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Development and Transferability of EST-SSR Markers forPinus koraiensisfrom Cold-Stressed Transcriptome through Illumina Sequencing

Li, Xiang and Liu, Xiaoting and Wei, Jiatong and Li, Yan and Tigabu, Mulualem and Zhao, Xiyang (2020). Development and Transferability of EST-SSR Markers forPinus koraiensisfrom Cold-Stressed Transcriptome through Illumina Sequencing. Genes. 11 , 500 , 1-14
[Journal article]

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Abstract

Pinus koraiensishas significant economic and ecological value in Northeast China. However, due to the lack of suitable molecular markers, only a few available microsatellite markers were developed for further population genetics studies. In this study, for the first time we developed expressed sequence tag-simple sequence repeat (EST-SSR) markers from the cold-stressed transcriptome ofP. koraiensisusing Illumina Sequencing. We identified a total of 7,235 EST-SSRs from 97,376 sequences, and we tested their transferability among seven related Pinus species. The results showed that trinucleotides were the most abundant type of repeat (1287, 18.74%) excluding mononucleotides, followed by dinucleotides (1284, 18.7%) and tetranucleotides (72, 1.05%). The most dominant dinucleotides and trinucleotide repeat motifs were AT/AT (535, 7.79%) and AAT/ATT (103, 1.5%). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.002 to 0.986 and 0.017 to 0.743, respectively, and the polymorphism information content (PIC) values and number of alleles (Na) varied from 0.029 to 0.794 and 2 to 23, respectively. A total of 8 naturalP. koraiensispopulations were divided into two main genetic clusters. Furthermore, nine of twenty polymorphic primer pairs were successfully amplified in seven Pinus species, and at least 80% of the successfulP. koraiensisEST-SSR primers could be amplified in more than four species (16, 80%). Combined results for the development of EST-SSR markers inP. koraiensisand transferability among related species would contribute to improved studies on the genetic diversity and population structure inP. koraiensisand phylogenetic relationships among Pinus species. They would also provide a significant source for quantitative trait locus analysis.

Authors/Creators:Li, Xiang and Liu, Xiaoting and Wei, Jiatong and Li, Yan and Tigabu, Mulualem and Zhao, Xiyang
Title:Development and Transferability of EST-SSR Markers forPinus koraiensisfrom Cold-Stressed Transcriptome through Illumina Sequencing
Year of publishing :2020
Volume:11
Article number:500
Number of Pages:14
Publisher:MDPI
ISSN:2073-4425
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
Keywords:Pinus koraiensis, microsatellite markers, population structure, RNA-Seq, interspecific transferability
URN:NBN:urn:nbn:se:slu:epsilon-p-106939
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-106939
Additional ID:
Type of IDID
DOI10.3390/genes11050500
Web of Science (WoS)000542276700109
ID Code:17342
Faculty:S - Faculty of Forest Sciences
Department:(S) > Southern Swedish Forest Research Centre
Deposited By: SLUpub Connector
Deposited On:28 Aug 2020 08:06
Metadata Last Modified:28 Aug 2020 08:06

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