Genomic prediction within and across maize landrace derived populations using haplotypes.

Genomic prediction (GP) using haplotypes is considered advantageous compared to GP solely reliant on single nucleotide polymorphisms (SNPs), owing to haplotypes' enhanced ability to capture ancestral information and their higher linkage disequilibrium with quantitative trait loci (QTL). Many empirical studies supported the advantages of haplotype-based GP over SNP-based approaches. Nevertheless, the performance of haplotype-based GP can vary significantly depending on multiple factors, including the traits being studied, the genetic structure of the population under investigation, and the particular method employed for haplotype construction. In this study, we compared haplotype and SNP based prediction accuracies in four populations derived from European maize landraces. Populations comprised either doubled haploid lines (DH) derived directly from landraces, or gamete capture lines (GC) derived from crosses of the landraces with an inbred line. For two different landraces, both types of populations were generated, genotyped with 600k SNPs and phenotyped as lines per se for five traits. Our study explores three prediction scenarios: (i) within each of the four populations, (ii) across DH and GC populations from the same landrace, and (iii) across landraces using either DH or GC populations. Three haplotype construction methods were evaluated: 1. fixed-window blocks (FixedHB), 2. LD-based blocks (HaploView), and 3. IBD-based blocks (HaploBlocker). In within population predictions, FixedHB and HaploView methods performed as well as or slightly better than SNPs for all traits. HaploBlocker improved accuracy for certain traits but exhibited inferior performance for others. In prediction across populations, the parameter setting from HaploBlocker which controls the construction of shared haplotypes between populations played a crucial role for obtaining optimal results. When predicting across landraces, accuracies were low for both, SNP and haplotype approaches, but for specific traits substantial improvement was observed with HaploBlocker. This study provides recommendations for optimal haplotype construction and identifies relevant parameters for constructing haplotypes in the context of genomic prediction.

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Copyright © 2024 Lin, Mayer, Valle Torres, Pook, Hölker, Presterl, Ouzunova and Schön.

Déclaration de conflit d'intérêts

Author MM was employed by the company Bayer CropScience Deutschland GmbH. Author DVT was employed by the company Strube Research GmbH & Co. KG. Authors AH, ThP, and MO were employed by the company KWS SAAT SE & Co. KGaA. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare that this study received funding from Federal Ministry of Education and Research (BMBF, Germany) under the Plant Breeding Research for the Bioeconomy initiative (funding ID: 031B0195, project MAZE), the Bavarian State Ministry of the Environment and Consumer Protection through the BayKlimaFit project network (project TGC01GCUFuE69741, “Improving cold tolerance in maize”), and KWS SAAT SE & Co. KGaA (KWS) through PhD fellowships (MM and AH). The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.