Accurate recombination estimation from pooled genotyping and sequencing: a case study on barley.
Breeding value estimation
Genetic map
Pool sequencing
Population genetics
Recombination rate
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
25 Jun 2022
25 Jun 2022
Historique:
received:
06
04
2022
accepted:
15
06
2022
entrez:
25
6
2022
pubmed:
26
6
2022
medline:
29
6
2022
Statut:
epublish
Résumé
Sexual reproduction involves meiotic recombination and the creation of crossing over between homologous chromosomes, which leads to new allele combinations. We present a new approach that uses the allele frequency differences and the physical distance of neighboring polymorphisms to estimate the recombination rate from pool genotyping or sequencing. This allows a considerable cost reduction compared to conventional mapping based on genotyping or sequencing data of single individuals. We evaluated the approach based on computer simulations at various genotyping depths and population sizes as well as applied it to experimental data of 45 barley populations, comprising 4182 RIL. High correlations between the recombination rates from this new pool genetic mapping approach and conventional mapping in simulated and experimental barley populations were observed. The proposed method therefore provides a reliable genetic map position and recombination rate estimation in defined genomic windows.
Identifiants
pubmed: 35752769
doi: 10.1186/s12864-022-08701-7
pii: 10.1186/s12864-022-08701-7
pmc: PMC9233355
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
468Informations de copyright
© 2022. The Author(s).
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