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Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species

Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR su...

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Autores principales: Singh, Jagveer, Sharma, Ankush, Sharma, Vishal, Gaikwad, Popat Nanaso, Sidhu, Gurupkar Singh, Kaur, Gurwinder, Kaur, Nimarpreet, Jindal, Taveena, Chhuneja, Parveen, Rattanpal, H. S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322976/
https://www.ncbi.nlm.nih.gov/pubmed/37407627
http://dx.doi.org/10.1038/s41598-023-37024-0
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author Singh, Jagveer
Sharma, Ankush
Sharma, Vishal
Gaikwad, Popat Nanaso
Sidhu, Gurupkar Singh
Kaur, Gurwinder
Kaur, Nimarpreet
Jindal, Taveena
Chhuneja, Parveen
Rattanpal, H. S.
author_facet Singh, Jagveer
Sharma, Ankush
Sharma, Vishal
Gaikwad, Popat Nanaso
Sidhu, Gurupkar Singh
Kaur, Gurwinder
Kaur, Nimarpreet
Jindal, Taveena
Chhuneja, Parveen
Rattanpal, H. S.
author_sort Singh, Jagveer
collection PubMed
description Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
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spelling pubmed-103229762023-07-07 Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species Singh, Jagveer Sharma, Ankush Sharma, Vishal Gaikwad, Popat Nanaso Sidhu, Gurupkar Singh Kaur, Gurwinder Kaur, Nimarpreet Jindal, Taveena Chhuneja, Parveen Rattanpal, H. S. Sci Rep Article Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species. Nature Publishing Group UK 2023-07-05 /pmc/articles/PMC10322976/ /pubmed/37407627 http://dx.doi.org/10.1038/s41598-023-37024-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Singh, Jagveer
Sharma, Ankush
Sharma, Vishal
Gaikwad, Popat Nanaso
Sidhu, Gurupkar Singh
Kaur, Gurwinder
Kaur, Nimarpreet
Jindal, Taveena
Chhuneja, Parveen
Rattanpal, H. S.
Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
title Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
title_full Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
title_fullStr Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
title_full_unstemmed Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
title_short Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
title_sort comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322976/
https://www.ncbi.nlm.nih.gov/pubmed/37407627
http://dx.doi.org/10.1038/s41598-023-37024-0
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