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.

Training Population

ID	GSTP007
Species	Rice
Sample type	Hybrid Line
Sample number	1495
SNP number	1,654,030
Traits	12
Paper	Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. https://pubmed.ncbi.nlm.nih.gov/25651972/

User submitted samples

TCD000211_demo

Sample	Calling SNP ratio
Line1_XXX_Line2	44.83%
Line1_XXX_Line3	49.48%
Line1_XXX_Line4	47.85%
Line1_XXX_Line5	46.24%
Line1_XXX_Line6	41.98%
Line2_XXX_Line3	44.80%
Line2_XXX_Line4	43.81%
Line2_XXX_Line5	43.21%
Line2_XXX_Line6	40.50%
Line3_XXX_Line4	49.93%
Line3_XXX_Line5	47.52%
Line3_XXX_Line6	42.93%
Line4_XXX_Line5	45.27%
Line4_XXX_Line6	41.48%
Line5_XXX_Line6	40.94%

Note:
* Calling SNP ratio: the ratio of the total number of SNPs in [ the sample mapped to the reference dataset ] / [ the total number of SNPs in the reference dataset ]

Height (cm) -- Best Linear Unbiased Prediction

Models

Model	Prediction accuracy	MSE	RMSE
rrBLUP	0.856	13.46	3.65
GBLUP	0.854	13.56	3.67
BayesCpi	0.852	13.62	3.69
BayesL	0.855	13.24	3.63
BayesR	0.857	13.20	3.62
LightGBM	0.841	14.62	3.82

Prediction

Sample	rrBLUP		GBLUP		BayesCpi		BayesL		BayesR		LightGBM
Sample	Prediction	Pred/Max	Prediction	Pred/Max	Prediction	Pred/Max	Prediction	Pred/Max	Prediction	Pred/Max	Prediction	Pred/Max
Line1_XXX_Line2	93.78	76.51%	94.34	76.96%	94.45	77.06%	93.59	76.35%	93.13	75.98%	98.14	80.07%
Line1_XXX_Line3	93.08	75.94%	95.02	77.52%	93.46	76.25%	94.40	77.01%	93.47	76.26%	97.22	79.31%
Line1_XXX_Line4	94.82	77.36%	94.95	77.46%	95.72	78.09%	95.47	77.89%	94.89	77.41%	99.06	80.82%
Line1_XXX_Line5	96.65	78.85%	95.72	78.09%	98.66	80.49%	97.14	79.25%	94.72	77.28%	99.36	81.06%
Line1_XXX_Line6	95.04	77.54%	94.41	77.02%	95.76	78.12%	95.68	78.06%	93.88	76.59%	98.52	80.38%
Line2_XXX_Line3	95.35	77.79%	96.54	78.76%	95.18	77.65%	95.98	78.30%	96.52	78.74%	96.23	78.51%
Line2_XXX_Line4	96.11	78.41%	96.63	78.83%	97.04	79.17%	96.58	78.80%	97.78	79.77%	98.14	80.06%
Line2_XXX_Line5	96.16	78.45%	96.07	78.38%	97.49	79.54%	96.59	78.80%	95.34	77.78%	99.47	81.15%
Line2_XXX_Line6	97.47	79.52%	97.24	79.33%	97.05	79.18%	97.25	79.34%	97.05	79.18%	96.51	78.73%
Line3_XXX_Line4	95.60	77.99%	98.54	80.40%	95.61	78.00%	97.61	79.63%	98.17	80.09%	97.20	79.30%
Line3_XXX_Line5	96.88	79.04%	97.34	79.41%	98.08	80.01%	98.87	80.66%	97.25	79.34%	96.55	78.77%
Line3_XXX_Line6	97.56	79.59%	99.06	80.82%	97.22	79.31%	99.54	81.21%	98.21	80.12%	98.54	80.39%
Line4_XXX_Line5	97.76	79.75%	97.33	79.41%	98.48	80.34%	98.82	80.62%	97.65	79.67%	99.14	80.88%
Line4_XXX_Line6	98.06	80.00%	99.09	80.84%	99.02	80.78%	99.61	81.26%	99.00	80.77%	97.89	79.86%
Line5_XXX_Line6	98.51	80.37%	97.83	79.82%	100.28	81.81%	99.82	81.43%	97.44	79.50%	97.62	79.64%

LeadSNP

The lead SNPs for GWAS significant signals based on our CropGS-Hub GWAS database are also listed below for users who are interested in traditional marker-assisted selection (MAS)

SNPid	Chromosome	Position	Ref	Alt	P value	Genetic Effect (Alt - Ref)
Chr1_5088861	Chr1	5088861	C	T	6.1509e-06	-2.4658
Chr2_15070264	Chr2	15070264	G	A	6.6595e-08	3.0146
Chr3_1254972	Chr3	1254972	A	G	1.9089e-09	2.8958
Chr4_25115617	Chr4	25115617	G	T	5.3960e-06	-0.6773
Chr6_2899259	Chr6	2899259	C	G	1.8111e-06	2.4843
Chr8_4670027	Chr8	4670027	G	A	6.4227e-06	-2.7599
Chr8_6101818	Chr8	6101818	T	C	8.6624e-09	3.9511
Chr8_28059937	Chr8	28059937	T	C	2.4897e-07	-1.8969
Chr12_23352645	Chr12	23352645	T	G	5.9812e-06	-2.2893

Lead SNPs in this database have been idefined using PLINK. The parameters are set as follows:
--clump-p1 $cutt-off --clump-p2 0.05 --clump-r2 0.1 --clump-kb 1000