Identification and Development of Polymorphic Genic-SSRs in Tamarix ramosissima in Alxa Region Based on Transcriptome
- 1Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau/Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
2Inner Mongolia Academy of Forestry Sciences, Hohhot 010010, China
3Daqing Mountains Forest Ecosystem Research Station, Hohhot 010010, China
Received date: 2020-11-20
Accepted date: 2021-05-27
Online published: 2021-05-27
Abstract
Simple sequence repeats located in gene transcribed regions (Genic-SSR) can play important roles in plant adaptation to environmental changes. In this study, the transcriptomes of Tamarix ramosissima from five different locations in Alax were sequenced, assembled, and compared. By using CandiSSR software, a total of 1 185 polymorphic Genic-SSRs representing 157 motif types were identified in 1 123 transcripts. Among them, the trinucleotide repeats (596, 50.30%) were the most abundant, followed by dinucleotide repeats (486, 41.01%). Location analysis showed that 411, 239, and 163 Genic-SSRs were located in CDSs, 5′UTRs, and 3′UTRs of the relevant transcripts, respectively; 78.47% of the trinucleotide SSRs were located in CDSs, and 94.07% of the dinucleotide SSRs were located in UTRs. Among SSRs distributed in CDSs, AGC/GCT, AGG/CCT, AAG/CTT, CCG/CGG, and ATC/GAT were relatively abundant, accounting for 64.48% of all the Genic-SSRs; AG/CT and AT/AT were the most abundant repeat types in UTRs, which together account for 55.22% of all the Genic-SSRs in UTRs. Functional annotation showed that polymorphic Genic-SSRs containing genes enriched in a wide range of GO terms and KEGG pathways that highly related to stress response in T. ramosissima. Of the 15 randomly selected Genic-SSRs, 14 were successfully amplified by using polymerase chain reaction technology and 64 alleles were found in these SSR loci. Genetic polymorphism estimation showed that the mean of expected and observed heterozygosity (He, Ho), polymorphism information content (PIC) of these SSRs were 0.553, 0.421, and 0.493, respectively, demonstrating the feasibility of developing SSR markers by RNA-seq.
Key words： Genic-SSR; polymorphism; RNA-seq; Tamarix ramosissima
Cite this article
Yanan Zhang, Lei Huang, Jiabin Li, Lei Zhang, Zhenhua Dang . Identification and Development of Polymorphic Genic-SSRs in Tamarix ramosissima in Alxa Region Based on Transcriptome[J]. Chinese Bulletin of Botany, 2021 , 56(4) : 433 -442 . DOI: 10.11983/CBB20185
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