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Item Isolation and characterisation of cell wall polysaccharides from taewa (Māori potatoes; Solanum tuberosum L.)(Elsevier B.V., 2026-02) Luiten CA; Hinkley SFR; Roskruge NR; Semese SA; Heath A-LM; Perry TL; Rehrer NJ; Sims IMTaewa are varieties of potato introduced to New Zealand by European explorers in the late 18th century. The aim of this research was to extract and characterise cell wall polysaccharides from three varieties of taewa (Huakaroro, Tutaekuri, Moemoe) and compare their composition and structure with a modern potato variety (Agria). The yield of cell walls ranged from 22.8 mg to 42 mg per gram fresh weight potato and was higher for Tutaekuri than other taewa varieties and Agria. Cell walls of Tutaekuri also contained the highest amounts of galactose and the highest level of pectic polysaccharides compared with other varieties. Sequential fractionation of the cell walls gave two pectic polysaccharides fractions (imidazole + Na2CO3 and residue wash), and a hemicellulose fraction (4 M KOH). The residue wash fractions contained higher proportions of rhamnogalacturonan-I than the imidazole + Na2CO3 fraction. Constituent sugar and glycosyl linkage compositions indicated that there were differences in the detailed structural features of the pectic polysaccharides among the taewa varieties and Agria. The imidazole + Na2CO3 fraction from Moemoe had a lower rhamnogalacturonan-I/homogalacturonan ratio and a lower side-chain/rhamnose ratio than the other varieties. Glycosyl linkage analysis indicated that Moemoe had shorter galactan side-chains than the other varieties. Constituent sugar and glycosyl linkage analysis of the 4 M KOH fractions gave linkages that were typical of solanaceous xyloglucans. This knowledge provides added value to taewa suggesting that as well as their important role as a taonga species for Māori, they could contribute to human health outcomes.Item Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package.(MDPI (Basel, Switzerland), 2024-09-25) Angelin-Bonnet O; Vignes M; Biggs PJ; Baldwin S; Thomson S; Hojsgaard DBackground/Objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature. This tool is applicable to all ploidy levels; we notably provide functionalities to facilitate the visualisation of GWAS results obtained for autotetraploid organisms with the GWASpoly package. Results: We illustrate the capabilities of hidecan with examples from two autotetraploid potato datasets. Conclusions: The hidecan package is implemented in R and is publicly available on the CRAN repository and on GitHub. A description of the package, as well as a detailed tutorial, is made available alongside the package. It is also part of the VIEWpoly tool for the visualisation and exploration of results from polyploids computational tools.Item Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes(BioMed Central Ltd, 2023-05-05) Angelin-Bonnet O; Thomson S; Vignes M; Biggs PJ; Monaghan K; Bloomer R; Wright K; Baldwin SBACKGROUND: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype. Here, we used capture sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis (GWAS) for tuber bruising. In addition, we collected transcriptomic data to enrich the GWAS results. However, there is currently no satisfactory method to represent both GWAS and transcriptomics analysis results in a single visualisation and to compare them with existing knowledge about the biological system under study. RESULTS: When investigating population structure, we found that the STRUCTURE algorithm yielded greater insights than discriminant analysis of principal components (DAPC). Importantly, we found that markers with the highest (though non-significant) association scores were consistent with previous findings on tuber bruising. In addition, new genomic regions were found to be associated with tuber bruising. The GWAS results were backed by the transcriptomics differential expression analysis. The differential expression notably highlighted for the first time the role of two genes involved in cellular strength and mechanical force sensing in tuber resistance to bruising. We proposed a new visualisation, the HIDECAN plot, to integrate the results from the genomics and transcriptomics analyses, along with previous knowledge about genomic regions and candidate genes associated with the trait. CONCLUSION: This study offers a unique genome-wide exploration of the genetic components of tuber bruising. The role of genetic components affecting cellular strength and resistance to physical force, as well as mechanosensing mechanisms, was highlighted for the first time in the context of tuber bruising. We showcase the usefulness of genomic data from breeding programmes in identifying genomic regions whose association with the trait of interest merit further investigation. We demonstrate how confidence in these discoveries and their biological relevance can be increased by integrating results from transcriptomics analyses. The newly proposed visualisation provides a clear framework to summarise of both genomics and transcriptomics analyses, and places them in the context of previous knowledge on the trait of interest.Item Traditional knowledge systems and crops : case studies on the introduction of kūmara (Ipomoea batatas) and taewa Māori (Solanum tuberosum) to Aotearoa/New Zealand : a thesis presented in partial fulfilment of the requirement for the degree of Master of AgriScience in Horticultural Science at Massey University, Manawatū, New Zealand(Massey University, 2015) Estrada de la Cerda, RodrigoKūmara (Ipomoea batatas) and taewa Māori, or Māori potato (Solanum tuberosum), are arguably the most important Māori traditional crops. Over many centuries, Māori have developed a very intimate relationship to kūmara, and later with taewa, in order to ensure the survival of their people. There are extensive examples of traditional knowledge aligned