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Appl. Sci. 2015, 5(4), 1050-1063; doi:10.3390/app5041050

Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.)

1
Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China
2
College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Academic Editor: Takayoshi Kobayashi
Received: 14 September 2015 / Revised: 13 October 2015 / Accepted: 23 October 2015 / Published: 5 November 2015
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Abstract

Transcriptome analysis is an efficient way to explore molecular markers in plant species, for which genome sequences have not been published. To address the limited number of markers published for the Welsh onion, this study found 6486 loci of genic simple sequence repeats (SSR), which consisted of 1–5 bp repeat motifs, based on next-generation sequencing (NGS) technology and the RNA-Seq approach. The most abundant motif was mononucleotide (52.33%), followed by trinucleotide (31.96%), and dinucleotide (14.57%). A total of 2525 primer pairs were successfully designed, and 91 out of 311 tested primers were polymorphisms. Overall, 38 genic SSR markers were randomly selected to further validate the degree of genetic diversity, and 22 genic SSR markers (57.89%) showed high levels of polymorphism. The average polymorphism information content (PIC) value and the number of alleles (Na) were 0.63 and 5.27, respectively, and the unweighted pair-group method with arithmetic average (UPGMA) cluster analysis grouped the 22 Allium accessions into three groups with Nei’s similarity coefficients ranging from 0.37 to 0.99. This result suggested that these genic SSR markers could be used to develop a higher resolution genetic map and/or to analyze the phylogenetic relationships among Allium plants in the near future. View Full-Text
Keywords: simple sequence repeats (SSR); genic marker; transcriptome; genetic diversity; Allium fistulosum L. simple sequence repeats (SSR); genic marker; transcriptome; genetic diversity; Allium fistulosum L.
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Yang, L.; Wen, C.; Zhao, H.; Liu, Q.; Yang, J.; Liu, L.; Wang, Y. Development of Polymorphic Genic SSR Markers by Transcriptome Sequencing in the Welsh Onion (Allium fistulosum L.). Appl. Sci. 2015, 5, 1050-1063.

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