Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks.
In silico
Mallard duck
Microsatellite
Muscovy duck
SSR
Journal
Journal, genetic engineering & biotechnology
ISSN: 2090-5920
Titre abrégé: J Genet Eng Biotechnol
Pays: Netherlands
ID NLM: 101317150
Informations de publication
Date de publication:
19 Oct 2023
19 Oct 2023
Historique:
received:
05
07
2023
accepted:
08
10
2023
medline:
19
10
2023
pubmed:
19
10
2023
entrez:
19
10
2023
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
BACKGROUND
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
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
CONCLUSIONS
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.
Identifiants
pubmed: 37856056
doi: 10.1186/s43141-023-00556-z
pii: 10.1186/s43141-023-00556-z
pmc: PMC10587045
doi:
Types de publication
Journal Article
Langues
eng
Pagination
105Subventions
Organisme : University of Bisha
ID : UB-GRP-7-1444
Informations de copyright
© 2023. Academy of Scientific Research and Technology.
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