Open AccessLong-term comparison between index selection and optimal independent culling in plant breeding programs with genomic prediction
Author(s) -
Lorena Batista,
R. Chris Gaynor,
Gabriel Rodrigues Alves Margarido,
T. J. Byrne,
P. R. Amer,
Gregor Gorjanc,
John M. Hickey
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0235554
Subject(s) - culling , selection (genetic algorithm) , genetic gain , genomic selection , biology , context (archaeology) , index selection , statistics , evolutionary biology , genetics , genetic variation , computer science , genotype , mathematics , zoology , gene , herd , artificial intelligence , single nucleotide polymorphism , paleontology
In the context of genomic selection, we evaluated and compared breeding programs using either index selection or independent culling for recurrent selection of parents. We simulated a clonally propagated crop breeding program for 20 cycles using either independent culling or an economic index with two unfavourably correlated traits under selection. Cycle time from crossing to selection of parents was kept the same for both strategies. Both methods led to increasingly unfavourable genetic correlations between traits and, compared to independent culling, index selection led to larger changes in the genetic correlation between the two traits. When linkage disequilibrium was not considered, the two methods had similar losses of genetic diversity. Two independent culling approaches were evaluated, one using optimal culling levels and one using the same selection intensity for both traits. Optimal culling levels outperformed the same selection intensity even when traits had the same economic importance. Therefore, accurately estimating optimal culling levels is essential for maximizing gains when independent culling is performed. Once optimal culling levels are achieved, independent culling and index selection lead to comparable genetic gains.