Estimation of Molecular Pairwise Relatedness in Autopolyploid Crops.

Autor: Amadeu RR; Horticultural Sciences Department, University of Florida, Gainesville, FL.; Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Brazil., Lara LAC; The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.; Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Brazil., Munoz P; Horticultural Sciences Department, University of Florida, Gainesville, FL., Garcia AAF; Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Brazil augusto.garcia@usp.br.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2020 Dec 03; Vol. 10 (12), pp. 4579-4589. Date of Electronic Publication: 2020 Dec 03.
DOI: 10.1534/g3.120.401669
Abstrakt: A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.
(Copyright © 2020 Amadeu et al.)
Databáze: MEDLINE
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