Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.)
Abstract Background Hexaploid oat (Avena sativa L.) is a commercially important cereal crop due to its soluble dietary fiber β-glucan, a hemicellulose known to prevent cardio-vascular diseases. To maximize health benefits associated with the consumption of oat-based food products, breeding efforts h...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-11174-5 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832594974886068224 |
|---|---|
| author | Sumandeep Kaur Bazzer Guilherme Oliveira Jason D. Fiedler Raja Sekhar Nandety Jean-Luc Jannink Melanie Caffe |
| author_facet | Sumandeep Kaur Bazzer Guilherme Oliveira Jason D. Fiedler Raja Sekhar Nandety Jean-Luc Jannink Melanie Caffe |
| author_sort | Sumandeep Kaur Bazzer |
| collection | DOAJ |
| description | Abstract Background Hexaploid oat (Avena sativa L.) is a commercially important cereal crop due to its soluble dietary fiber β-glucan, a hemicellulose known to prevent cardio-vascular diseases. To maximize health benefits associated with the consumption of oat-based food products, breeding efforts have aimed at increasing the β-glucan content in oat groats. However, progress has been limited. 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 conduct a genome-wide association study (GWAS) to increase our understanding of the genetic control of beta-glucan content in oats and to compare strategies to implement genomic selection (GS) to increase genetic gain for β-glucan content in oat. Results Large variation for β-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 β-glucan content. Comparison based on physical position showed that 12 out of 22 loci coincided with previously identified β-glucan QTLs, and three loci are in the vicinity of cellulose synthesis genes, Cellulose synthase-like (Csl). To perform a GWAS analysis across all breeding datasets, the β-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 for individual environments and 37 coincided with previously reported β-glucan QTLs not identified when performing the GWAS in single years. In addition, 21 novel loci were identified that were not reported in the previous studies. The proposed approach increased our ability to detect significantly associated markers. The comparison of multiple GS 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-3 K 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 β-glucan content. The proposed genomic strategies 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 β-glucan content and other traits. |
| format | Article |
| id | doaj-art-654eb09ffd404f1c95d00afa79a32d4b |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-654eb09ffd404f1c95d00afa79a32d4b2025-01-19T12:11:33ZengBMCBMC Genomics1471-21642025-01-0126112210.1186/s12864-024-11174-5Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.)Sumandeep Kaur Bazzer0Guilherme Oliveira1Jason D. Fiedler2Raja Sekhar Nandety3Jean-Luc Jannink4Melanie Caffe5Department of Agronomy, Horticulture, and Plant Science, South Dakota State University (SDSU)Department of Agronomy, Horticulture, and Plant Science, South Dakota State University (SDSU)Cereal Crops Improvement Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARSCereal Crops Improvement Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARSR.W. Holley Center for Agriculture and Health, USDA-ARSDepartment of Agronomy, Horticulture, and Plant Science, South Dakota State University (SDSU)Abstract Background Hexaploid oat (Avena sativa L.) is a commercially important cereal crop due to its soluble dietary fiber β-glucan, a hemicellulose known to prevent cardio-vascular diseases. To maximize health benefits associated with the consumption of oat-based food products, breeding efforts have aimed at increasing the β-glucan content in oat groats. However, progress has been limited. 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 conduct a genome-wide association study (GWAS) to increase our understanding of the genetic control of beta-glucan content in oats and to compare strategies to implement genomic selection (GS) to increase genetic gain for β-glucan content in oat. Results Large variation for β-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 β-glucan content. Comparison based on physical position showed that 12 out of 22 loci coincided with previously identified β-glucan QTLs, and three loci are in the vicinity of cellulose synthesis genes, Cellulose synthase-like (Csl). To perform a GWAS analysis across all breeding datasets, the β-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 for individual environments and 37 coincided with previously reported β-glucan QTLs not identified when performing the GWAS in single years. In addition, 21 novel loci were identified that were not reported in the previous studies. The proposed approach increased our ability to detect significantly associated markers. The comparison of multiple GS 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-3 K 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 β-glucan content. The proposed genomic strategies 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 β-glucan content and other traits.https://doi.org/10.1186/s12864-024-11174-5Avena sativa L.Β-glucan contentGWASQuantitative trait loci (QTL)Cellulose synthase-like (Csl)Genomic selection (GS) |
| spellingShingle | Sumandeep Kaur Bazzer Guilherme Oliveira Jason D. Fiedler Raja Sekhar Nandety Jean-Luc Jannink Melanie Caffe Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.) BMC Genomics Avena sativa L. Β-glucan content GWAS Quantitative trait loci (QTL) Cellulose synthase-like (Csl) Genomic selection (GS) |
| title | Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.) |
| title_full | Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.) |
| title_fullStr | Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.) |
| title_full_unstemmed | Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.) |
| title_short | Genomic strategies to facilitate breeding for increased β-Glucan content in oat (Avena sativa L.) |
| title_sort | genomic strategies to facilitate breeding for increased β glucan content in oat avena sativa l |
| topic | Avena sativa L. Β-glucan content GWAS Quantitative trait loci (QTL) Cellulose synthase-like (Csl) Genomic selection (GS) |
| url | https://doi.org/10.1186/s12864-024-11174-5 |
| work_keys_str_mv | AT sumandeepkaurbazzer genomicstrategiestofacilitatebreedingforincreasedbglucancontentinoatavenasatival AT guilhermeoliveira genomicstrategiestofacilitatebreedingforincreasedbglucancontentinoatavenasatival AT jasondfiedler genomicstrategiestofacilitatebreedingforincreasedbglucancontentinoatavenasatival AT rajasekharnandety genomicstrategiestofacilitatebreedingforincreasedbglucancontentinoatavenasatival AT jeanlucjannink genomicstrategiestofacilitatebreedingforincreasedbglucancontentinoatavenasatival AT melaniecaffe genomicstrategiestofacilitatebreedingforincreasedbglucancontentinoatavenasatival |