Supplementary Table 1. Distribution of morphological, physiological, agronomic and fiber quality traits related QTL for drought and salt tolerance under greenhouse and/or field conditions.

Chromosome / PH / FSW / FRW / DSW / DRW / LA / CHL / Pn / SC / TR / CIR / CT / OP / SCY / LY / BW / LP / FL / FU / FS / FE / MIC
c1 / 5 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c2 / 0 / 1 / 0 / 0 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 1 / 2 / 0 / 2 / 0 / 0 / 0 / 0 / 1 / 0
c3 / 0 / 0 / 0 / 0 / 0 / 2 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 7 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c4 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c5 / 12 / 1 / 2 / 0 / 1 / 2 / 3 / 0 / 0 / 0 / 0 / 1 / 0 / 1 / 0 / 4 / 0 / 0 / 0 / 0 / 0 / 0
c6 / 4 / 1 / 0 / 0 / 0 / 5 / 0 / 1 / 0 / 0 / 0 / 2 / 2 / 3 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c7 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0
c8 / 0 / 0 / 0 / 0 / 0 / 1 / 3 / 0 / 0 / 3 / 0 / 1 / 0 / 0 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0
c9 / 3 / 1 / 0 / 4 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0
c10 / 2 / 4 / 0 / 1 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c11 / 3 / 6 / 0 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 2 / 1 / 2 / 1
c12 / 4 / 4 / 0 / 0 / 0 / 3 / 2 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0
c13 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0
c14 / 0 / 1 / 0 / 0 / 1 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 1 / 1 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 0
c15 / 0 / 3 / 5 / 5 / 0 / 0 / 1 / 2 / 0 / 1 / 1 / 2 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c16 / 3 / 0 / 0 / 1 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0
c17 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c18 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c19 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 2
c20 / 2 / 0 / 1 / 2 / 0 / 2 / 4 / 0 / 3 / 3 / 0 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c21 / 0 / 0 / 1 / 0 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0
c22 / 2 / 0 / 0 / 0 / 0 / 0 / 2 / 1 / 0 / 0 / 1 / 1 / 1 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0
c23 / 0 / 0 / 5 / 2 / 3 / 0 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c24 / 2 / 3 / 2 / 0 / 1 / 0 / 9 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0
c25 / 6 / 2 / 2 / 1 / 3 / 2 / 1 / 0 / 1 / 0 / 1 / 1 / 2 / 2 / 1 / 1 / 0 / 0 / 2 / 2 / 5 / 6
c26 / 4 / 0 / 2 / 6 / 6 / 2 / 0 / 0 / 0 / 0 / 0 / 2 / 0 / 0 / 2 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Total / 54 / 27 / 22 / 23 / 19 / 23 / 32 / 5 / 7 / 7 / 6 / 16 / 11 / 15 / 16 / 16 / 3 / 2 / 4 / 3 / 8 / 9

PH, plant height; FSW, fresh shoot weight; FRW, fresh root weight; DSW, dry shoot weight, DRW, dry root weight; LA, Leaf area index;; CHL, chlorophyll content; Pn, photosynthesis rate; SC, stomata conductance; TR, transpiration; CIR, carbon isotype ratio; CT, canopy temperature;; OP, osmotic potential; SCY, seedcotton yield; LY, lint yield; BW, boll weight; LP, lint percent;FL, fiber length; FU, fiber uniformity; FS, fiber strength; FE, fiber elongation; MIC, micronaire value