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Genome-wide identification and validation of simple sequence repeats (SSRs) from Asparagus officinalis

文献类型： 外文期刊

作者： Li, Shufen 1 ; Zhang, Guojun 2 ; Li, Xu 1 ; Wang, Lianjun 3 ; Yuan, Jinhong 1 ; Deng, Chuanliang 1 ; Gao, Wujun 1 ;

作者机构： 1.Henan Normal Univ, Coll Life Sci, Xinxiang 453007, Henan, Peoples R China

2.Xinxiang Med Univ, Sch Basic Med Sci, Xinxiang 453003, Henan, Peoples R China

3.Hubei Acad Agr Sci, Inst Food Corps, Wuhan 430064, Hubei, Peoples R China

关键词： Asparagus officinalis;Genetic diversity;Genomic SSRs;Microsatellites;Motif

期刊名称：MOLECULAR AND CELLULAR PROBES （ 影响因子：2.365； 五年影响因子：2.386 ）

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收录情况： SCI

摘要： Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species. (C) 2016 Elsevier Ltd. All rights reserved.

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