to kūmara and taewa that strengthen the relationship to the people and acknowledge that relationship as central to the human and crop dispersal from different locations, eventually to Aotearoa / New Zealand. This project looked at the diverse knowledge systems that exist relative to the relationship of Māori to these two food crops; kūmara and taewa. A mixed methodology was applied and information gained from diverse sources including scientific publications, literature in Spanish and English, and Andean, Pacific and Māori traditional knowledge. The evidence on the introduction of kūmara to Aotearoa/New Zealand by Māori is indisputable. Mātauranga Māori confirms the association of kūmara as important cargo for the tribes involved, even detailing the purpose for some of the voyages. Less conclusive is the earlier introduction of kūmara to the Pacific from South America. In the case of taewa, both traditional Māori knowledge and early literature confirm the potato as an introduction during the first decade of recorded European contact. The aim of this thesis was to look to various knowledge sources and determine what can contribute to a discussion around the early introduction of key food crops to Aotearoa / New Zealand and also to understand the most important factors affecting each crop’s mode of introduction, assisted or not. Various key factors which clearly define the Māori relationship to these foods have been identified. These include: the conduit the crops provided in determining and continuing a relationship between cultures across the South Pacific and including the South American continent and cultures; the contribution of scientific knowledge from western science including oceanography, ethnography, ethnobotany and horticulture generally; the perceived importance of these crops as witnessed at the time of European contact, by both the Spanish and Portuguese in the wider Pacific region, and subsequently the British, French, and other peoples including their missionary cohorts in Aotearoa / New Zealand, and; the extended value of these crops to the endurance of Māori culture (physically, socially and spiritually). Both crops retain an importance to Māori society which is beyond doubt.Item Physiological aging in taewa Māori (Māori potatoes, Solanum tuberosum) and the suitability of different cultivars for short season cropping : a thesis in partial fulfilment of the requirements for the degree of Master of Agriscience in Horticulture at Massey University, Palmerston North, New Zealand(Massey University, 2013) Hutchins, DanielAltering the storage regime of potato (Solanum tuberosum) seed tubers alters the performance of crops grown from those tubers. The size and nature of these effects are cultivar specific. Potato seed tubers progress through a number of stages during storage, a process known as physiological aging. The rate of aging is affected by many factors the most significant of which is the amount of warming (thermal time) the seed is exposed to during storage. Having seed tubers of an appropriate age can increase early crop growth and improve early yields. With the recent establishment of the Tomato-Potato Psyllid (Bactericera cockerelli, TPP) in New Zealand, shorter growing seasons have become desirable, as ongoing costs of controlling TPP on potatoes and other crops are significant. Taewa Māori (Māori potato; Solanum tuberosum ssp. tuberosum & andigena) have been grown in New Zealand for over 220 years and have developed into a range of potato cultivars unique to New Zealand. Taewa hold significant cultural value and are part of the story of early colonial New Zealand. Seed tubers from three cultivars of taewa, Moemoe, Kowiniwini and Waiporoporo, were exposed to different periods of warming (thermal time, degree-days) prior to planting. All three cultivars displayed some level of resistance to the effects of physiological aging over the range of thermal time studied. However some effects were observed. There was an increase in tuber number with an increased thermal time in the cultivar Moemoe, but no change in tuber fresh weight in any treatment. The tuber dry matter in Waiporoporo was highest in tubers exposed to 728 degree- days indicating there may be an optimal amount of degree-days in terms of this parameter. The resistance of these taewa to physiological aging means growers might save on cool-storage costs by reducing storage time. The early harvests and physiology of the three cultivars were assessed for their suitability to a short (90 day) season. The cultivar Waiporoporo showed the best yield characteristics for a table potato crop over a 90-day season. Waiporoporo set fewer tubers than the other two cultivars but the tubers it produced were larger and more suited to the table market. Waiporoporo had a higher tuber fresh weight than Kowiniwini and greater leaf area than Moemoe at 90 days after planting (DAP). Moemoe showed the best potential in terms of the salad potato, new potato and gourmet markets that require smaller tubers than the table market. Taewa growers looking to shorten their cropping season should consider using the cultivar Waiporoporo for the table market, and Moemoe for markets that require smaller potatoes.Item Phytochemical-rich potato extracts and potential for risk reduction in tamoxifen treatment of breast cancer : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Nutritional Science at Massey University, Palmerston North, New Zealand(Massey University, 2013) Chong, Esther Swee LanExisting data suggest an inverse correlation between breast cancer risk and vegetable consumption, and the anticancer effects of vegetables are attributed to the diversity and abundance of phytochemicals. Standard endocrine therapies for breast cancer are associated with significant side effects and not always effective. Undoubtedly, there is a need for improved treatment of breast cancer. In the quest for better breast cancer treatments