thornei from wheat root samples. The standard curve was validated by estimating P. thornei from sixteen wheat lines with known levels of resistance. Overall, the assay was 2.4-fold less expensive compared to the commercial service (PreDicta B test, SARDI). The DNA extraction protocol was inexpensive as it works without using a commercial DNA extraction kit. In order to identify metabolites associated with resistance loci, the GC-MS based metabolic profiles of root exudates and root tissues from the resistant lines were compared with the susceptible lines. In root exudates, 21 metabolites were found to be associated with resistance QTL. Likewise, from root tissue, 15 metabolites were found to be associated with the resistance QTL. These metabolites were derived from diverse biochemical groups, including amino acids and amines, organic acids, sugars, sugar alcohols and sugar phosphates. The possible roles of these resistance compounds in P. thornei resistance is largely unknown. However, their nematotoxic properties against other plant parasitic nematodes were discussed. In response to P. thornei infection, the histological and histochemical responses of wheat roots were investigated. The use of the fluorescent dye PKH26 (for P. thornei labelling) and confocal microscopy enabled visualisation of live P. thornei both out and inside wheat root tissue. In response to P. thornei infection, secondary cell wall thickening (deposition of cellulose, callose, lignin and suberin) was observed in the P. thornei resistant cultivar, Sokoll. Secondary cell wall thickening might result in physical reinforcement of the cell wall restricting P. thornei migration in the resistant root tissues.en
dc.description.dissertationThesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food & Wine, 2020en
dc.identifier.urihttp://hdl.handle.net/2440/123683
dc.language.isoenen
dc.provenanceThis electronic version is made publicly available by the University of Adelaide in accordance with its open access policy for student theses. Copyright in this thesis remains with the author. This thesis may incorporate third party material which has been used by the author pursuant to Fair Dealing exceptions. If you are the owner of any included third party copyright material you wish to be removed from this electronic version, please complete the take down form located at: http://www.adelaide.edu.au/legalsen
dc.subjectRoot lesion nematodeen
dc.subjectpratylenchus thorneien
dc.subjectwheaten
dc.subjectQTLen
dc.subjectfine mappingen
dc.subjectdisease resistanceen
dc.subjectmetabolic analysisen
dc.subjectroot exudateen
dc.subjectnematode quantificationen
dc.subjecthistopathologyen
dc.subjectconfocal microscopyen
dc.titleGenetic and biological analysis of root lesion nematode (Pratylenchus thornei) resistance loci in wheaten
dc.typeThesisen

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