A DNA-based diagnostic for differentiating among New Zealand endemic Podocarpus

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• 作者：Christina W. Marshall ; David Chagné ; Oliver Deusch…
• 关键词：Podocarpus ; DNA markers ; High ; resolution melting ; Tōtara ; Hall’s tōtara ; Interspecific variation
• 刊名：Tree Genetics & Genomes
• 出版年：2015
• 出版时间：August 2015
• 年：2015
• 卷：11
• 期：4
• 全文大小：590 KB
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• 作者单位：Christina W. Marshall (1)
  David Chagné (2)
  Oliver Deusch (1)
  Nicole Gruenheit (3)
  John McCallum (4)
  David Bergin (5)
  Peter J. Lockhart (1)
  Phillip L. Wilcox (6) (7)
  
  1. Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
  2. The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Palmerston North, New Zealand
  3. Faculty of Life Sciences, University of Manchester, Manchester, UK
  4. Plant & Food Research, Lincoln Research Centre, Lincoln, New Zealand
  5. Enivronmental Restoration Ltd., 53 Te Puea Road, RD4, Rotorua, 3074, New Zealand
  6. Scion, 49 Sala St, Private Bag 3020, Rotorua, New Zealand
  7. Department of Biochemistry, University of Otago, Dunedin, New Zealand
  
• 刊物主题：Forestry; Plant Genetics & Genomics; Plant Breeding/Biotechnology; Tree Biology; Biotechnology;
• 出版者：Springer Berlin Heidelberg
• ISSN：1614-2950

文摘

Species of the genus Podocarpus are primarily found in the Southern Hemisphere. In New Zealand, there are four endemic species—Podocarpus acutifolius, Podocarpus nivalis, Podocarpus totara and Podocarpus cunninghamii. The last mentioned two species, tōtara and Hall’s tōtara, are the most economically and culturally important and have been used extensively for carving, timber and medicinal purposes. However, these species are often difficult to distinguish morphologically as seedlings and adults. Useable Po. totara and Po. cunninghamii timber resources are now scarce, and replanting of tōtara is very costly; therefore, cheap diagnostics for ensuring species identity would be useful for replanting. Using expressed sequence tag (EST)-aligned genomic DNA sequences from putative Po. totara × Po. cunninghamii hybrids, we designed 120 primers for high-resolution melting (HRM) assays. These were evaluated in a multi-stage screening process to identify markers that discriminate among New Zealand endemic Podocarpus species. Ten markers reproducibly differentiated at least one species from the other three, and six differentiated two or more species. One marker differentiated all four species. Moreover, two markers were able to identify ‘artifical’ F₁ hybrids of Po. totara and Po. cunninghamii that had been created from mixing equal amounts of DNA from one genotype of each species. Markers also differentiated a non-New Zealand endemic, Podocarpus lawrencei. Phylogenetic analyses indicated that Po. acutifolius accessions were genetically most similar to those of Po. totara, while Po. nivalis was the most genetically distinct species. Our results show that HRM markers can be easily developed from small amounts of next-generation sequence data and used to identify species and determine their phylogenetic relationships.