Reference

rrBLUP (rrBLUP [R-Package])

Endelman,J.B. (2011) Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP. Plant Genome, 4, 250–255.

GBLUP (sommer [R-Package])

Covarrubias-Pazaran,G. (2016) Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer. PLoS ONE, 11, e0156744.

Bayes (hibayes [R-Package])

Yin,L., Zhang,H., Li,X., Zhao,S. and Liu,X. (2022) hibayes: An R Package to Fit Individual-Level, Summary-Level and Single-Step Bayesian Regression Models for Genomic Prediction and Genome-Wide Association Studies. bioRxiv, 10.1101/2022.02.12.480230.

LightGBM (lightgbm [Python-package])

Yan,J., Xu,Y., Cheng,Q., Jiang,S., Wang,Q., Xiao,Y., Ma,C., Yan,J. and Wang,X. (2021) LightGBM: accelerated genomically designed crop breeding through ensemble learning. Genome Biol, 22, 271.

Plant_height

10xCV result

BayesCpi	Prediction correlation	MSE	RMSE
1	0.576	290.901	17.056
2	0.692	204.047	14.285
3	0.583	260.813	16.150
4	0.742	306.618	17.511
5	0.842	168.780	12.992
6	0.720	214.089	14.632
7	0.719	250.979	15.842
8	0.681	228.117	15.104
9	0.644	413.162	20.326
10	0.814	145.377	12.057
Prediction accuracy	0.701	248.288	15.595

Prediction

Dataset:

Validation

Testing

Sample	BayesCpi
Sample	Prediction	Pred/Max
Sample290	100.68	51.81%
Sample249	130.44	67.12%
Sample018	134.31	69.11%
Sample130	99.89	51.40%
Sample169	146.03	75.15%
Sample187	132.83	68.35%
Sample153	110.85	57.04%
Sample078	124.18	63.90%
Sample020	97.73	50.29%
Sample199	117.60	60.52%
Sample058	117.65	60.54%
Sample015	118.84	61.15%
Sample281	111.38	57.31%
Sample112	109.40	56.29%
Sample159	132.03	67.94%
Sample042	95.35	49.06%
Sample289	99.38	51.14%
Sample045	129.65	66.71%
Sample055	129.29	66.53%
Sample105	114.27	58.80%
Sample107	141.50	72.81%
Sample103	132.52	68.19%
Sample067	115.10	59.23%
Sample109	131.77	67.81%
Sample271	112.13	57.70%
Sample046	106.32	54.71%
Sample120	97.36	50.10%
Sample144	119.67	61.58%
Line1	104.24	53.64%
Line2	104.25	53.64%