Breeding strategies to enhance ß-glucan content in oats (Avena sativa L.)

Authors: BAZZZER, SUMANDEEP - South Dakota State University; OLIVEIRA, GUIHERME - South Dakota State University; Fiedler, Jason; Nandety, Raja Sekhar; Jannink, Jean Luc; CAFFE, MELANIE - South Dakota State University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2024
Publication Date: 1/14/2025
Citation: Bazzzer, S., Oliveira, G., Fiedler, J.D., Nandety, R., Jannink, J., Caffe, M. 2025. Breeding strategies to enhance ß-glucan content in oats (Avena sativa L.). BMC Genomics. Article 0001a. https://doi.org/10.1186/s12864-024-11174-5.
DOI: https://doi.org/10.1186/s12864-024-11174-5

Interpretive Summary: Oat is an important cereal grain crop that provides human health benefits due to the presence of soluble dietary fiber ß-glucan in its grain. To maintain high amounts of this beneficial component in new varieties that are subject to diverse growing conditions, gene regions that influence this trait can be leveraged. To find these regions of the genome to deploy, we screened 1,230 breeding lines from the South Dakota State University breeding program for B-glucan concentration over several years. Upon analysis, we identified many areas of the oat genome that influence this important trait, validating previous work and uncovering potentially new genes. We also developed statistical models that take all the genome information to predict the traits. Taken together this knowledge enables the selection of breeding lines without direct screening and increases the rate at which we can develop new varieties for the producers.

Technical Abstract: Background: Hexaploid oat (Avena sativa L.) is a commercially important cereal crop due to its soluble dietary fiber ß-glucan, a hemicellulose known to benefit human health. Increasing ß-glucan content is among the primary objectives of oat breeding programs focusing on improving oats for the food market worldwide. To accelerate oat breeding efforts, we leveraged existing breeding datasets (1,230 breeding lines from South Dakota State University oat breeding program grown in multiple environments between 2015 and 2022) to conducta genome-wide association study (GWAS) that identified quantitative trait loci (QTLs) associated with ß-glucan content, and compared strategies to implement genomic selection (GS) to increase ß-glucan content in oat. Results: Large variation for ß-glucan content was observed with values ranging between 3.02 and 7.24 %. An independent GWAS was performed for each breeding panel in each environment and identified 22 loci distributed over fourteen oat chromosomes significantly associated with ß-glucan content. Comparison based on physical position showed that 12 out of 22 loci coincided with previously identified ß-glucan QTLs, and three loci are in the vicinity of cellulose synthesis genes, Cellulose synthase-like (Csl). To perform a GWAS analysis across all panels, the ß-glucan content of each breeding line was predicted for each of the 26 environments. The overall GWAS identified 73 loci, of which 15 coincided with loci identified with individual environments and 37 coincided with previously reported ß-glucan QTLs but that were not identified when performing the GWAS in single years, therefore increasing the ability to detect significantly associated markers. In addition, 21 novel loci were identified that were not reported in the previous studies. The comparison of multiple genomic selection scenarios indicated that using a specific set of markers as a fixed effect in GS models did not increase the prediction accuracy. However, the use of multi-environment data in the training population resulted in an increase in prediction accuracy (0.61-0.72) as compared to single-year (0.28-0.48) data. The use of USDA-SoyWheOatBar-3K genotyping array data resulted in a similar level of prediction accuracy as did genotyping-by-sequencing data. Conclusion: This study identified and confirmed the location of multiple loci associated with ß-glucan content. The proposed strategies allowed us to leverage existing breeding data and significantly increase both our ability to detect significant markers in GWAS and the accuracy of genomic predictions. The findings of this study can be useful to accelerate the genetic improvement of ß-glucan content and other traits.