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

作   者：Nan Li, Yong-Qi Zheng, Hong-Mei Ding, He-Peng Li, Hua-Zheng Peng, Bo Jiang, Hai-Bo Li
期刊名称：Trees
影响因子：1.842
卷 期 号：2017-9
页     码：
关键词：Casuarina Allocasuarina Simple sequence repeat marker Transcriptome Genetic relationship
论文摘要：
Abstract 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.
Keywords Casuarina Allocasuarina Simple sequence
repeat marker Transcriptome Genetic relationship