Data and analysis code for "Selection-aware metrics provide complementary decision-level information in plant genomic prediction"

This record contains fold-level within-environment prediction results, directed maize cross-environment prediction results, source data and submitted figure files underlying Figures 1–6, the source table underlying Table 1, exact CSV versions of Supplementary Tables S1–S6, original analysis scripts, experiment configurations, marker lists, and quality-control summaries associated with the manuscript “Selection-aware metrics provide complementary decision-level information in plant genomic prediction.”

The study analyzes publicly available maize and switchgrass genotype and phenotype datasets. The original switchgrass benchmark data are available from Dryad (DOI: 10.5061/dryad.xksn02vb9). The maize NCII6210 data are available through the ZEAMAP/MaizeGo CUBIC-related resource associated with Xiao et al. (2021; DOI: 10.1186/s13059-021-02370-7). The original public datasets are not redistributed in this record.

MeNet is third-party academic software. The original MeNet software and the study-specific adaptation scripts are not redistributed. Numerical MeNet outputs needed to verify the manuscript results are included with the required notice: Copyright, GANLAB. See LICENSES.md and third_party/MeNet_LICENCE.txt.

Related manuscript: Frontiers in Plant Science, Plant Breeding. Manuscript ID: 1951182.

Funding: This work was supported by the National Natural Science Foundation of China (32341036) and the Pinduoduo-China Agricultural University Research Fund (PC2024A01003).