Genomic prediction with haplotype blocks in wheat

Frontiers in Plant Science

Plant Science

László Cselényi¹  Michael Koch²  Markus Wolf³  Andreas Stahl⁴  Benjamin Wittkop⁵  Anna Luise Langstroff⁵  Rod J. Snowdon⁵  Sven Weber⁵  Uche Joshua Okoye⁶  Yohannes Fekadu Difabachew⁶  Carola Zenke-Philippi⁶  Matthias Frisch⁶  Martin Kirchhoff⁷  Jutta Förster⁸ 

[1] Department of Cereal Breeding, W. von Borries-Eckendorf GmbH & Co. KG, Leopoldshöhe, Germany;Deutsche Saatveredelung AG, Lippstadt, Germany;German Seed Alliance GmbH, Holtsee, Germany;Saaten-Union Biotec GmbH, Leopoldshöhe, Germany;Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany;Institute of Agronomy and Plant Breeding I, Justus Liebig University, Gießen, Germany;Institute of Agronomy and Plant Breeding II, Justus Liebig University, Gießen, Germany;Nordsaat Saatzucht GmbH, Langenstein, Germany;Saaten-Union Biotec GmbH, Leopoldshöhe, Germany;

关键词: genomic prediction;    wheat;    haplotype blocks;    prediction accuracy;    cross-validation;   

DOI  :  10.3389/fpls.2023.1168547

 received in 2023-02-17, accepted in 2023-04-17,  发布年份 2023

来源: Frontiers

【 摘 要 】

Haplotype blocks might carry additional information compared to single SNPs and have therefore been suggested for use as independent variables in genomic prediction. Studies in different species resulted in more accurate predictions than with single SNPs in some traits but not in others. In addition, it remains unclear how the blocks should be built to obtain the greatest prediction accuracies. Our objective was to compare the results of genomic prediction with different types of haplotype blocks to prediction with single SNPs in 11 traits in winter wheat. We built haplotype blocks from marker data from 361 winter wheat lines based on linkage disequilibrium, fixed SNP numbers, fixed lengths in cM and with the R package HaploBlocker. We used these blocks together with data from single-year field trials in a cross-validation study for predictions with RR-BLUP, an alternative method (RMLA) that allows for heterogeneous marker variances, and GBLUP performed with the software GVCHAP. The greatest prediction accuracies for resistance scores for B. graminis, P. triticina, and F. graminearum were obtained with LD-based haplotype blocks while blocks with fixed marker numbers and fixed lengths in cM resulted in the greatest prediction accuracies for plant height. Prediction accuracies of haplotype blocks built with HaploBlocker were greater than those of the other methods for protein concentration and resistances scores for S. tritici, B. graminis, and P. striiformis. We hypothesize that the trait-dependence is caused by properties of the haplotype blocks that have overlapping and contrasting effects on the prediction accuracy. While they might be able to capture local epistatic effects and to detect ancestral relationships better than single SNPs, prediction accuracy might be reduced by unfavorable characteristics of the design matrices in the models that are due to their multi-allelic nature.

【 授权许可】

Unknown   
Copyright © 2023 Difabachew, Frisch, Langstroff, Stahl, Wittkop, Snowdon, Koch, Kirchhoff, Cselényi, Wolf, Förster, Weber, Okoye and Zenke-Philippi