Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments
Abstract Background In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-groun...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | Plant Methods |
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| Online Access: | https://doi.org/10.1186/s13007-023-01121-y |
| _version_ | 1797355733939912704 |
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| author | Biructawit B. Tessema Miguel A. Raffo Xiangyu Guo Simon F. Svane Lene Krusell Jens Due Jensen Anja Karine Ruud Marta Malinowska Kristian Thorup-Kristensen Just Jensen |
| author_facet | Biructawit B. Tessema Miguel A. Raffo Xiangyu Guo Simon F. Svane Lene Krusell Jens Due Jensen Anja Karine Ruud Marta Malinowska Kristian Thorup-Kristensen Just Jensen |
| author_sort | Biructawit B. Tessema |
| collection | DOAJ |
| description | Abstract Background In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits were obtained through digital images measuring the root length at different depths. Two nearest-neighbor adjustments (M1 and M2) to model spatial variation were used for genetic parameter estimation and genomic prediction (GP). M1 and M2 used (co)variance structures and differed in the distance function to calculate between-neighbor correlations. M2 was the most developed adjustment, as accounted by the Euclidean distance between neighbors. Results The estimated heritabilities ( $${\widehat{h}}^{2}$$ h ^ 2 ) ranged from low to medium for root and above-ground traits. The genetic coefficient of variation ( $$GCV$$ GCV ) ranged from 3.2 to 7.0% for above-ground and 4.7 to 10.4% for root traits, indicating good breeding potential for the measured traits. The highest $$GCV$$ GCV observed for root traits revealed that significant genetic change in root development can be achieved through selection. We studied the genotype-by-water availability interaction, but no relevant interaction effects were detected. GP was assessed using leave-one-line-out (LOO) cross-validation. The predictive ability (PA) estimated as the correlation between phenotypes corrected by fixed effects and genomic estimated breeding values ranged from 0.33 to 0.49 for above-ground and 0.15 to 0.27 for root traits, and no substantial variance inflation in predicted genetic effects was observed. Significant differences in PA were observed in favor of M2. Conclusions The significant $$GCV$$ GCV and the accurate prediction of breeding values for above-ground and root traits revealed that developing genetically superior barley lines with improved root systems is possible. In addition, we found significant spatial variation in the experiment, highlighting the relevance of correctly accounting for spatial effects in statistical models. In this sense, the proposed nearest-neighbor adjustments are flexible approaches in terms of assumptions that can be useful for semi-field or field experiments. |
| first_indexed | 2024-03-08T14:16:17Z |
| format | Article |
| id | doaj.art-8dedd7489b0b4799adb6078b3954e215 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-03-08T14:16:17Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-8dedd7489b0b4799adb6078b3954e2152024-01-14T12:24:38ZengBMCPlant Methods1746-48112024-01-0120111510.1186/s13007-023-01121-yGenomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustmentsBiructawit B. Tessema0Miguel A. Raffo1Xiangyu Guo2Simon F. Svane3Lene Krusell4Jens Due Jensen5Anja Karine Ruud6Marta Malinowska7Kristian Thorup-Kristensen8Just Jensen9Center for Quantitative Genetics and Genomics, Aarhus UniversityCenter for Quantitative Genetics and Genomics, Aarhus UniversityCenter for Quantitative Genetics and Genomics, Aarhus UniversityDepartment of Plant and Environmental Science, University of CopenhagenSejet Plant Breeding I/SNordic Seed A/SCenter for Quantitative Genetics and Genomics, Aarhus UniversityCenter for Quantitative Genetics and Genomics, Aarhus UniversityDepartment of Plant and Environmental Science, University of CopenhagenCenter for Quantitative Genetics and Genomics, Aarhus UniversityAbstract Background In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits were obtained through digital images measuring the root length at different depths. Two nearest-neighbor adjustments (M1 and M2) to model spatial variation were used for genetic parameter estimation and genomic prediction (GP). M1 and M2 used (co)variance structures and differed in the distance function to calculate between-neighbor correlations. M2 was the most developed adjustment, as accounted by the Euclidean distance between neighbors. Results The estimated heritabilities ( $${\widehat{h}}^{2}$$ h ^ 2 ) ranged from low to medium for root and above-ground traits. The genetic coefficient of variation ( $$GCV$$ GCV ) ranged from 3.2 to 7.0% for above-ground and 4.7 to 10.4% for root traits, indicating good breeding potential for the measured traits. The highest $$GCV$$ GCV observed for root traits revealed that significant genetic change in root development can be achieved through selection. We studied the genotype-by-water availability interaction, but no relevant interaction effects were detected. GP was assessed using leave-one-line-out (LOO) cross-validation. The predictive ability (PA) estimated as the correlation between phenotypes corrected by fixed effects and genomic estimated breeding values ranged from 0.33 to 0.49 for above-ground and 0.15 to 0.27 for root traits, and no substantial variance inflation in predicted genetic effects was observed. Significant differences in PA were observed in favor of M2. Conclusions The significant $$GCV$$ GCV and the accurate prediction of breeding values for above-ground and root traits revealed that developing genetically superior barley lines with improved root systems is possible. In addition, we found significant spatial variation in the experiment, highlighting the relevance of correctly accounting for spatial effects in statistical models. In this sense, the proposed nearest-neighbor adjustments are flexible approaches in terms of assumptions that can be useful for semi-field or field experiments.https://doi.org/10.1186/s13007-023-01121-yGenomic predictionSpring barleySemi-fieldRootsYieldSpatial adjustment |
| spellingShingle | Biructawit B. Tessema Miguel A. Raffo Xiangyu Guo Simon F. Svane Lene Krusell Jens Due Jensen Anja Karine Ruud Marta Malinowska Kristian Thorup-Kristensen Just Jensen Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments Plant Methods Genomic prediction Spring barley Semi-field Roots Yield Spatial adjustment |
| title | Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments |
| title_full | Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments |
| title_fullStr | Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments |
| title_full_unstemmed | Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments |
| title_short | Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments |
| title_sort | genomic prediction for root and yield traits of barley under a water availability gradient a case study comparing different spatial adjustments |
| topic | Genomic prediction Spring barley Semi-field Roots Yield Spatial adjustment |
| url | https://doi.org/10.1186/s13007-023-01121-y |
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