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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...

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Autores principales: Nishio, Sogo, Kunihisa, Miyuki, Taniguchi, Fumiya, Kajiya-Kanegae, Hiromi, Moriya, Shigeki, Takeuchi, Yukie, Sawamura, Yutaka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
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.
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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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