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Grierson ERP, Thrimawithana AH, van Klink JW, Lewis DH, Carvajal I, Shiller J, Miller P, Deroles SC, Clearwater MJ, Davies KM, Chagné D, Schwinn KE. A phosphatase gene is linked to nectar dihydroxyacetone accumulation in mānuka (Leptospermum scoparium). THE NEW PHYTOLOGIST 2024. [PMID: 38532557 DOI: 10.1111/nph.19714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
Floral nectar composition beyond common sugars shows great diversity but contributing genetic factors are generally unknown. Mānuka (Leptospermum scoparium) is renowned for the antimicrobial compound methylglyoxal in its derived honey, which originates from the precursor, dihydroxyacetone (DHA), accumulating in the nectar. Although this nectar trait is highly variable, genetic contribution to the trait is unclear. Therefore, we investigated key gene(s) and genomic regions underpinning this trait. We used RNAseq analysis to identify nectary-associated genes differentially expressed between high and low nectar DHA genotypes. We also used a mānuka high-density linkage map and quantitative trait loci (QTL) mapping population, supported by an improved genome assembly, to reveal genetic regions associated with nectar DHA content. Expression and QTL analyses both pointed to the involvement of a phosphatase gene, LsSgpp2. The expression pattern of LsSgpp2 correlated with nectar DHA accumulation, and it co-located with a QTL on chromosome 4. The identification of three QTLs, some of the first reported for a plant nectar trait, indicates polygenic control of DHA content. We have established plant genetics as a key influence on DHA accumulation. The data suggest the hypothesis of LsSGPP2 releasing DHA from DHA-phosphate and variability in LsSgpp2 gene expression contributing to the trait variability.
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Affiliation(s)
- Ella R P Grierson
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3216, New Zealand
| | | | - John W van Klink
- PFR, Chemistry Department, University of Otago, Dunedin, 9016, New Zealand
| | - David H Lewis
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | | | - Jason Shiller
- PFR, Te Puke Research Centre, Te Puke, 3182, New Zealand
| | - Poppy Miller
- PFR, Te Puke Research Centre, Te Puke, 3182, New Zealand
| | | | - Michael J Clearwater
- Te Aka Mātuatua - School of Science, University of Waikato, Hamilton, 3216, New Zealand
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
| | - Kathy E Schwinn
- The New Zealand Institute for Plant and Food Research Limited (PFR), Palmerston North, 4472, New Zealand
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2
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Clark A, Wilcox P, Morrison S, Munshi D, Kurian P, Mika J, Chagne D, Allan A, Hudson M. Identifying Māori perspectives on gene editing in Aotearoa New Zealand. Commun Biol 2024; 7:221. [PMID: 38388561 PMCID: PMC10883908 DOI: 10.1038/s42003-024-05896-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
A comment article summarizing a range of research activities that contribute to understanding evolving Māori perspectives on Gene Editing and how they might contribute to future regulation.
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Affiliation(s)
- Amanda Clark
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Phillip Wilcox
- Department of Statistics, University of Otago, Dunedin, New Zealand
| | - Sandy Morrison
- Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - Priya Kurian
- Faculty of Arts, Law, Psychology and Social Sciences, University of Waikato, Hamilton, New Zealand
| | - Jason Mika
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
- Management School, University of Waikato, Hamilton, New Zealand
| | - David Chagne
- Plant and Food Research, Palmerston North, New Zealand
| | - Andrew Allan
- Plant and Food Research, Auckland, New Zealand
- Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand.
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3
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Montanari S, Deng C, Koot E, Bassil NV, Zurn JD, Morrison-Whittle P, Worthington ML, Aryal R, Ashrafi H, Pradelles J, Wellenreuther M, Chagné D. A multiplexed plant-animal SNP array for selective breeding and species conservation applications. G3 (BETHESDA, MD.) 2023; 13:jkad170. [PMID: 37565490 PMCID: PMC10542201 DOI: 10.1093/g3journal/jkad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023]
Abstract
Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.
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Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Ltd, Motueka 7198, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Ltd, Auckland 1025, New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Jason D Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson 7010, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
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4
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Liggins L, Arranz V, Braid HE, Carmelet-Rescan D, Elleouet J, Egorova E, Gemmell MR, Hills SFK, Holland LP, Koot EM, Lischka A, Maxwell KH, McCartney LJ, Nguyen HTT, Noble C, Olmedo Rojas P, Parvizi E, Pearman WS, Sweatman JAN, Kaihoro TR, Walton K, Aguirre JD, Stewart LC. The future of molecular ecology in Aotearoa New Zealand: an early career perspective. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2097709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Vanessa Arranz
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Heather E. Braid
- AUT Lab for Cephalopod Ecology and Systematics, School of Science, Auckland University of Technology, Auckland, New Zealand
| | | | | | - Ekaterina Egorova
- Massey Geoinformatics Collaboratory, School of Mathematical and Computational Sciences, Auckland, New Zealand
| | - Michael R. Gemmell
- Plant Health and Environment Lab, Ministry for Primary Industries, Auckland, New Zealand
| | - Simon F. K. Hills
- Ngāti Porou
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Emily M. Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, New Zealand
| | - Alexandra Lischka
- AUT Lab for Cephalopod Ecology and Systematics, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Kimberley H. Maxwell
- Ngāti Porou
- Te Whakatōhea, Te Whānau-a-Apanui, Ngāitai, Ngāti Tūwharetoa
- Te Kōtahi Research Institute, Faculty of Māori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - Hang T. T. Nguyen
- Faculty of Fisheries, University of Agriculture and Forestry, Hue University, Vietnam
| | - Cory Noble
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | | | - Elahe Parvizi
- School of Science, University of Waikato, Hamilton, New Zealand
| | | | | | | | - Kerry Walton
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - J. David Aguirre
- School of Natural Sciences, Massey University, Auckland, New Zealand
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