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 (ρ) 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, ρ was close to zero for all DHL and traits. Whereas scenario cLi showed improved ρ values compared to sL, ρ for cLe remained at the low level observed for LwL. Forecasting ρ with deterministic equations yielded inflated values compared to empirical estimates of ρ 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.

Keywords: GenPred; Genomic Prediction; doubled-haploid; maize landraces; shared data resources.

Figure 1

Prediction accuracy (ρ) of seven agronomic traits from genomic prediction for the scenario sL obtained with Genomic Best Linear Unbiased Prediction by leave-one-out cross-validation using increasing sample size (${\text{N}}_i$) from doubled-haploid lines sampled from the landraces Satu Mare or Walliser.

Figure 2

(A) Linkage disequilibrium (LD) and (B) cluster analysis based on modified Rogers’ distance for each doubled-haploid line from landraces GB (Gelber Badischer), SF (Strenzfelder), SM (Satu Mare), WA (Walliser), CG (Campan Galade), and RT (Rheintaler), as well as the elite flint (EF) lines.

Figure 3

Linkage phase similarity (LPS) of pairwise combinations of doubled-haploid (DH) lines (A) from SM (Satu Mare) with the elite flint (EF) lines, as well as all other DH lines from landraces GB (Gelber Badischer), SF (Strenzfelder), SM, WA (Walliser), CG (Campan Galade), and RT (Rheintaler); (B) from WA with the EF lines as well as DH lines from landraces CG, GB, RT, and SF, and from GB with DH lines from landrace SF.