Dataset Information

Simple sequence repeat markers for kanuka (Kunzea spp.; Myrtaceae) present in New Zealand.

ABSTRACT: PREMISE OF THE STUDY:We developed simple sequence repeat (SSR) markers to facilitate population genetic studies on k?nuka (Kunzea spp.; Myrtaceae). METHODS AND RESULTS:A shotgun sequencing library was constructed from leaf material of K. robusta using a Roche 454 Junior sequencer, and a total of 3174 putative SSR regions were identified. Sixteen polymorphic markers were optimized for multiplex PCR on 10 endemic New Zealand Kunzea species. Each of these loci cross-amplified in all tested species. The amplified di-, tri-, and pentanucleotide repeats resulted in eight to 24 alleles per locus for a total of 220 specimens. The mean observed and expected heterozygosity per locus ranged from 0.18 to 0.77 and 0.33 to 0.82, respectively. CONCLUSIONS:The SSR markers we produced are valuable for phylogenetic and population studies on all endemic Kunzea spp. and may also be useful for studies on closely related Kunzea species from Australia.

SUBMITTER: Goeke DF

PROVIDER: S-EPMC5400435 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Simple sequence repeat markers for kānuka (<i>Kunzea</i> spp.; Myrtaceae) present in New Zealand.

Goeke Dagmar F DF Mitchell Caroline M CM Lange Claudia C Houliston Gary J GJ

Applications in plant sciences 20170411 4

<h4>Premise of the study</h4>We developed simple sequence repeat (SSR) markers to facilitate population genetic studies on kānuka (<i>Kunzea</i> spp.; Myrtaceae).<h4>Methods and results</h4>A shotgun sequencing library was constructed from leaf material of <i>K. robusta</i> using a Roche 454 Junior sequencer, and a total of 3174 putative SSR regions were identified. Sixteen polymorphic markers were optimized for multiplex PCR on 10 endemic New Zealand <i>Kunzea</i> species. Each of these loci cr ...[more]

PMID: 28439479

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Project description:Claviceps purpurea is a pathogen that infects most members of Pooideae, a subfamily of Poaceae, and causes ergot, a floral disease in which the ovary is replaced with a sclerotium. When the ergot body is accidently consumed by either man or animal in high enough quantities, there is extreme pain, limb loss and sometimes death.This study was initiated to develop simple sequence repeat (SSRs) markers for rapid identification of C. purpurea. SSRs were designed from sequence data stored at the National Center for Biotechnology Information database. The study consisted of 74 ergot isolates, from four different host species, Lolium perenne, Poa pratensis, Bromus inermis, and Secale cereale plus three additional Claviceps species, C. pusilla, C. paspali and C.fusiformis. Samples were collected from six different counties in Oregon and Washington over a 5-year period. Thirty-four SSR markers were selected, which enabled the differentiation of each isolate from one another based solely on their molecular fingerprints. Discriminant analysis of principle components was used to identify four isolate groups, CA Group 1, 2, 3, and 4, for subsequent cluster and molecular variance analyses. CA Group 1 consisting of eight isolates from the host species P. pratensis, was separated on the cluster analysis plot from the remaining three groups and this group was later identified as C. humidiphila. The other three groups were distinct from one another, but closely related. These three groups contained samples from all four of the host species. These SSRs are simple to use, reliable and allowed clear differentiation of C. humidiphila from C. purpurea. Isolates from the three separate species, C. pusilla, C. paspali and C.fusiformis, also amplified with these markers.The SSR markers developed in this study will be helpful in defining the population structure and genetics of Claviceps strains. They will also provide valuable tools for plant breeders needing to identify resistance in crops or for researchers examining fungal movements across environments.

Dataset Information

Simple sequence repeat markers for kanuka (Kunzea spp.; Myrtaceae) present in New Zealand.

Publications

Simple sequence repeat markers for kānuka (<i>Kunzea</i> spp.; Myrtaceae) present in New Zealand.

Similar Datasets

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