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Table 5 Performances of the Least Absolute Shrinkage and Selection Operator (LASSO), Partial Least Square (PLS) and Sparse Partial Least Squares (SPLS), Bayes A, Bayes B and Genomic Best Linear Unbiased Prediction (GBLUP) methods to predict phenotypes measure in field trials in 2003 and 2007, with or without taking into account the genetic structures revealed by DAPC and INSTRUCT

From: Genetic diversity and trait genomic prediction in a pea diversity panel

 

Thousand seed weight

Beginning of flowering ( \( \sum T{}^{\circ}C \) )

Seed number

 

2003

2007

2003

2007

2003

2007

MSEP

      

LASSO

1931 (360)

2185 (398)

16074 (2469)

10953 (1511)

7722 (1035)

1047 (180)

LASSO-DAPC

2334 (404)

2761 (458)

17893 (3018)

13080 (1814)

9700 (1598)

1342 (206)

LASSO-INSTRUCT

1882 (364)

2455 (511)

18019 (2623)

13013 (1805)

9566 (1629)

1310 (213)

PLS

1737 (283)

2011 (312)

14733 (2196)

9883 (1247)

7978 (1019)

1003 (163)

PLS-DAPC

2058 (296)

2414 (333)

16292 (2371)

11882 (1317)

10531 (1481)

1234 (215)

PLS-INSTRUCT

1790 (249)

2040 (300)

17357 (2346)

11947 (1430)

9786 (1410)

1226 (211)

SPLS

1947 (286)

2215 (332)

16064 (2160)

11546 (1441)

7820 (985)

1079 (188)

SPLS-DAPC

2355 (321)

2696 (399)

18929 (2493)

13115 (1725)

10476 (2216)

1337 (214)

SPLS-INSTRUCT

1906 (285)

2204 (316)

18250 (2653)

12644 (1537)

9947 (1887)

1336 (215)

Bayes A

1822 (329)

2084 (344)

14823 (2517)

10099 (1431)

7631 (1020)

1304 (421)

Bayes B

1814 (327)

2051 (350)

14722 (2471)

10206 (1474)

7660 (1002)

1328 (408)

GBLUP

1759 (288)

2017 (342)

14237 (2287)

9858 (1301)

7593 (988)

1296 (409)

R 2

      

LASSO

0.78 (0.06)

0.81 (0.04)

0.56 (0.11)

0.71 (0.09)

0.65 (0.07)

0.62 (0.11)

LASSO-DAPC

0.79 (0.08)

0.88 (0.04)

0.55 (0.15)

0.70 (0.11)

0.59 (0.11)

0.52 (0.16)

LASSO-INSTRUCT

0.88 (0.06)

0.91 (0.06)

0.49 (0.15)

0.70 (0.11)

0.59 (0.12)

0.52 (0.16)

PLS

0.77 (0.01)

0.79 (0.01)

0.56 (0.02)

0.76 (0.02)

0.70 (0.02)

0.69 (0.02)

PLS-DAPC

0.79 (0.01)

0.80 (0.01)

0.50 (0.02)

0.56 (0.02)

0.68 (0.02)

0.51 (0.03)

PLS-INSTRUCT

0.83 (0.01)

0.84 (0.01)

0.47 (0.03)

0.69 (0.02)

0.61 (0.02)

0.62 (0.02)

SPLS

0.74 (0.02)

0.77 (0.02)

0.59 (0.03)

0.79 (0.02)

0.67 (0.02)

0.55 (0.03)

SPLS-DAPC

0.71 (0.02)

0.73 (0.02)

0.40 (0.03)

0.73 (0.02)

0.46 (0.03)

0.41 (0.03)

SPLS-INSTRUCT

0.88 (0.01)

0.85 (0.01)

0.41 (0.03)

0.61 (0.02)

0.57 (0.03)

0.55 (0.03)

Bayes A

0.84 (0.03)

0.87 (0.02)

0.69 (0.06)

0.81 (0.03)

0.70 (0.04)

0.62 (0.11)

Bayes B

0.83 (0.03)

0.87 (0.02)

0.68 (0.06)

0.81 (0.04)

0.70 (0.04)

0.62 (0.10)

GBLUP

0.85 (0.02)

0.88 (0.02)

0.69 (0.05)

0.82 (0.03)

0.70 (0.04)

0.62 (0.10)

Q 2

      

LASSO

0.50 (0.07)

0.58 (0.06)

0.20 (0.07)

0.40 (0.71)

0.38 (0.08)

0.32 (0.07)

LASSO-DAPC

0.40 (0.10)

0.47 (0.09)

0.11 (0.12)

0.30 (0.09)

0.23 (0.10)

0.11 (0.09)

LASSO-INSTRUCT

0.52 (0.09)

0.53 (0.10)

0.11 (0.08)

0.29 (0.09)

0.25 (0.10)

0.14 (0.10)

PLS

0.55 (0.06)

0.61 (0.05)

0.27 (0.07)

0.46 (0.06)

0.35 (0.09)

0.34 (0.08)

PLS-DAPC

0.47 (0.07)

0.54 (0.06)

0.19 (0.08)

0.35 (0.07)

0.17 (0.11)

0.19 (0.11)

PLS-INSTRUCT

0.54 (0.06)

0.61 (0.05)

0.13 (0.09)

0.35 (0.08)

0.22 (0.11)

0.19 (0.11)

SPLS

0.49 (0.07)

0.58 (0.05)

0.20 (0.09)

0.36 (0.08)

0.37 (0.09)

0.29 (0.08)

SPLS-DAPC

0.39 (0.09)

0.48 (0.08)

0.06 (0.11)

0.28 (0.10)

0.17 (0.18)

0.12 (0.10)

SPLS-INSTRUCT

0.51 (0.08)

0.58 (0.06)

0.10 (0.09)

0.30 (0.09)

0.21 (0.15)

0.12 (0.12)

Bayes A

0.53 (0.06)

0.61 (0.05)

0.26 (0.07)

0.45 (0.07)

0.39 (0.07)

0.27 (0.11)

Bayes B

0.53 (0.06)

0.61 (0.05)

0.27 (0.07)

0.44 (0.07)

0.38 (0.08)

0.26 (0.10)

GBLUP

0.54 (0.06)

0.62 (0.05)

0.29 (0.070)

0.46 (0.07)

0.39 (0.08)

0.28 (0.10)

  1. The best predictions are highlighted in bold. Mean square error of prediction (MSEP) indicates expected squared Euclidian distance between predicted and observed phenotypes, R 2 expressed the proportion of variance explained by the model and Q 2 evaluates the prediction quality of the model. Standard deviations are in parentheses.