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Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea
- Source :
- Plants, Vol 10, Iss 12, p 2796 (2021)
- Publication Year :
- 2021
- Publisher :
- MDPI AG, 2021.
-
Abstract
- Developing new varieties in fruit and tea breeding programs is very costly and labor-intensive. Thus, establishing a variety discrimination system is important for protecting breeders’ rights and producers’ profits. Simple sequence repeat (SSR) databases that can be utilized for both next-generation sequencing (SSR-GBS) and polymerase chain reaction–capillary electrophoresis (PCR-CE) would be very useful in variety discrimination. In the present study, SSRs with tri-, tetra- and pentanucleotide repeats were examined in apple, pear and tea. Out of 37 SSRs that showed clear results in PCR-CE, 27 were suitable for SSR-GBS. Among the remaining markers, there was allele dropout for some markers that caused differences between the results of PCR-CE and SSR-GBS. For the selected 27 markers, the alleles detected by SSR-GBS were comparable to those detected by PCR-CE. Furthermore, we developed a computational pipeline for automated genotyping using SSR-GBS by setting a value “α” for each marker, a criterion whether a genotype is homozygous or heterozygous based on allele frequency. The set of 27 markers contains 10, 8 and 9 SSRs for apple, pear and tea, respectively, that are useful for both PCR-CE and SSR-GBS and suitable for automation. The databases help researchers discriminate varieties in various ways depending on sample size, markers and methods.
- Subjects :
- variety discrimination
microsatellite
automation
Botany
QK1-989
Subjects
Details
- Language :
- English
- ISSN :
- 10122796 and 22237747
- Volume :
- 10
- Issue :
- 12
- Database :
- Directory of Open Access Journals
- Journal :
- Plants
- Publication Type :
- Academic Journal
- Accession number :
- edsdoj.1b4bc190b8d45279a7cc230c190e7a4
- Document Type :
- article
- Full Text :
- https://doi.org/10.3390/plants10122796