Development and validation of SSR markers based on transcriptome sequencing of Casuarina equisetifolia

• Published in: Trees (Berlin, West) West), 2018-02, Vol.32 (1), p.41-49
• Main Authors: Li, Nan, Zheng, Yong-Qi, Ding, Hong-Mei, Li, He-Peng, Peng, Hua-Zheng, Jiang, Bo, Li, Hai-Bo
• Format: Article
• Language: English
• Subjects: Agriculture; Biological evolution; Biomedical and Life Sciences; Breeding; Casuarina; Casuarina equisetifolia; Cold tolerance; Cultivars; Expressed sequence tags; Forestry; Functional Genomics; Gene expression; Gene polymorphism; Genetic analysis; Genetic diversity; Genetic relationship; Genotype & phenotype; Genotypes; Life Sciences; Loci; Low temperature resistance; Markers; Original Article; Plant Anatomy/Development; Plant breeding; Plant Pathology; Plant Physiology; Plant Sciences; Polymorphism; Population genetics; Population studies; Shelters; Species
• ISSN: 0931-1890; 1432-2285
• DOI: 10.1007/s00468-017-1607-6

Key message Based on Casuarina equisetifolia transcriptome data, the present study developed and validated 15 transferable EST-SSR markers across Casuarina and Allocasuarina species. Casuarina species are valued as pioneer trees for coastal shelter forest construction. To accelerate Casuarina breeding for more robust, attractive, and cold-resistant cultivars, it is essential to introduce molecular marker-assisted breeding. Based on Casuarina equisetifolia transcriptome data, 10,291 EST-SSR loci with the types of 2–6 nucleotide repeats were identified from assembled 118,270 unigenes. An average of one EST-SSR was found every 13.54 kb, and the distribution frequency of SSRs was 8.7%. The most common repeat motifs were dinucleotide with AG/CT and trinucleotide with AAG/CTT. A total of 150 SSR markers were randomly selected for validation, among which 15 produced clear, reproducible and polymorphic bands, and thus were employed for genetic relationship analysis among 26 genotypes from four Casuarina and three Allocasuarina species. A total of 42 bands were identified, varying from 2 to 5 bands per locus with an average of 2.8. Polymorphism information content ranged from to 0.2624 to 0.6177 with a mean value of 0.4265, indicating a high level of polymorphism. The UPGMA dendrogram revealed a high genetic variation resided among species within two genera, Allocasuarina and Casuarina . Meanwhile, the 15 highly polymorphic Casuarina SSR markers were also proved to be transferable across Casuarina and Allocasuarina species. These valuable SSR markers can be applied further for population and evolutionary genetic studies in Casuarinaceae, and will be useful in selection and breeding of Casuarina species for improving cold tolerance.