with fewer side effects, food and nutrition represent a logical strategy to explore. Potato (Solanum tuberosum L.) was chosen for the present project as the target vegetable for investigation. Pigmented potato has recently attracted research attention because of its potential health benefits. Two potato extracts were prepared from a white and purple variety (‘Urenika’) and referred to as WPE and PPE respectively. Tamoxifen and estradiol exhibited paradoxical effects: each of them was inhibitory at high doses but stimulatory at low to moderate doses, on proliferation of two breast cancer cell lines, MCF-7 and T-47D. In contrast, both PPE and WPE inhibited cell proliferation in a dose-dependent manner without paradoxical effects. The potato extracts also blocked estradiol- or tamoxifeninduced cell proliferation of these two cell lines. These findings imply that both potato extracts may have a role to play in prevention of breast cancer, or complementing tamoxifen to achieve desirable treatment efficacy. Since both PPE and WPE were equivalent in efficacy, one (PPE) was selected for further study, given the intention of developing a nutraceutical or therapeutic product of New Zealand proprietary value. Phytochemical compositions of the potato extracts were identified and quantified using ultra high performance liquid chromatography-mass spectrometry, many of which were reported for the first time in variety ‘Urenika’. Several compounds were found at doses which have been reported individually to exert bioactive effects against cancer. It is possible the antiproliferative effects of potato extracts resulted from more than one of these bioactive compounds working together. Dose-dependent apoptotic effects of PPE were observed in T-47D culture, and a combined effect seems to exist between PPE and tamoxifen in modulating the S and G2/M phase. In summary, the key contributions and significance of current thesis are: (1) demonstration of the “risk” zone for tamoxifen (10-8 to 10-6 M) and estradiol (10-10 to 10-8 M) concentrations which may stimulate breast cancer cell growth. Note that these concentrations of tamoxifen or estradiol are physiologically achievable. Furthermore, one key novel finding is regarding the estradiol dependency of tamoxifen action. Specifically, at low to moderate doses (10-9 to 10-8 M) of tamoxifen, there is a threshold of estradiol (> 10-8 M) which allows a significant inhibitory action to occur. The stimulatory action of tamoxifen and complex interaction between tamoxifen and estradiol observed in vitro may partially explain the failure of tamoxifen treatment in some patients. Owing to the vast differences between cell culture experiments and the human body, a more systematic in vivo investigation of clinical effects of tamoxifen over a range of different doses under various estradiol concentrations is warranted; (2) pioneering data on the efficacy of ‘Urenika’ extract against breast cancer in vitro; (3) a metastatic breast cancer animal model which successfully generated metastasis to distant sites (lymph nodes, lungs, livers and spleens), mimicking advanced stage of breast cancer in humans. This model could be used in future testing of the effect of PPE and the combined treatments (PPE with tamoxifen) on establishment and metastasis; and (4) a ‘refined’ non-invasive feeding methodology, which is more ethical than oral gavages, for tamoxifen administration in mice was developed and results obtained were comparable to the method of intraperitoneal injection. Using this model and the non-invasive feeding method, a dose-dependent stimulatory effect of tamoxifen on growth of 4T1 tumours was observed in mice. The current thesis has derived a new hypothesis which may be worth clinical investigation: tamoxifen may induce excessive leukocytosis which contributes to tumour invasiveness and growth. This thesis also represents a significant contribution to the potential use of potato extracts in reducing the risk of tamoxifen in stimulating cancer growth.Item The deconstruction of pectic rhamnogalacturonan I unmasks the occurrence of a novel arabinogalactan oligosaccharide epitope(Oxford University Press (OUP), 1/11/2015) Buffetto F; Cornuault VRG; Rydahl MG; Ropartz D; Alvarado C; Echasserieau V; Le Gall S; Bouchet B; Tranquet O; Verhertbruggen Y; Willats WGT; Knox JP; Ralet MC; Guillon FRhamnogalacturonan I (RGI) is a pectic polysaccharide composed of a backbone of alternating rhamnose and galacturonic acid residues with side chains containing galactose and/or arabinose residues. The structure of these side chains and the degree of substitution of rhamnose residues are extremely variable and depend on species, organs, cell types and developmental stages. Deciphering RGI function requires extending the current set of monoclonal antibodies (mAbs) directed to this polymer. Here, we describe the generation of a new mAb that recognizes a heterogeneous subdomain of RGI. The mAb, INRA-AGI-1, was produced by immunization of mice with RGI oligosaccharides isolated from potato tubers. These oligomers consisted of highly branched RGI backbones substituted with short side chains. INRA-AGI-1 bound specifically to RGI isolated from galactan-rich cell walls and displayed no binding to other pectic domains. In order to identify its RGI-related epitope, potato RGI oligosaccharides were fractionated by anion-exchange chromatography. Antibody recognition was assessed for each chromatographic fraction. INRA-AGI-1 recognizes a linear chain of (1→4)-linked galactose and (1→5)-linked arabinose residues. By combining the use of INRA-AGI-1 with LM5, LM6 and INRA-RU1 mAbs and enzymatic pre-treatments, evidence is presented of spatial differences in RGI motif distribution within individual cell walls of potato tubers and carrot roots. These observations raise questions about the biosynthesis and assembly of pectin structural domains and their integration and remodeling in cell walls.
