The Introduction of Hi-SSRseq
Microsatellites (short tandem repeats, STR, or simple sequence repeats, SSR) are widely used markers in population genetics. Despite accurate and efficient genotyping of SSRs constitutes the basis of SSRs as an effective genetic marker with various applications, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. single‐nucleotide polymorphisms (SNPs) or insertions/deletions (indel) polymorphisms in the nucleotide sequence of that fragment, either within the repetitive array or in the flanking regions (FR), remain undetected by length assessment alone. Moreover, indels in the flanking regions might be incorrectly confounded with size mutations of the SSR.
As a consequence, the traditional assessment of fragment length may lead to underestimating genetic variability, inaccurate results, or even wrong evolutionary interpretations. To overcome such errors, information about the nucleotide sequence of each allele is needed. CD Genomics provided a technology called Hi-SSRseq that combined the multiplexed amplification of traditional 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, which also greatly reduces the cost and time of genotyping, and the comparison between samples can be directly based on the base sequence.
Our objectives were (a) to generate nucleotide sequence data of several non‐model plant species, for which prior genomic data did not exist, from both the SSR and the flanking regions, (b) to record the length of the repetitive region, as well as SNP and indel variation within the SSR and the FR, (3) to estimate the amount of molecularly accessible size homoplasy of each locus, and (4) to compare the degree of genetic variability between different datasets based on the number of repeat units, fragment length, and sequence identity.
Key Features and Advantages
With state-of-the-art sequencing platforms and deep collaboration with highly experienced technicians and scientists across departments in CD Genomics, an Hi-SSRseq technique is offered that allows to genotype hundreds of individuals at many custom‐designed SSR loci simultaneously, combining multiplex PCR and Illumina sequencing. If you have additional requirements or questions, please feel free to contact us.