Cargando…

Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications

Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre atten...

Descripción completa

Detalles Bibliográficos
Autores principales: Kumari, Ratna, Wankhede, Dhammaprakash Pandhari, Bajpai, Akansha, Maurya, Avantika, Prasad, Kartikay, Gautam, Dikshant, Rangan, Parimalan, Latha, M., John K., Joseph, A., Suma, Bhat, Kangila V., Gaikwad, Ambika B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6910694/
https://www.ncbi.nlm.nih.gov/pubmed/31834893
http://dx.doi.org/10.1371/journal.pone.0226002
_version_ 1783479138259042304
author Kumari, Ratna
Wankhede, Dhammaprakash Pandhari
Bajpai, Akansha
Maurya, Avantika
Prasad, Kartikay
Gautam, Dikshant
Rangan, Parimalan
Latha, M.
John K., Joseph
A., Suma
Bhat, Kangila V.
Gaikwad, Ambika B.
author_facet Kumari, Ratna
Wankhede, Dhammaprakash Pandhari
Bajpai, Akansha
Maurya, Avantika
Prasad, Kartikay
Gautam, Dikshant
Rangan, Parimalan
Latha, M.
John K., Joseph
A., Suma
Bhat, Kangila V.
Gaikwad, Ambika B.
author_sort Kumari, Ratna
collection PubMed
description Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species.
format Online
Article
Text
id pubmed-6910694
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-69106942019-12-27 Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications Kumari, Ratna Wankhede, Dhammaprakash Pandhari Bajpai, Akansha Maurya, Avantika Prasad, Kartikay Gautam, Dikshant Rangan, Parimalan Latha, M. John K., Joseph A., Suma Bhat, Kangila V. Gaikwad, Ambika B. PLoS One Research Article Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species. Public Library of Science 2019-12-13 /pmc/articles/PMC6910694/ /pubmed/31834893 http://dx.doi.org/10.1371/journal.pone.0226002 Text en © 2019 Kumari et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kumari, Ratna
Wankhede, Dhammaprakash Pandhari
Bajpai, Akansha
Maurya, Avantika
Prasad, Kartikay
Gautam, Dikshant
Rangan, Parimalan
Latha, M.
John K., Joseph
A., Suma
Bhat, Kangila V.
Gaikwad, Ambika B.
Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications
title Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications
title_full Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications
title_fullStr Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications
title_full_unstemmed Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications
title_short Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications
title_sort genome wide identification and characterization of microsatellite markers in black pepper (piper nigrum): a valuable resource for boosting genomics applications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6910694/
https://www.ncbi.nlm.nih.gov/pubmed/31834893
http://dx.doi.org/10.1371/journal.pone.0226002
work_keys_str_mv AT kumariratna genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT wankhededhammaprakashpandhari genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT bajpaiakansha genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT mauryaavantika genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT prasadkartikay genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT gautamdikshant genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT ranganparimalan genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT latham genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT johnkjoseph genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT asuma genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT bhatkangilav genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications
AT gaikwadambikab genomewideidentificationandcharacterizationofmicrosatellitemarkersinblackpepperpipernigrumavaluableresourceforboostinggenomicsapplications