Supplementary Table S1. QTLs associated with disease severity index (DSI) of leaves, vascular stem and root staining (VRS), percentage plant survival (PS) of Fusarium wilt (FOV race 4)in an interspecific recombinantinbred line and F2mapping populations from twogreenhouse tests andtwo field experiments data detected by nonparametric mapping.Simple sequence repeats (SSR) markers placed on cotton chromosomes.

Populationa / Siteb / Trait / Chromosome / SSR Marker / K*c / Mean-ad / Mean-hd / Mean-bd / P valuee
Pop 1a / UC Davis / VRS / 3 / BNL226 / 9.40 / 1.64 / 0.94 / ****
Pop 1a / UC Davis / DSI / 3 / BNL226 / 5.47 / 1.80 / 1.35 / **
Pop 3 / Field Kern County / VRS / 3 / BNL226 / 4.07 / 1.71 / 1.29 / 0.81 / *
Pop 1a / UC Davis / VRS / 3 / MUSB0639 / 8.73 / 1.59 / 1.08 / ****
Pop 1a / UC Davis / DSI / 3 / MUSB0639 / 4.94 / 1.79 / 1.35 / **
Pop 2 / Field Kern County / VRS / 3 / MUSB0639 / 4.34 / 1.78 / 0.69 / **
Pop 1a / UC Davis / VRS / 3 / NAU1068 / 6.41 / 1.59 / 1.00 / **
Pop 3 / Field Kern County / DSI / 3 / NAU1068 / 2.80 / 1.40 / 1.21 / *
Pop 1a / UC Davis / VRS / 6 / MUSB0754 / 4.92 / 0.96 / 1.51 / **
Pop 1c / Field Kern County / PS / 6 / MUSB0754 / 3.40 / 41.36 / 49.67 / *
Pop 1c / Field Kern County / DSI / 6 / MUSB0754 / 5.52 / 0.92 / 1.21 / **
Pop 1c / Field Kern County / VRS / 6 / MUSB0754 / 4.30 / 2.27 / 2.56 / **
Pop 3 / Field Kern County / DSI / 6 / MUSB0754 / 3.03 / 1.31 / 1.11 / *
Pop 3 / Field Kern County / VRS / 6 / MUSB0754 / 3.05 / 1.33 / 0.72 / *
Pop 3 / Field Kern County / DSI / 6 / NAU2714 / 8.30 / 2.10 / 0.93 / 1.38 / **
Pop 1b / UC Kearney / VRS / 8 / MUSB0255 / 4.85 / 1.32 / 1.85 / **
Pop 1c / Field Kern County / PS / 8 / MUSB0255 / 8.57 / 37.99 / 50.12 / ****
Pop 1c / Field Kern County / VRS / 8 / MUSB0255 / 4.23 / 2.64 / 2.35 / **
Pop 2 / Field Kern County / VRS / 8 / MUSB0255 / 4.85 / 2.31 / 1.21 / 1.50 / *
Pop 3 / Field Kern County / VRS / 8 / MUSB0255 / 4.82 / 2.00 / 1.13 / 1.09 / *
Pop 1a / UC Davis / VRS / 8 / Gh465 / 3.97 / 1.51 / 1.16 / **
Pop 1b / UC Kearney / VRS / 8 / Gh465 / 3.06 / 1.40 / 1.81 / *
Pop 1c / Field Kern County / PS / 8 / Gh465 / 11.69 / 38.19 / 51.23 / *****
Pop 1c / Field Kern County / DSI / 8 / Gh465 / 13.16 / 0.86 / 1.31 / ******
Pop 1c / Field Kern County / VRS / 8 / Gh465 / 4.74 / 1.40 / 1.92 / **
Pop 1b / UC Kearney / VRS / 8 / Gh272 / 4.63 / 1.32 / 1.92 / **
Pop 1c / Field Kern County / PS / 8 / Gh272 / 10.63 / 38.71 / 52.04 / ****
Pop 1c / Field Kern County / VRS / 8 / Gh272 / 4.07 / 2.32 / 2.57 / **
Pop 2 / Field Kern County / DSI / 8 / Gh272 / 6.10 / 1.13 / 0.31 / 0.40 / **
Pop 3 / Field Kern County / VRS / 8 / Gh272 / 6.30 / 2.06 / 1.24 / 0.88 / **
Pop 1c / Field Kern County / PS / 8 / Gh237 / 10.03 / 38.38 / 51.36 / ****
Pop 1c / Field Kern County / VRS / 8 / Gh237 / 5.80 / 2.59 / 2.29 / **
Pop 2 / Field Kern County / DSI / 8 / Gh237 / 6.37 / 1.13 / 0.30 / 0.43 / **
Pop 3 / Field Kern County / VRS / 8 / Gh237 / 7.40 / 2.20 / 1.17 / 0.96 / **
Pop 1c / Field Kern County / PS / 8 / Gh171 / 15.84 / 35.53 / 53.06 / *******
Pop 1c / Field Kern County / VRS / 8 / Gh171 / 6.65 / 2.27 / 2.65 / ***
Pop 1c / Field Kern County / DSI / 8 / Gh171 / 11.10 / 1.36 / 0.90 / *****
