Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding

• Published in: PLoS computational biology Vol. 19; no. 9; p. e1010290
• Main Authors: Tchounke, Billy, Sanchez, Leopoldo, Bell, Joseph Martin, Cros, David
• Format: Journal Article
• Language: English
• Published: San Francisco Public Library of Science 01.09.2023; PLOS; Public Library of Science (PLoS)
• Subjects: Algorithms; Biology and Life Sciences; Breeding; Cell division; Elaeis guineensis; Fertilization; Fruits; Genetic aspects; Genetic improvement; Genomics; Haplotypes; Heuristic methods; Inbreeding; Life Sciences; Mate selection; Mathematical optimization; Methods; Mutation; Oil palm; Optimization; Optimization algorithms; Parameter identification; Physical Sciences; Plant breeding; Prohibition; Research and Analysis Methods; Seeds; Self-fertilization; Simulated annealing; Simulation; Cameroon; PLOS COMPUTATIONAL BIOLOGY
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1010290

Genomic selection (GS) is an effective method for the genetic improvement of complex traits in plants and animals. Optimization approaches could be used in conjunction with GS to further increase its efficiency and to limit inbreeding, which can increase faster with GS. Mate selection (MS) typically uses a metaheuristic optimization algorithm, simulated annealing, to optimize the selection of individuals and their matings. However, in species with long breeding cycles, this cannot be studied empirically. Here, we investigated this aspect with forward genetic simulations on a high-performance computing cluster and massively parallel computing, considering the oil palm hybrid breeding example. We compared MS and simple methods of inbreeding management (limitation of the number of individuals selected per family, prohibition of self-fertilization and combination of these two methods), in terms of parental inbreeding and genetic progress over four generations of genomic selection and phenotypic selection. The results showed that, compared to the conventional method without optimization, MS could lead to significant decreases in inbreeding and increases in annual genetic progress, with the magnitude of the effect depending on MS parameters and breeding scenarios. The optimal solution retained by MS differed by five breeding characteristics from the conventional solution: selected individuals covering a broader range of genetic values, fewer individuals selected per full-sib family, decreased percentage of selfings, selfings preferentially made on the best individuals and unbalanced number of crosses among selected individuals, with the better an individual, the higher the number of times he is mated. Stronger slowing-down in inbreeding could be achieved with other methods but they were associated with a decreased genetic progress. We recommend that breeders use MS, with preliminary analyses to identify the proper parameters to reach the goals of the breeding program in terms of inbreeding and genetic gain.