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Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

文献类型： 外文期刊

作者： Li, Xiaoying 1 ; Xu, Hongxia 1 ; Feng, Jianjun 2 ; Chen, Junwei 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Hort, Hangzhou 310021, Zhejiang, Peoples R China

2.Ninghai Agr & Forestry Bur, Ningbo 315600, Zhejiang, Peoples R China

关键词： cluster;genetic analysis;microsatellite;species;transferability

期刊名称：JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE （ 影响因子：1.144； 五年影响因子：1.617 ）

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收录情况： SCI

摘要： Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotryajaponica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus xdomestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, approximate to 12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.

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