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Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea
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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8703814/ https://www.ncbi.nlm.nih.gov/pubmed/34961266 http://dx.doi.org/10.3390/plants10122796 |
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author | Nishio, Sogo Kunihisa, Miyuki Taniguchi, Fumiya Kajiya-Kanegae, Hiromi Moriya, Shigeki Takeuchi, Yukie Sawamura, Yutaka |
author_facet | Nishio, Sogo Kunihisa, Miyuki Taniguchi, Fumiya Kajiya-Kanegae, Hiromi Moriya, Shigeki Takeuchi, Yukie Sawamura, Yutaka |
author_sort | Nishio, Sogo |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8703814 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-87038142021-12-25 Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea Nishio, Sogo Kunihisa, Miyuki Taniguchi, Fumiya Kajiya-Kanegae, Hiromi Moriya, Shigeki Takeuchi, Yukie Sawamura, Yutaka Plants (Basel) Article 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. MDPI 2021-12-17 /pmc/articles/PMC8703814/ /pubmed/34961266 http://dx.doi.org/10.3390/plants10122796 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Nishio, Sogo Kunihisa, Miyuki Taniguchi, Fumiya Kajiya-Kanegae, Hiromi Moriya, Shigeki Takeuchi, Yukie Sawamura, Yutaka Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea |
title | Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea |
title_full | Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea |
title_fullStr | Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea |
title_full_unstemmed | Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea |
title_short | Development of SSR Databases Available for Both NGS and Capillary Electrophoresis in Apple, Pear and Tea |
title_sort | development of ssr databases available for both ngs and capillary electrophoresis in apple, pear and tea |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8703814/ https://www.ncbi.nlm.nih.gov/pubmed/34961266 http://dx.doi.org/10.3390/plants10122796 |
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