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A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetabl...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962762/ https://www.ncbi.nlm.nih.gov/pubmed/27602231 http://dx.doi.org/10.1038/hortres.2016.36 |
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author | Hulse-Kemp, Amanda M Ashrafi, Hamid Plieske, Joerg Lemm, Jana Stoffel, Kevin Hill, Theresa Luerssen, Hartmut Pethiyagoda, Charit L Lawley, Cindy T Ganal, Martin W Van Deynze, Allen |
author_facet | Hulse-Kemp, Amanda M Ashrafi, Hamid Plieske, Joerg Lemm, Jana Stoffel, Kevin Hill, Theresa Luerssen, Hartmut Pethiyagoda, Charit L Lawley, Cindy T Ganal, Martin W Van Deynze, Allen |
author_sort | Hulse-Kemp, Amanda M |
collection | PubMed |
description | The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F(2) individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network. |
format | Online Article Text |
id | pubmed-4962762 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-49627622016-09-06 A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding Hulse-Kemp, Amanda M Ashrafi, Hamid Plieske, Joerg Lemm, Jana Stoffel, Kevin Hill, Theresa Luerssen, Hartmut Pethiyagoda, Charit L Lawley, Cindy T Ganal, Martin W Van Deynze, Allen Hortic Res Article The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F(2) individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network. Nature Publishing Group 2016-07-27 /pmc/articles/PMC4962762/ /pubmed/27602231 http://dx.doi.org/10.1038/hortres.2016.36 Text en Copyright © 2016 The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Hulse-Kemp, Amanda M Ashrafi, Hamid Plieske, Joerg Lemm, Jana Stoffel, Kevin Hill, Theresa Luerssen, Hartmut Pethiyagoda, Charit L Lawley, Cindy T Ganal, Martin W Van Deynze, Allen A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding |
title | A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding |
title_full | A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding |
title_fullStr | A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding |
title_full_unstemmed | A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding |
title_short | A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding |
title_sort | hapmap leads to a capsicum annuum snp infinium array: a new tool for pepper breeding |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962762/ https://www.ncbi.nlm.nih.gov/pubmed/27602231 http://dx.doi.org/10.1038/hortres.2016.36 |
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