Dataset Information

Genomic Prediction Within and Among Doubled-Haploid Libraries from Maize Landraces.

ABSTRACT: Thousands of maize landraces are stored in seed banks worldwide. Doubled-haploid libraries (DHL) produced from landraces harness their rich genetic diversity for future breeding. We investigated the prospects of genomic prediction (GP) for line per se performance in DHL from six European landraces and 53 elite flint (EF) lines by comparing four scenarios: GP within a single library (sL); GP between pairs of libraries (LwL); and GP among combined libraries, either including (cLi) or excluding (cLe) lines from the training set (TS) that belong to the same DHL as the prediction set. For scenario sL, with N = 50 lines in the TS, the prediction accuracy (?) among seven agronomic traits varied from -0.53 to 0.57 for the DHL and reached up to 0.74 for the EF lines. For LwL, ? was close to zero for all DHL and traits. Whereas scenario cLi showed improved ? values compared to sL, ? for cLe remained at the low level observed for LwL. Forecasting ? with deterministic equations yielded inflated values compared to empirical estimates of ? for the DHL, but conserved the ranking. In conclusion, GP is promising within DHL, but large TS sizes (N > 100) are needed to achieve decent prediction accuracy because LD between QTL and markers is the primary source of information that can be exploited by GP. Since production of DHL from landraces is expensive, we recommend GP only for very large DHL produced from a few highly preselected landraces.

SUBMITTER: Brauner PC

PROVIDER: S-EPMC6283160 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Genomic Prediction Within and Among Doubled-Haploid Libraries from Maize Landraces.

Brauner Pedro C PC Müller Dominik D Schopp Pascal P Böhm Juliane J Bauer Eva E Schön Chris-Carolin CC Melchinger Albrecht E AE

Genetics 20180926 4

Thousands of maize landraces are stored in seed banks worldwide. Doubled-haploid libraries (DHL) produced from landraces harness their rich genetic diversity for future breeding. We investigated the prospects of genomic prediction (GP) for line <i>per se</i> performance in DHL from six European landraces and 53 elite flint (EF) lines by comparing four scenarios: GP within a single library (sL); GP between pairs of libraries (LwL); and GP among combined libraries, either including (cLi) or exclud ...[more]

PMID: 30257934

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Project description: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.

Dataset Information

Genomic Prediction Within and Among Doubled-Haploid Libraries from Maize Landraces.

Publications

Genomic Prediction Within and Among Doubled-Haploid Libraries from Maize Landraces.

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