Pop 3 / Field Kern County / VRS / 8 / Gh171 / 5.94 / 2.00 / 1.15 / 1.00 / *
Pop 1a / UC Davis / VRS / 8 / MUSB0780 / 5.53 / 1.06 / 1.63 / **
Pop 1b / UC Kearney / VRS / 8 / MUSB0780 / 7.66 / 1.41 / 2.06 / ***
Pop 3 / Field Kern County / VRS / 8 / MUSB0780 / 4.67 / 1.42 / 1.40 / 0.62 / *
Pop 1a / UC Davis / VRS / 14 / MUSS354 / 2.89 / 1.23 / 1.53 / *
Pop 1b / UC Kerneay / VRS / 14 / MUSS354 / 8.45 / 1.21 / 1.84 / ****
Pop 1c / Field Kern County / PS / 14 / MUSS354 / 10.72 / 52.14 / 38.53 / ****
Pop 2 / Field Kern County / VRS / 14 / MUSS354 / 9.96 / 1.91 / 0.59 / ****
Pop 3 / Field Kern County / VRS / 14 / MUSS354 / 9.53 / 1.65 / 0.80 / ****
Pop 1a / UC Davis / VRS / 14 / BNL0834 / 10.95 / 1.10 / 1.68 / *****
Pop 1a / UC Davis / DSI / 14 / BNL0834 / 15.26 / 1.12 / 1.86 / *******
Pop 1b / UC Kerneay / VRS / 14 / BNL0834 / 8.53 / 1.08 / 1.54 / ****
Pop 1c / Field Kern County / PS / 14 / BNL0834 / 14.95 / 37.05 / 52.29 / ******
Pop 1c / Field Kern County / VRS / 14 / BNL0834 / 6.30 / 2.70 / 2.29 / **
Pop 2 / Field Kern County / VRS / 14 / BNL0834 / 9.90 / 2.53 / 1.38 / 0.93 / ***
Pop 3 / Field Kern County / VRS / 14 / BNL0834 / 8.61 / 1.95 / 1.27 / 0.61 / **
Pop 1a / UC Davis / VRS / 17 / BNL2496 / 7.50 / 1.17 / 1.67 / ***
Pop 1a / UC Davis / DSI / 17 / BNL2496 / 5.62 / 1.37 / 1.79 / **
Pop 2 / Field Kern County / VRS / 17 / BNL2496 / 4.78 / 1.83 / 1.88 / 0.94 / *
Pop 3 / Field Kern County / VRS / 17 / BNL2496 / 6.19 / 1.65 / 1.21 / 0.63 / **
Pop 1a / UC Davis / VRS / 19 / BNL3347 / 4.52 / 1.56 / 1.19 / **
Pop 1a / UC Davis / DSI / 19 / BNL3347 / 4.02 / 1.40 / 1.80 / **
Pop 1c / Field Kern County / VRS / 19 / BNL3347 / 2.76 / 2.34 / 2.59 / *
Pop 2 / Field Kern County / VRS / 19 / BNL3347 / 5.95 / 2.23 / 1.19 / 1.92 / *
Pop 1a / UC Davis / VRS / 19 / Gh109 / 3.87 / 1.52 / 1.09 / **
Pop 1b / UC Kerneay / VRS / 19 / Gh109 / 4.29 / 1.24 / 1.73 / **
Pop 2 / Field Kern County / VRS / 19 / Gh109 / 8.51 / 2.46 / 1.14 / 1.92 / **
Pop 3 / Field Kern County / DSI / 19 / MUSB1155 / 4.91 / 0.18 / 0.44 / **
Pop 3 / Field Kern County / VRS / 19 / MUSB1155 / 3.31 / 1.67 / 0.96 / *
Pop 2 / Field Kern County / VRS / 19 / MUSB1155 / 0.07 / 1.62 / 1.55
Pop 2 / Field Kern County / VRS / 19 / MUSB1155 / 3.98 / 3.42 / 0.40 / 1.62 / ***
Pop 1a / UC Davis / VRS / 25 / Gh537 / 3.89 / 1.20 / 1.55 / **
Pop 1a / UC Davis / DSI / 25 / Gh537 / 2.98 / 1.49 / 1.85 / *
Pop 1c / Field Kern County / VRS / 25 / Gh537 / 7.06 / 2.30 / 2.68 / ***
Pop 2 / Field Kern County / VRS / 25 / Gh537 / 6.50 / 1.80 / 1.93 / 0.79 / **
Pop 1c / Field Kern County / PS / 25 / Gh224 / 4.85 / 40.13 / 48.53 / **
Pop 1c / Field Kern County / VRS / 25 / Gh224 / 10.02 / 2.24 / 2.69 / ****
Pop 1c / Field Kern County / DSI / 25 / Gh224 / 4.57 / 0.96 / 1.24 / **
Pop 3 / Field Kern County / DSI / 25 / Gh224 / 4.75 / 1.00 / 1.23 / 1.41 / *
Pop 1c / Field Kern County / PS / 25 / JESPR224 / 5.80 / 39.47 / 48.86 / **
Pop 1c / Field Kern County / VRS / 25 / JESPR224 / 15.98 / 2.19 / 2.74 / *******
Pop 1a / UC Davis / VRS / 25 / BNL3103 / 6.96 / 1.02 / 1.66 / ***
Pop 1c / Field Kern County / VRS / 25 / BNL3103 / 6.52 / 2.34 / 2.68 / **

