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Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

BACKGROUND: Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing who...

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Autores principales: Safaa, Hosam, Khaled, Rawan, Isaac, Suzy, Mostafa, Rofida, Ragab, Mohamed, Elsayed, Dalia A. A., Helal, Mostafa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10587045/
https://www.ncbi.nlm.nih.gov/pubmed/37856056
http://dx.doi.org/10.1186/s43141-023-00556-z
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author Safaa, Hosam
Khaled, Rawan
Isaac, Suzy
Mostafa, Rofida
Ragab, Mohamed
Elsayed, Dalia A. A.
Helal, Mostafa
author_facet Safaa, Hosam
Khaled, Rawan
Isaac, Suzy
Mostafa, Rofida
Ragab, Mohamed
Elsayed, Dalia A. A.
Helal, Mostafa
author_sort Safaa, Hosam
collection PubMed
description BACKGROUND: Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. RESULTS: The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. CONCLUSION: The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.
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spelling pubmed-105870452023-10-21 Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks Safaa, Hosam Khaled, Rawan Isaac, Suzy Mostafa, Rofida Ragab, Mohamed Elsayed, Dalia A. A. Helal, Mostafa J Genet Eng Biotechnol Research BACKGROUND: Microsatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. RESULTS: The total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. CONCLUSION: The current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach. Springer Berlin Heidelberg 2023-10-19 /pmc/articles/PMC10587045/ /pubmed/37856056 http://dx.doi.org/10.1186/s43141-023-00556-z 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 Research
Safaa, Hosam
Khaled, Rawan
Isaac, Suzy
Mostafa, Rofida
Ragab, Mohamed
Elsayed, Dalia A. A.
Helal, Mostafa
Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks
title Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks
title_full Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks
title_fullStr Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks
title_full_unstemmed Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks
title_short Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks
title_sort genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in mallard and muscovy ducks
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10587045/
https://www.ncbi.nlm.nih.gov/pubmed/37856056
http://dx.doi.org/10.1186/s43141-023-00556-z
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