An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions.

ABSTRACT:

Background

With the broad application of high-throughput sequencing and its reduced cost, simple sequence repeat (SSR) genotyping by sequencing (SSR-GBS) has been widely used for interpreting genetic data across different fields, including population genetic diversity and structure analysis, the construction of genetic maps, and the investigation of intraspecies relationships. The development of accurate and efficient typing strategies for SSR-GBS is urgently needed and several tools have been published. However, to date, no suitable accurate genotyping method can tolerate single nucleotide variations (SNVs) in SSRs and flanking regions. These SNVs may be caused by PCR and sequencing errors or SNPs among varieties, and they directly affect sequence alignment and genotyping accuracy

SUBMITTER: Huo Y 

PROVIDER: S-EPMC8424866 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature