ArticleBMC genomics2019
Application of high-throughput amplicon sequencing-based SSR genotyping in genetic background screening.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A High-Throughput Genotyping Workflow and an Optimized SSR Panel for High-Accuracy Parentage Analysis in Largemouth Black Bass.Marine biotechnology (New York, N.Y.) · 2026Article
- Substantial enhancement ofHorticulture research · 2025Article
- The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity inInternational journal of molecular sciences · 2024Article
- CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis inInternational journal of molecular sciences · 2023Article
- Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2.Microbiology spectrum · 2023Article
- Development and verification of SSR markers from drought stress-responsive miRNAs in Dongxiang wild rice (Oryza rufipogon Griff.).Functional & integrative genomics · 2022Article
- De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity.PloS one · 2021Article
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Authors and funding
16 authors.
Funding
Abstract
backgroundHost genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-assisted backcrossing (MAB), transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) editing are three commonly used genetic engineering techniques. However, methods for genetic background screening between genetically engineered organisms and corresponding recipients suffer from low efficiency, low accuracy or high cost.
resultsHere, we improved our previously reported AmpSeq-SSR method, an amplicon sequencing-based simple sequence repeat (SSR) genotyping method, by selecting SSR loci with high polymorphism among varieties. Ultimately, a set of 396 SSRs was generated and applied to evaluate the genetic backgrounds identity between rice lines developed through MAB, transgenesis, and CRISPR/Cas9 editing and the respective recipient rice. We discovered that the percentage of different SSRs between the MAB-developed rice line and its recipient was as high as 23.5%. In contrast, only 0.8% of SSRs were different between the CRISPR/Cas9-system-mediated rice line and its recipient, while no SSRs showed different genotypes between the transgenic rice line and its recipient. Furthermore, most differential SSRs induced by MAB technology were located in non-coding regions (62.9%), followed by untranslated regions (21.0%) and coding regions (16.1%). Trinucleotide repeats were the most prevalent type of altered SSR. Most importantly, all altered SSRs located in coding regions were trinucleotide repeats.
conclusionsThis method is not only useful for the background evaluation of genetic resources but also expands our understanding of the unintended effects of different genetic engineering techniques. While the work we present focused on rice, this method can be readily extended to other organisms.
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