Genetic control and prospects of predictive breeding for European winter wheat’s Zeleny sedimentation values and Hagberg-Perten falling number

Key message Sedimentation values and falling number in the last decades have helped maintain high baking quality despite rigorous selection for grain yield in wheat. Allelic combinations of major loci sustained the bread-making quality while improving grain yield. Glu-D1, Pinb-D1, and non-gluten proteins are associated with sedimentation values and falling number in European wheat. Abstract Zeleny sedimentation values (ZSV) and Hagberg-Perten falling number (HFN) are among the most important parameters that help determine the baking quality classes of wheat and, thus, influence the monetary benefits for growers. We used a published data set of 372 European wheat varieties evaluated in replicated field trials in multiple environments. ZSV and HFN traits hold a wide and significant genotypic variation and high broad-sense heritability. The genetic correlations revealed positive and significant associations of ZSV and HFN with each other, grain protein content (GPC) and grain hardness; however, they were all significantly negatively correlated with grain yield. Besides, GPC appeared to be the major predictor for ZSV and HFN. Our genome-wide association analyses based on high-quality SSR, SNP, and candidate gene markers revealed a strong quantitative genetic nature of ZSV and HFN by explaining their total genotypic variance as 41.49% and 38.06%, respectively. The association of known Glutenin (Glu-1) and Puroindoline (Pin-1) with ZSV provided positive analytic proof of our studies. We report novel candidate loci associated with globulins and albumins—the non-gluten monomeric proteins in wheat. In addition, predictive breeding analyses for ZSV and HFN suggest using genomic selection in the early stages of breeding programs with an average prediction accuracy of 81 and 59%, respectively. Supplementary Information The online version contains supplementary material available at 10.1007/s00122-023-04450-7.


Figure S2 .
Figure S2.Association of wheat's grain yield with four quality traits namely (a) Zeleny sedimentation values, (b) Hagberg-Perten falling number, (c) grain protein content, and (d) grain hardness based on their BLUEs calculated across environments. 2 and  denote the multiple squared regression coefficient and its respective significance.The red dashed line represent the linear regression line whereas the golden dots represent the above average values for both traits in each scatter plot.

Figure S3 .
Figure S3.Scatterplot and boxplots showing the distribution of the (a) identified QZsv.ipk-1AQTL for Zeleny sedimentation value represented by the marker AX-95236907 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of AX-95236907 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs) of varieties, varieties harboring the major (reference) allele and the minor (alternate) allele, respectively.The annotated function of the corresponding gene for AX-95236907 is Peroxidase, as highlighted blue in (a).

Figure S4 .
Figure S4.Scatterplot and boxplots showing the distribution of the (a) identified QZsv.ipk-1B for Zeleny sedimentation value represented by the marker AX-95017670 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of AX-95017670 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs)of varieties, varieties harboring the major (reference) and the minor (alternate) allele, respectively.

Figure S5 .
Figure S5.Scatterplot and boxplots showing the distribution of the (a) identified QZsv.ipk-1D for Zeleny sedimentation value represented by the marker UMN25 and UMN26 for Glu-D1 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of Glu-D1 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs) of varieties, varieties harboring the major (reference) and the minor (alternate) allele, respectively.

Figure S6 .
Figure S6.Scatterplot and boxplots showing the distribution of the (a) identified QZsv.ipk-1D for Zeleny sedimentation value represented by the marker BS00022768_51 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of BS00022768_51 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs) of varieties, varieties harboring the major (reference) and the minor (alternate) allele, respectively.The annotated function of the corresponding gene for BS00022768_51 is Globulin, as highlighted blue in (a).

Figure S7 .
Figure S7.Scatterplot and boxplots showing the distribution of the (a) identified QZsv.ipk-5D for Zeleny sedimentation value represented by the marker BS00000020_51 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of BS00000020_51 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs) of varieties, varieties harboring the major (reference) and the minor (alternate) allele, respectively.The annotated function of the corresponding gene for BS00000020_51 is Puroindoline-b, as highlighted blue in (a).

Figure S8 .
Figure S8.Scatterplot and boxplots showing the distribution of the (a) identified QHfn.ipk-1A for Hagberg-Perten falling number represented by the marker AX-94430348 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of AX-94430348 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs) of varieties, varieties harboring the major (reference) and the minor (alternate) allele, respectively.The annotated function of the corresponding gene for AX-94430348 is Albumin-2 protein, as highlighted blue in (a).

Figure S9 .
Figure S9.Scatterplot and boxplots showing the distribution of the (a) identified QHfn.ipk-5B for Hagberg-Perten falling number represented by the marker wsnp_Ku_rep_c71565_71299640 as a function of first two principal components based on high-quality marker genotypes, and the allelic influence of wsnp_Ku_rep_c71565_71299640 on (b) Zeleny sedimentation value, (c) Hagberg-Perten falling number, (d) Grain protein content, (e) grain hardness, and (f) grain yield.The blue, black, and red boxplots show the overall genotypic values (BLUEs) of varieties, varieties harboring the major (reference) and the minor (alternate) allele, respectively.