Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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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.