Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean

Nonoy B. Bandillo, Diego Jarquin, Luis G. Posadas, Aaron J. Lorenz, George L. Graef

Research output: Contribution to journalArticlepeer-review


Increasing the rate of genetic gain for seed yield remains the primary breeding objective in both public and private soybean [Glycine max (L.) Merr.] breeding programs. Genomic selection (GS) has the potential to accelerate the rate of genetic gain for soybean seed yield. Limited studies to date have validated GS accuracy and directly compared GS with phenotypic selection (PS), and none have been reported in soybean. This study conducted the first empirical validation of GS for increasing seed yield using over 1,500 lines and over 7 yr (2010–2016) of replicated experiments in the University of Nebraska–Lincoln soybean breeding program. The study was designed to capture the varying genetic relatedness of the training population to three validation sets: two large biparental populations (TBP-1 and TBP-2) and a large validation set comprised of 457 preselected advanced lines derived from 45 biparental populations (TMP). We found that prediction accuracy (.54) realized in our validation experiments was comparable with what we obtained from a series of cross-validation experiments (.64). Both GS and PS were more effective for increasing the population mean performance compared with random selection (RS). We found a selection advantage of GS over PS, where higher genetic gain and identification of top-performing lines was maximized at 10–20% selected proportion. Genomic selection led to small increases in genetic similarity when compared with PS and RS presumably because of a significant shift on allelic frequencies toward the extremes, suggesting that it could erode genetic diversity more quickly. Overall, we found that GS can perform as effectively as PS but that measures should be considered to protect against loss of genetic variance when using GS.

Original languageEnglish (US)
Article numbere20285
JournalPlant Genome
Issue number1
StatePublished - Mar 2023

Bibliographical note

Funding Information:
The authors would like to acknowledge funding for this project from the University of Nebraska–Lincoln and the Nebraska Soybean Board for funding N. Bandillo's graduate research assistantship and the ongoing soybean breeding program at the University of Nebraska.

Publisher Copyright:
© 2022 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't


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