Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies a...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Venugopal Vidya, Duraisamy Prasath, Mohandas Snigdha, Ramasamy Gobu, Charles Sona, Chandan Suravi Maiti
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2021
Materias:
R
Q
Acceso en línea:https://doaj.org/article/42cd520246584939bce150cc5a63c3c5
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:42cd520246584939bce150cc5a63c3c5
record_format dspace
spelling oai:doaj.org-article:42cd520246584939bce150cc5a63c3c52021-11-04T06:49:43ZDevelopment of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)1932-6203https://doaj.org/article/42cd520246584939bce150cc5a63c3c52021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8550423/?tool=EBIhttps://doaj.org/toc/1932-6203Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.Venugopal VidyaDuraisamy PrasathMohandas SnigdhaRamasamy GobuCharles SonaChandan Suravi MaitiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Venugopal Vidya
Duraisamy Prasath
Mohandas Snigdha
Ramasamy Gobu
Charles Sona
Chandan Suravi Maiti
Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)
description Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.
format article
author Venugopal Vidya
Duraisamy Prasath
Mohandas Snigdha
Ramasamy Gobu
Charles Sona
Chandan Suravi Maiti
author_facet Venugopal Vidya
Duraisamy Prasath
Mohandas Snigdha
Ramasamy Gobu
Charles Sona
Chandan Suravi Maiti
author_sort Venugopal Vidya
title Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)
title_short Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)
title_full Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)
title_fullStr Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)
title_full_unstemmed Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)
title_sort development of est-ssr markers based on transcriptome and its validation in ginger (zingiber officinale rosc.)
publisher Public Library of Science (PLoS)
publishDate 2021
url https://doaj.org/article/42cd520246584939bce150cc5a63c3c5
work_keys_str_mv AT venugopalvidya developmentofestssrmarkersbasedontranscriptomeanditsvalidationingingerzingiberofficinalerosc
AT duraisamyprasath developmentofestssrmarkersbasedontranscriptomeanditsvalidationingingerzingiberofficinalerosc
AT mohandassnigdha developmentofestssrmarkersbasedontranscriptomeanditsvalidationingingerzingiberofficinalerosc
AT ramasamygobu developmentofestssrmarkersbasedontranscriptomeanditsvalidationingingerzingiberofficinalerosc
AT charlessona developmentofestssrmarkersbasedontranscriptomeanditsvalidationingingerzingiberofficinalerosc
AT chandansuravimaiti developmentofestssrmarkersbasedontranscriptomeanditsvalidationingingerzingiberofficinalerosc
_version_ 1718445082089095168