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Table 3 Genotype-phenotype association analysis results including markers that showed significant associations with berry fresh weight (BFW) (A), bunch weight (BWe) (B), berry length (BL) (C), berry width (BWi) (D) and berry volume (BV) (E), as determined in a set 13 RxS segregants with contrasting phenotypes for berry size. P-values of associations and variance explained by each SNP/InDel marker (R2) are indicated for the GLM models obtained for seasons 2010, 2011 and 2012. Statistically significant associations are highlighted with an asterisk (p < 0.05)

From: Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches

A.
   BFW 2010 BFW 2011 BFW 2012
Marker Chr p-value R2(%) p-value R2(%) p-value R2(%)
TSRNAINDELS120073669 6 0.0173* 41.6 0.1572 18.9 0.0365* 34
TSRNAINDELS120073728 6 0.0419* 32.5 0.3932 7.4 0.0925 23.6
TSRNAINDELS120073761 6 0.0419* 32.5 0.3932 7.4 0.0925 23.6
TSRNAINDELS120073788 6 0.0419* 32.5 0.3932 7.4 0.0925 23.6
TSRNASNP120668018 8 0.2449 12.1 0.0073* 12.1 0.1162 12.1
TSRNASNP120671217 8 0.2449 12.1 0.0073* 12.1 0.1162 12.1
TSRNASNP120671218 8 0.2449 12.1 0,0073* 12.1 0.1162 12.1
TSRNASNP120671409 8 0.2449 12.1 0,0073* 12.1 0.1162 12.1
TSRNASNP120206984 15 0.0339* 49.2 0.2812 49.2 0.1126 49.2
TSRNASNP120273500 17 0.0019* 59.9 0.0191* 59.9 0.0005* 59.9
TSRNASNP120275823 17 0.0019* 59.9 0.0191* 59.9 0.0005* 59.9
TSRNASNP120277213 17 0.0019* 59.9 0.0191* 59.9 0.0005* 59.9
TSRNASNP120278360 17 0.0019* 59.9 0.0191* 59.9 0.0005* 59.9
TSRNASNP120279487 17 0.0019* 59.9 0.0191* 59.9 0.0005* 59.9
TSRNASNP120280865 17 0.0019* 59.9 0.0191* 59.9 0.0005* 59.9
TSRNASNP120275548 17 0.0134* 44.0 0.1049 44.0 0.0108* 44.0
B.
   BWe 2010   BWe 2011 BWe 2012
Marker Chr p-value R2(%) p-value R2(%) p-value R2(%)
TSRNASNP120273500 17 0.0430* 32.2 0.2441 13.3 0.0010* 67.8
TSRNASNP120275823 17 0.0430* 32.2 0.2441 13.3 0.0010* 67.8
TSRNASNP120277213 17 0.0430* 32.2 0.2441 13.3 0.0010* 67.8
TSRNASNP120278360 17 0,0430* 32.2 0.2441 13.3 0.0010* 67.8
TSRNASNP120279487 17 0.0430* 32.2 0.2441 13.3 0.0010* 67.8
TSRNASNP120280865 17 0.0430* 32.2 0.2441 13.3 0.0010* 67.8
TSRNASNP120275548 17 0.09226 23.6 0.1669 18.2 0.0025* 61.7
C.
   BL 2010   BL 2011   BL 2012  
Marker Chr p-value R2(%) p-value R2(%) p-value R2(%)
TSRNAINDELS120073669 6 0.0463* 31.4 0.0334* 34.9 0.0589 28.8
TSRNASNP120668018 8 0.0952 23.2 0.0273* 37.1 0.3045 9.5
TSRNASNP120671217 8 0.0952 23.2 0.0273* 37.1 0,3045 9.5
TSRNASNP120671218 8 0.0952 23.2 0.0273* 37.1 0.3045 9.5
TSRNASNP120671409 8 0.0952 23.2 0.0273* 37.1 0.3045 9.5
TSRNAINDELS120025818 15 0.2293 25.5 0.3628 0.18 0.0312* 50.0
TSRNASNP120206984 15 02293 25.5 0.3628 0.18 0.0312* 50.0
TSRNASNP120273500 17 0.0083* 48.3 0.0140* 43.6 0.0059* 51.2
TSRNASNP120275823 17 0.0083* 48.3 0.0140* 43.6 0.0059* 51.2
TSRNASNP120277213 17 0.0083* 48.3 0.0140* 43.6 0.0059* 51.2
TSRNASNP120278360 17 0.0083* 48.3 0.0140* 43.6 0.0059* 51.2
TSRNASNP120279487 17 0.0083* 48.3 0.0140* 43.6 0.0059* 51.2
TSRNASNP120280865 17 0.0083* 48.3 0.0140* 43.6 0.0059* 51.2
TSRNASNP120275548 17 0.0738 26.2 0.0471* 31.2 0.0153* 42.8
D.
   BWi 2010   BWi 2011 BWi 2012  
Marker Chr p-value R2(%) p-value R2(%) p-value R2(%)
TSRNAINDELS120073669 6 0.0223* 39.1 0.0104* 46.4 0.0214* 39.5
TSRNASNP120728591 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNAINDELS120095050 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120729221 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120729235 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120730012 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120731088 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120731107 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNAINDELS120095636 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120734745 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNAINDELS120095711 9 0.0383* 33,5 0.0434* 32.1 0.0652 27.7
TSRNASNP120735535 9 0.0383* 33.5 0.0434* 32.1 0.0652 27.7
TSRNAINDELS120025818 15 0.1045 36.3 0.4111 16.3 0.0486* 45.4
TSRNASNP120206984 15 0.1045 36.3 0.4111 16.3 0.0486* 45.4
TSRNASNP120273500 17 0.0142* 43.5 0.0053* 52.2 0.0012* 62.8
TSRNASNP120275823 17 0.0142* 43.5 0.0053* 52.2 0.0012* 62.8
TSRNASNP120277213 17 0.0142* 43.5 0.0053* 52.2 0.0012* 62.8
TSRNASNP120278360 17 0.0142* 43.5 0.0053* 52.2 0.0012* 62.8
TSRNASNP120279487 17 0.0142* 43.5 0.0053* 52.2 0.0012* 62.8
TSRNASNP120280865 17 0.0142* 43.5 0.0053* 52.2 0.0012* 62.8
TSRNASNP120275548 17 0.0461* 31.5 0.0379* 33.6 0.0067* 50.2
E.
   BV 2010 BV 2011 BV 2012
Marker Chr p-value R2(%) p-value R2(%) p-value R2(%)
TSRNAINDELS120073669 6 0.0480* 31.0 0.0244* 38.2 0.08 25.3
TSRNASNP120185697 14 0.2961 9.9 0.0452* 31.7 0.7015 1.4
TSRNASNP120273500 17 0.0017* 60.8 0.0123* 44.8 0.011* 45.9
TSRNASNP120275823 17 0.0017* 60.8 0.0123* 44.8 0.011* 45.9
TSRNASNP120277213 17 0.0017* 60.8 0.0123* 44.8 0.011* 45.9
TSRNASNP120278360 17 0.0017* 60.8 0.0123* 44.8 0.011* 45.9
TSRNASNP120279487 17 0.0017* 60.8 0.0123* 44.8 0.011* 45.9
TSRNASNP120280865 17 0.0017* 60.8 0.0123* 44.8 0.011* 45.9
TSRNASNP120275548 17 0.0274* 37.0 0.0450* 31.7 0.0430* 32.2