Tom Okpul (2011). SWEETPOTATO (IPOMOEA BATATAS (L.) LAM.)YIELD DECLINE: THE ACTIVITY AND INVOLVEMENT OF RETROTRANSPOSONS PhD Thesis, School of Agriculture and Food Sciences, The University of Queensland.

Attached Files (Some files may be inaccessible until you login with your UQ eSpace credentials)
Name Description MIMEType Size Downloads
s41341201_phd_finalthesis.pdf Corrected PhD thesis application/pdf 2.14MB 0
Author Tom Okpul
School, Centre or Institute School of Agriculture and Food Sciences
Institution The University of Queensland
Publication date 2011-08-01
Thesis type PhD Thesis
Supervisor Prof. Ian D. Godwin
Dr. Mark J. Dieters
Prof. Robert M. Harding
Total pages 124
Total black and white pages 124
Language eng
Subjects 070305 Crop and Pasture Improvement (Selection and Breeding)
060404 Epigenetics (incl.Genome Methylation and Epigenomics)
Abstract/Summary Sweetpotato, Ipomoea batatas Lam. (Convolvulaceae), is an important food crop that is now grown in all tropical and sub-tropical countries. There are numerous constraints to the production of sweetpotato, but the most serious of these is the progressive decline in yield and/ or vigour over generations of clonal propagation, a phenomenon commonly referred to as yield decline. Yield decline has been attributed to both pathological (particularly viruses) and genetic (mutations, especially those associated with transposable elements (TEs)) causal agents, which can accumulate over clonal generations. A better understanding of TEs that are integrated into the sweetpotato genome is essential to develop strategies to overcome yield decline. Four experiments were conducted to better the understanding of factors contributing to yield decline by investigating sweetpotato retrotransposons and the use of pathogen-tested (PT) planting materials. The first experiment screened and isolated sequence fragments of long terminal repeat (LTR), reverse transcriptase and gypsy-like RT and envelop-like domains of LTR retrotransposons, and two partial sequences of non-LTR long interspersed element (LINE) in the sweetpotato genome. Using dot blot hybridisation, these elements were found to be present in abundance with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. This is the first report of gypsy-like retrotransposons in sweetpotato; and they were found to be homologous to the transcriptionally active Bagy-2 of barley (Hordeum vulgare). In order to determine whether a sub-set of these isolated elements are transcriptionally active in sweetpotato, the second experiment was conducted to evaluate the effect of water deficit stress on their levels of transcription. Using two sweetpotato cultivars, Wanmun and Beauregard, it was possible to test for genotypic differences in retrotransposon transcription under different water regimes using semi-quantitative RT-PCR. The retrotransposons studied were active under normal conditions, and the prolonged periods of water deficit stress did influence their transcription levels, particularly for IbLtr-1, IbGy-1 and IbRt-1. This is also the first report of constitutive expression of a number of retrotransposons in sweetpotato. The third experiment was conducted to investigate the utility of retrotransposon-based markers in assessing diversity in 50 sweetpotato cultivars originating from Papua New Guinea (PNG), the Solomon Islands, Tonga, Australia and the United States. Their genetic diversity and relatedness were assessed using phenotypic, Inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), and simple sequence repeats (SSR) and Inter-SSR (ISSR) markers. The phenotypic markers grouped the cultivars differently from the DNA markers. The DNA markers amplified a total of 182 loci. REMAP markers were the most informative and revealed a higher level of diversity together with ISSR and IRAP markers. Most of this variation was attributed to the PNG germplasm (Hʹ = 0.39, SI = 0.57) although the differences compared to those from other areas were not significant (P>0.05). The narrow diversity observed between these genepools could be attributed to the possible introgression of PNG genes into the Australian germplasm. The IRAP, REMAP and ISSR markers were able to distinguish the cultivars and reveal a clonal variant, which proves them to be useful markers to uncover genetic and epigenetic variation in sweetpotato. The fourth experiment evaluated the productivity of PT and naturally-infected clones of 14 sweetpotato cultivars at Bundaberg, Australia. The field-derived clones were exposed to the endemic viruses, while the PT clones were subjected to thermotherapy and meristem-tip culture to eliminate viral pathogens prior to trialling. The plants were indexed for viruses before and after trialling using nitrocellulose membrane enzyme-linked immunosorbent assay and graft-inoculations onto I. setosa. The PT method proved to be beneficial but cultivar-dependent. No improvements in total yield were observed from the use of PT material for the PNG cultivars, Wosaken, Markham and Wanmun. A similar observation was noted on cv. Wanmun in a study previously conducted at Kerevat, PNG indicating its increased tolerance to the endemic viruses present at the respective trial sites. The cultivars exhibiting such responses may be useful sources of tolerance or resistance for future breeding work. This current study has demonstrated that numerous classes of retrotransposons are present in the Ipomoea genome, with LINEs, gypsy- and copia-like elements abundant. These classes of elements are transcriptionally active, with good evidence that there are genotypic, environmental and possibly developmental factors influencing their transcription. Yield decline is inevitable in cultivars of clonally-propagated plants such as that observed in sweetpotato. The accumulation of viruses over clonal generations is now evident as a significant contributor to yield decline. Notwithstanding, the involvement of TEs remains to be studied further as it seem to be rooted into the plant defence, physiological and epigenetic response machineries and their intertwining networks.
Keyword Sweetpotato, yield decline, retrotransposons, molecular markers, water stress
Additional Notes Landscape pages: 29, 75, 76, 83, 94, 95, 99.

Citation counts: Google Scholar Search Google Scholar
Created: Wed, 07 Mar 2012, 06:08:08 EST by Mr Tom Okpul on behalf of Library - Information Access Service