Genomic Assisted Selection for Enhancing Line Breeding 27.04.2017 Sebastian Michel 1
Selection through the years… 2
Selection through the years… • Great progress in the genetic improvement of crop plants by breeders 3
Selection through the years… • Great progress in the genetic improvement of crop plants by breeders >>>But: not all expectations were met ? ! 4
Selection through the years… • Great progress in the genetic improvement of crop plants by breeders >>>But: not all expectations were met and yield progress is insufficient ? ! >>> Development of new technologies & tools for breeding crop plants! 5 Source: Ray et al. (2013)
Genomic selection across years • 960 F 4:6 wheat lines with subpopulations tested in METs 2010-2016 6
Genomic selection across years • 960 F 4:6 wheat lines with subpopulations tested in METs 2010-2016 • Within-year prediction accuarcy was high 7
Genomic selection across years • 960 F 4:6 wheat lines with subpopulations tested in METs 2010-2016 • Within-year prediction accuarcy was high but overestimated 8
Genomic selection across years • 960 F 4:6 wheat lines with subpopulations tested in METs 2010-2016 • Within-year prediction accuarcy was high but overestimated • Great promise to genomically predict major traits across years • protein content r CV:ACROSS = 0.57 • grain yield r CV:ACROSS = 0.37 9
Genomic selection across years • 960 F 4:6 wheat lines with subpopulations tested in METs 2010-2016 • Within-year prediction accuarcy was high but overestimated • Great promise to genomically predict major traits across years • protein content r CV:ACROSS = 0.57 • grain yield r CV:ACROSS = 0.37 >>>Can GS support the selection of laborious to phenotype traits? 10
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations 11 Source: LflL (2008); modified after Laidig et al. (2016)
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations >>>Breeders postpone thoroughly quality testing into later generations >>>Indirect selection for quality by protein content in early generations 12 Source: LflL (2008); modified after Laidig et al. (2016)
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations >>>Breeders postpone thoroughly quality testing into later generations >>>Indirect selection for quality by protein content in early generations Accuracy of indirect selection? 13 Source: LflL (2008); modified after Laidig et al. (2016)
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations >>>Breeders postpone thoroughly quality testing into later generations >>>Indirect selection for quality by protein content in early generations Accuracy of indirect selection? Validation! Loaf volume (ml/100g) Protein content (%) 14 Source: LflL (2008); modified after Laidig et al. (2016)
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations >>>Breeders postpone thoroughly quality testing into later generations >>>Indirect selection for quality by protein content in early generations Accuracy of indirect selection? Validation! Loaf volume (ml/100g) Protein content (%) >>> Additional assessment of the protein quality seems necessary… 15 Source: LflL (2008); modified after Laidig et al. (2016)
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations >>>Breeders postpone thoroughly quality testing into later generations >>>Indirect selection for quality by protein content in early generations >>> Additional assessment of the protein quality seems necessary… >>> Additional assessment of the protein quality seems necessary… >>> Rheological tests are highly informative 16 Source: Brabender (2017); LflL (2008)
Baking quality in bread wheat • Assessment of baking quality time-consuming, labor-intensive & costly • Too little grain available from selection candidates in early generations >>>Breeders postpone thoroughly quality testing into later generations >>>Indirect selection for quality by protein content in early generations >>> Additional assessment of the protein quality seems necessary… >>> Rheological tests are highly informative but time-consuming & costly 17 Source: Brabender (2017); LflL (2008)
Forward prediction of quality traits • Training with rheological data from several locations 2009-2012 • Validating the trained statistical model with data from 2013-2015 18
Forward prediction of quality traits • Training with rheological data from several locations 2009-2012 • Validating the trained statistical model with data from 2013-2015 19
Forward prediction of quality traits • Training with rheological data from several locations 2009-2012 • Validating the trained statistical model with data from 2013-2015 • GS enables an earlier selection for quality traits with high intensity 20
Forward prediction of quality traits • Training with rheological data from several locations 2009-2012 • Validating the trained statistical model with data from 2013-2015 • GS enables an earlier selection for quality traits with high intensity >>>Predict labor-intensive and costly quality traits in early generations! Trait Accuracy Farinograph Development 0.43 Stability 0.36 Extensograph Resistance 0.37 Energy 0.60 21
Forward prediction of quality traits • Training with rheological data from several locations 2009-2012 • Validating the trained statistical model with data from 2013-2015 • GS enables an earlier selection for quality traits with high intensity >>>Predict labor-intensive and costly quality traits in early generations! Trait Accuracy Farinograph Development 0.43 Stability 0.36 Extensograph Resistance 0.37 Energy 0.60 >>> How can a breeder implement GS into a line breeding program? 22
Line breeding with genomic selection • Pedigree selection until F 4:5 generation preliminary yield trials • Genotyping and prediction of genomic breeding values 23 Source: Löschenberger et al. (2008); Elshire et al. (2011)
Line breeding with genomic selection • Pedigree selection until F 4:5 generation preliminary yield trials • Genotyping and prediction of genomic breeding values • Selected lines are retested in multi-environment trials >>> How good is genomic in comparison to phenotypic selection? 24 Source: Löschenberger et al. (2008); Elshire et al. (2011)
Predict line performance across years • Accuarcy of phenotypic selection: >>>Correlation between observed line performance in preliminary yield trials and multi-environment trials the following year 25
Predict line performance across years • Accuarcy of phenotypic selection: >>>Correlation between observed line performance in preliminary yield trials and multi-environment trials the following year • Accuarcy of genomic selection: >>>Correlation between predicted line performance and observed performance in multi-environment trials the following year 2010 2011 2012 2013 2014 2015 2016 Training GS PYT Validation 26
Predict line performance across years • Accuarcy of phenotypic selection: >>>Correlation between observed line performance in preliminary yield trials and multi-environment trials the following year • Accuarcy of genomic selection: >>>Correlation between predicted line performance and observed performance in multi-environment trials the following year 2010 2011 2012 2013 2014 2015 2016 Training GS PYT Validation >>> Cross-validation with 10 training x 5 validation population combinations 27
Phenotypic versus genomic selection • Genomic selection was superior to early generation phenotypic selection based on unreplicated preliminary yield trials >>> Low quality of the derived phenotypic data (!?) r = 0.20 r = 0.42 r = 0.38 r = 0.49 + 20% + 90% 28
Phenotypic versus genomic selection • Genomic selection was superior to early generation phenotypic selection based on unreplicated preliminary yield trials >>> Low quality of the derived phenotypic data (!?) r = 0.20 r = 0.42 r = 0.38 r = 0.49 + 20% + 90% >>> Utilizing marker data for enhancing phenotypic selection… 29
Breeding values in preliminary yield trials • Modeling kinship to enhance phenotypic breeding values (KBLUP) 30
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