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MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data

文献类型： 外文期刊

作者： Guo, Liang 1 ; Yang, Quan 1 ; Yang, Jing-Wen 1 ; Zhang, Nan 1 ; Liu, Bao-Suo 1 ; Zhu, Ke-Cheng 1 ; Guo, Hua-Yang 1 ; Jian 1 ;

作者机构： 1.Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Key Lab South China Sea Fishery Resources Exploit, Minist Agr & Rural Affairs, Guangzhou 510300, Guangdong, Peoples R China

2.Guangdong Prov Engineer Technol Res Ctr Marine Bi, Guangzhou, Peoples R China

3.Shanghai Ocean Univ, Natl Demonstrat Ctr Expt Fisheries Sci Educ, Shanghai, Peoples R China

关键词： multiplex SSR-PCR; pedigree construction; pipeline; resequencing

期刊名称：ECOLOGY AND EVOLUTION （ 影响因子：2.912； 五年影响因子：3.271 ）

ISSN： 2045-7758

年卷期： 2020 年 10 卷 6 期

页码：

收录情况： SCI

摘要： Next-generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end-to-end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping and allelotyping of dimeric patterns was ten times higher than those for other patterns. The error rate of allelotyping was less than that of genotyping. The allele length range reached approximate saturation with 10 individuals. This pipeline uses allele numbers to select highly polymorphic loci, masks loci with variation, and applies in silico PCR to improve primer specificity. The application of the developed multiplex SSR-PCR assays validated the pipeline's robustness, showing higher polymorphism and stability for the developed simple sequence repeats and a lower cost for genotyping and providing low-depth resequencing data from less than a dozen individuals for the development of markers. This pipeline fills the gap between next-generation sequencing and multiplex SSR-PCR.

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