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Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea

Authors :
Sogo Nishio
Miyuki Kunihisa
Fumiya Taniguchi
Hiromi Kajiya-Kanegae
Shigeki Moriya
Yukie Takeuchi
Yutaka Sawamura
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.

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