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Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)

The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit...

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Autores principales: Solomon, Abate Mekonnen, Kim, Tae-Gun, Han, Koeun, Lee, Hea-Young, Patil, Abhinandan, Siddique, Muhammad Irfan, Ahn, Jeonghwan, Kang, Byoung-Cheorl
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273576/
https://www.ncbi.nlm.nih.gov/pubmed/34262581
http://dx.doi.org/10.3389/fpls.2021.675474
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author Solomon, Abate Mekonnen
Kim, Tae-Gun
Han, Koeun
Lee, Hea-Young
Patil, Abhinandan
Siddique, Muhammad Irfan
Ahn, Jeonghwan
Kang, Byoung-Cheorl
author_facet Solomon, Abate Mekonnen
Kim, Tae-Gun
Han, Koeun
Lee, Hea-Young
Patil, Abhinandan
Siddique, Muhammad Irfan
Ahn, Jeonghwan
Kang, Byoung-Cheorl
author_sort Solomon, Abate Mekonnen
collection PubMed
description The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F(2) and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200–250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation.
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spelling pubmed-82735762021-07-13 Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.) Solomon, Abate Mekonnen Kim, Tae-Gun Han, Koeun Lee, Hea-Young Patil, Abhinandan Siddique, Muhammad Irfan Ahn, Jeonghwan Kang, Byoung-Cheorl Front Plant Sci Plant Science The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F(2) and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200–250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation. Frontiers Media S.A. 2021-06-28 /pmc/articles/PMC8273576/ /pubmed/34262581 http://dx.doi.org/10.3389/fpls.2021.675474 Text en Copyright © 2021 Solomon, Kim, Han, Lee, Patil, Siddique, Ahn and Kang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Solomon, Abate Mekonnen
Kim, Tae-Gun
Han, Koeun
Lee, Hea-Young
Patil, Abhinandan
Siddique, Muhammad Irfan
Ahn, Jeonghwan
Kang, Byoung-Cheorl
Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)
title Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)
title_full Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)
title_fullStr Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)
title_full_unstemmed Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)
title_short Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)
title_sort fine mapping and candidate gene identification for the capup locus controlling fruit orientation in pepper (capsicum spp.)
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273576/
https://www.ncbi.nlm.nih.gov/pubmed/34262581
http://dx.doi.org/10.3389/fpls.2021.675474
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