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Supplemental Material for Baertschi et al., 2021

dataset
posted on 02.09.2021, 15:14 by Cédric Baertschi, Tuong-Vi Cao, Jérôme Bartholomé, Yolima Ospina, Constanza Quintero, Julien Frouin, Jean-Marc Bouvet, Cécile Grenier

Figure S1. Density of SNP markers in the calibration set (334 S0 plants) in the 12-chromosome.

Figure S2. MAF distribution among the population of 334 S0 plants.

Figure S3. Linkage disequilibrium, measured as r2 between all pairs of markers considered in a 50 variants window.

Figure S4. Neighbor joining tree of Euclidean distance between the 334 S0 plants

Table S1. Genetic characterization of the population. A) Summary information on the distribution, MAF and heterozygosity of the 9 928 SNP loci. B) Observed heterozygosity (Ho) among the 334 genotypes

Table S2. Average linkage disequilibrium (r2) between marker pairs according to chromosomes and the distance between markers, considering loci with MAF >2.5%.

Table S3. Summary of the cross-validation (CV) procedures used in the study.

Table S4. Fixed effect and variance decomposition for 50 Temporal Checks randomly distributed across the design within each repetition, considering A) 50 S0:2 lines in the two sites in 2017 and 2018 trials and B) 50 S0:2 and 50 S0:3 lines in the two sites in the 2018 trials

Table S5. Average predictive ability for the SINSRO scenarios across all traits, years, GP methods and calibration set sizes

Table S6. Average predictive ability for the SINSRO, BAL1 and BAL2 scenarios across all traits, years and calibration set sizes using GBLUP

Table S7. Average predictive ability for the SINSRO and IMB scenarios across all traits, years and calibration set sizes using GBLUP

Table S8. Average predictive ability for the BAL1, BAL2, IMB and IMB scenarios across all traits, years and calibration set sizes using RKHS

DataSet file contains a ReadMe file as well as the genotype and phenotype information of the PCT27_TP334 population

History

Article title

Impact of early genomiC prediction for recurrent selection in AN upland rice synthetic population