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Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties

文献类型： 外文期刊

作者： Yang, Jingjing 1 ; Zhang, Jian 1 ; Han, Ruixi 3 ; Zhang, Feng 1 ; Mao, Aijun 1 ; Luo, Jiang 1 ; Dong, Bobo 1 ; Liu, Hui 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Natl Engn Res Ctr Vegetables, BVRC, Beijing, Peoples R China

2.Beijing Key Lab Vegetable Germplasm Improvement, Beijing, Peoples R China

3.Minist Agr & Rural Affairs Peoples Republ China, Dev Ctr Sci & Technol, Beijing, Peoples R China

4.Molbreeding Biotechnol Co, Shijiazhuang, Hebei, Peoples R China

关键词： simple sequence repeat; target SSR-seq; cucumber; genetic diversity; DNA fingerprint

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2019 年 10 卷

页码：

收录情况： SCI

摘要： Simple sequence repeats (SSR) - also known as microsatellites - have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289x at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.

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