| IDa | STS marker | Chr. | Position | QTL | Expressionb | Putative function | Candidate categoryc |
| TC_12018 | Coau2L06 | 2 | 75.8 | δ13C, FF | | Calcium-dependent protein kinase 2 | I′ | TC_1043, 2901, 4773, 4777, 8848 | pAR04H03 | 3 | 76.6 | Chl-a, δ13C | | Xyloglucan endotransglucosylase/hydrolase protein | I′ | TC_1191, 2292, 3741, 4297 | pAR0594 | 4 | 87.2 | Chl-a | ↑ leaf | Putative transport protein subunit | II′ | TC_15220, 5078 | P05-06 | 5 | 36.7 | DM | ↑ leaf | Probable WRKY transcription factor | II′ | TC_3299 | pAR0207b | 7 | 106.4 | FS | ↑ root | Putative linker histone H1 variant protein | II′ | TC_3097, 6916, 8776 | pAR03D05 | 7 | 172.1 | SC | | Putative CCR4 transcription complex | I′ | TC_11788, 6599, 6600 | Gafb22M15c | 7 | 187.9 | HI, BW, SC | | Probable xyloglucan endotransglucosylase | I′ | TC_12140, 370 | pAR0922 | 7 | 202.3 | HI, OP | | stress-induced protein | I′ | TC_11870, 12131, 4218, 5814, 9408 | Unig24G08d | 7 | 205.6 | HI, OP | | Luminal binding protein | I′ | TC_3660, 5958 | pGH843 | 7 | 207.4 | HI, OP, δ13C | ↓ leaf | Ubiquitin/ribosomal protein | II′ | TC_2075, 2076, 2077, 8440, 9924 | pAR3-26 | 7 | 210.3 | HI, OP, δ13C | ↓ leaf | Zinc finger | II′ | TC_15720, 6936 | Unig28D04 | 8 | 45.0 | Chl-a, Chl-b, δ13C | ↓ leaf | ATP synthase | II′ | TC_241, 8023, 8765 | Gate4CE02 | 10 | 95.6 | OP, SC, HI, CT | ↑ leaf, ↓ root | Transcription factor WRKY1 | II′ | TC_1092 | pAR0836 | 10 | 95.6 | OP, SC, HI, CT | | Photosystem II oxygen-evolving complex | I′ | TC_4882 | Gate4AH05 | 10 | 97.4 | OP, SC, HI, CT | ↑ root | Putative thioredoxin m2 | II′ | TC_7520, 7521, 7522, 7523, 7524 | pAR0783 | 10 | 100.6 | OP, SC, HI, CT | | Auxin-repressed 12.5 KD protein | I′ | TC_2988, 4865, 5435, 7627 | Coau4J19 | 10 | 106.7 | OP, SC, HI, CT | | Protein induced upon tuberization | I′ | TC_13398 | Unig26D12 | 10 | 106.7 | OP, SC, HI, CT | | Putative GTP-binding protein | I′ | TC_1142 | pAR0949 | 10 | 112.7 | OP, SC, HI, CT | | Metallothionein-like protein | I′ | TC_9516 | pGH663 | 10 | 112.9 | HI | ↑ leaf | Homeobox-leucine zipper protein | II′ | TC_159, 6239 | pAR0211 | 10 | 114.5 | HI | | Heat shock protein 70 | I′ | TC_7534 | Gate4CE05a | 10 | 122 | HI | | MYB-like DNA-binding domain protein | I′ | TC_3646, 3647, 3648 | Gate1CE04b | 11 | 45.7 | δ13C | ↑ leaf | Ubiquitin extension protein | II′ | TC_10672, 5735 | pAR08A01 | 11 | 45.7 | δ13C | ↑ root | Putative proline-rich protein | II′ | TC_14408 | Unig26E05 | 11 | 52.9 | δ13C | ↑ leaf | Transcription initiation factor TFIID subunit 9 | II′ | TC_4402, 5648, 7125, 7127, 7134 | Gate1CD11b | 12 | 0.0 | SC, HI, BW | | Transducer (GPA1), Arabidopsis thaliana GPA1 | I′ | TC_12229, 12900, 12901 | Gate4CG05a | 12 | 38.8 | FL | | Soluble epoxide hydrolase | I′ | TC_3419 | Gate4CA09b | 12 | 39.6 | FL | ↓ leaf | Zinc finger-like protein | II′ | TC_11086 | Gate4AE08b | 12 | 40.4 | FL | | Hsp20.1 protein | I′ | TC_3376, 7396, 7397 | pVNC146b | 12 | 41.5 | FL | | Omega-3 fatty acid desaturase, chloroplast precursor | I′ | TC_3270, 3271, 3272, 4970, 8481 | Gate4CG12 | 13 | 50.7 | SC, HI | | Thioredoxin-like protein 1 | I′ | TC_15659 | Coau2L21 | 13 | 131.5 | OP, BW | | Adenylyl cyclase associated protein | I′ | TC_4763, 8193, 8194, 8196, 8198 | Gate1AA03 | 13 | 135.0 | OP, BW | | Glycine-rich RNA-binding protein | I′ |
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| IDa | STS Marker | Chr | Position | QTL | Expressionb | Putative Function | Candidate Categoryc |
| Cotton12_00001_132 | Gate3CC07a | 2 | 76.2 | δ13C, FF | ↓ leaf | Putative epimerase/dehydratase | II | Cotton12_00007_02 | Coau1O15 | 3 | 76.0 | Chl-a | ↑ root, ↑ leaf | Unknown protein | II | Cotton12_18270_01 | Gate4BG06a | 4 | 74.4 | Chl-a | ↓ leaf | Homeobox-leucine zipper protein | II′ | Cotton12_00128_02 | Gate2BC04 | 4 | 103.5 | Chl-a | ↓ leaf | Unknown protein | II | Cotton12_14391_01 | P05-06 | 5 | 36.7 | DM | ↓ leaf | F23H11.2 protein (At1g59710/T30E16_31) | II | Cotton12_07910_01 | W07a | 5 | 105.3 | SC, HI, BW, FF | ↓ leaf | Gossypium putative major latex-like protein | II | Cotton12_25608_01 | A1737 | 6 | 49.8 | HI, BW | ↓ root | Hypothetical protein | II | Cotton12_00659_01 | pAR0537 | 7 | 97.0 | FS | ↓ leaf | Putative glycine hydroxymethyltransferase | II | Cotton12_16738_01 | pGH505 | 7 | 131.4 | FS | ↓ leaf | Hypothetical protein | II | Cotton12_00017_01 | P01-42 | 7 | 192.6 | SC, HI, BW | ↓ leaf | RNA-binding protein | II | Cotton12_12667_01 | P02-45 | 7 | 210.1 | HI, OP, δ13C | ↑ leaf | Expressed protein | II | Cotton12_04174_01 | Unig06B11 | 10 | 96.5 | OP, SC, HI, CT, FS | ↑ leaf | Hypothetical protein | II | Cotton12_04395_01 | pAR10F02 | 10 | 100.6 | OP, SC, HI, CT, FS | ↑ leaf | Putative ethylene response factor ERF3a | II′ | Cotton12_00370_02 | pAR0602 | 10 | 108.2 | OP, SC, HI, CT, FS | ↓ leaf | ATP synthase gamma chain, chloroplast precursor | II′ | Cotton12_01999_01 | Gate1DD01 | 10 | 112.7 | OP, SC, HI, CT, FS | ↓ leaf | Hypothetical protein | II | Cotton12_35202_01 | G1099 | 10 | 116.2 | OP, SC, HI, CT, FS | ↓ leaf | Glutamyl tRNA amidotransferase, subunit A | II | Cotton12_02930_01 | Gafb28K14 | 11 | 45.7 | δ13C | ↑ leaf | 4-Coumarate:CoA ligase | II′ | Cotton12_06698_01 | pAR01D04 | 11 | 54.4 | δ13C | ↑ root | Proline-rich protein APG-like | II′ | Cotton12_18985_01 | Gate4BD10a | 12 | 22.3 | SC, HI, BW | ↓ root, ↑ leaf | Hypothetical protein | II | Cotton12_18065_01 | Unig22D08 | 12 | 38.8 | FL | ↓ root | Hypothetical protein | II | Cotton12_19658_01 | W11 | 13 | 47.6 | OP, SC, HI, Chl-a | ↑ root | Hypothetical protein | II |
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