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Prediction of crossover recombination using parental genomes

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Title Prediction of crossover recombination using parental genomes
 
Creator Peñuela, Mauricio
Riccio-Rengifo, Camila
Finke, Jorge
Rocha, Camilo
Gkanogiannis, Anestis
Wing, Rod A.
Lorieux, Mathias
 
Subject genomes
plant breeding
oryza
recombination
crossing over
 
Description Meiotic recombination is a crucial cellular process, being one of the major drivers of evolution and adaptation of species. In plant breeding, crossing is used to introduce genetic variation among individuals and populations. While different approaches to predict recombination rates for different species have been developed, they fail to estimate the outcome of crossings between two specific accessions. This paper builds on the hypothesis that chromosomal recombination correlates positively to a measure of sequence identity. It presents a model that uses sequence identity, combined with other features derived from a genome alignment (including the number of variants, inversions, absent bases, and CentO sequences) to predict local chromosomal recombination in rice. Model performance is validated in an inter-subspecific indica x japonica cross, using 212 recombinant inbred lines. Across chromosomes, an average correlation of about 0.8 between experimental and prediction rates is achieved. The proposed model, a characterization of the variation of the recombination rates along the chromosomes, can enable breeding programs to increase the chances of creating novel allele combinations and, more generally, to introduce new varieties with a collection of desirable traits. It can be part of a modern panel of tools that breeders can use to reduce costs and execution times of crossing experiments.
 
Date 2023-02-16
2023-11-02T08:50:57Z
2023-11-02T08:50:57Z
 
Type Journal Article
 
Identifier Peñuela, M.; Riccio-Rengifo, C.; Finke, J.; Rocha, C.; Gkanogiannis, A.; Wing, R.A.; Lorieux, M. (2023) Prediction of crossover recombination using parental genomes. PLoS ONE 18(2): e0281804. ISSN: 1932-6203
1932-6203
https://hdl.handle.net/10568/132658
https://doi.org/10.1371/journal.pone.0281804
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format e0281804
application/pdf
 
Publisher Public Library of Science
 
Source PLoS ONE