aPopulations: Pop 1a, 1b, and 1c = RIL TM-1 x 3-79; Pop 2 = F2 TM-1 x Pima-S6; and Pop 3 = F2 Shorty x Pima-S6

bSites: DSI and VRS greenhouse evaluation conducted in 2007 at the University of California Davis, CA. (UC Davis); DSI and VRS greenhouse evaluation conducted in 2008 at the University of California Kearney Research and Extension Center, Parlier, CA. (UC Kearney); Pop 1 = DSI, PS, and VRS field evaluation conducted in 2007 on a infested field with FOV race 4 at the Kern County site (Field Kern County); and F2= DSI and VRS field evaluation conducted in 2010 on a infested field with FOV race 4 at the Kern County site(Field Kern County).

VRS scale: 0 = no vascular root staining evident to 5 = plant severely damaged or plant death .

cKruskal-Wallis analysis (K*) test regarded as the nonparametric equivalent of the one-way analysis of variance (Van Ooijen, 2004).

.dMean - QTL SSR markers associated with responses to FOV race 4using recorded DSI, PS, or VRS on the Pima-S6 and Pima 3-79 (Mean-b) , Heterozygote (Mean-h), Upland TM-1 and Upland Shorty (Mean-a). DSI or VRS index of SSR dominant markers scored onF2 mapping populations were placed Mean-a or Mean-b (instead of Mean-c or Mean-d) to fit the information in this table.

eP-valuesare designated as *P < 0.1,** P < 0.05, and *** P < 0.01