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) |