From: Genetic control of tolerance to drought stress in soybean
Locus ID | Candidate region | SNP ID | P | R2 | Allele effect | Gene of interest | Arabidopsis | Annotation | Reference | Known QTL |
---|---|---|---|---|---|---|---|---|---|---|
CW_SDS_1 | Gm03_7027565_7317565 | AX-93988673_G_A | 4.3 | 0.05 | -0.3 | N/A | N/A | N/A | N/A | N/A |
CW_SDS_2 | Gm03_16874434_17164434 | AX-93991327_G_C | 4.1 | 0.02 | 0.23 | N/A | N/A | N/A | N/A | N/A |
CW_SDS_3 | Gm03_45259915_45549915 | AX-93918502_C_A | 4.1 | 0.07 | -0.4 | Glyma.03G261500 | AT2G46820 (PSI-P) | Photosystem I P subunit (photosynthesis) | PubC 2, PubC 3 | |
Glyma.03G261400 | AT4G01410 (N/A) | LEA hydroxyproline-rich glycoprotein (lateral root formation) | N/A | N/A | ||||||
Glyma.03G258300 | AT3G61830 (ARF18) | Auxin response factor 18 (regulates cell growth and seed weight) | [69] | N/A | ||||||
CW_SDS_4 | Gm05_28547428_28867428 | AX-93921335_C_T | 5.2 | 0.06 | 0.27 | N/A | N/A | N/A | N/A | SCN 1 |
CW_SDS_5 | Gm06_14605039_14955039 | AX-93923547_T_C | 5.8 | 0.04 | -0.18 | N/A | N/A | N/A | N/A | PH 1, PH 2 |
CW_SDS_6 | Gm10_7752764_8022764 | AX-94072904_A_G | 4.2 | 0.05 | -0.3 | N/A | N/A | N/A | N/A | PH 3, PH 4 |
CW_SDS_7 | Gm12_268639_738639 | AX-94092624_A_G | 9.9 | 0.08 | -0.29 | Glyma.12G009100 | AT5G09680 (RLF) | Reduced lateral root formation (lateral root formation) | [70] | |
CW_SDS_8 | Gm13_30347735_30657735 | AX-93643614_G_A | 4 | 0.04 | 0.29 | N/A | N/A | N/A | N/A | WUE 1 |
CW_SDS_9a | Gm15_50341499_50871499 | AX-94142375_T_C | 4 | 0.06 | -0.38 | Glyma.15G269200 | AT2G32840 (N/A) | Proline-rich family protein (cell wall integrity and root elongation under drought) | [71] | Cu 1, Cu 2 |
CW_SDS_9b | Gm15_50369101_50899101 | AX-93945641_A_G | 4 | 0.06 | -0.38 | |||||
CW_LDS_1 | Gm02_8486923_8816923 | AX-93976757_G_A | 4.7 | 0.09 | 0.62 | Glyma.02G094700 | AT4G01470 (TIP1-3) | Tonoplast intrinsic protein 1;3 (transmembrane channels for water and small uncharged solutes) | [72] | N/A |
Glyma.02G094900 | AT3G55330 (PPL1) | PsbP-like protein 1 (reapir of PSII damage) | [73] | N/A | ||||||
Glyma.02G097700 | AT1G25480 (N/A) | Aluminium activated malate transporter family protein (stomatal opening) | [74] | N/A | ||||||
CW_LDS_2 | Gm06_50717337_51067337 | AX-93628808_T_C | 4.7 | 0.14 | 0.73 | Glyma.06G321900 | AT1G55670 (PSAG) | Photosystem I subunit G (satbility of photosystem I complex) | Seedset 1, Seeds | |
CW_LDS_3 | Gm08_47511280_47831280 | AX-93761082_G_T | 6.1 | 0.14 | 1.04 | Glyma.08G365700 | AT1G67080 (ABA4) | Abscisic acid (aba)-deficient 4 (stress-induced ABA accumulation) | [77] | WUE 2, WUE 3 |
CW_LDS_4 | Gm20_5309031_5709031 | AX-93900908_A_C | 4.6 | 0.14 | 0.76 | Glyma.20G037100 | AT5G12330 (LRP1) | Lateral root primordium (LRP) protein-related (root development) | [78] | N/A |
CW_LDS_5 | Gm20_43251405_43651405 | AX-93910009_G_T | 7.3 | 0.04 | 0.6 | Glyma.20G197600 | AT2G29460 (GSTU4) | Glutathione S-transferase tau 4 (oxidative stress response) | N/A | |
LSEN_SDS_1 | Gm03_35362990_35652990 | AX-93917720_G_A | 5.1 | 0.15 | -0.53 | Glyma.03G138000 | AT5G19450 (CPK8) | Calcium-dependent protein kinase 19 (ABA-mediated stomatal closure and ROS reduction) | [81] | P, Mg, Zn |
LSEN_SDS_2 | Gm15_49950789_50480789 | AX-94142205_C_T | 4.9 | 0.14 | -0.43 | Glyma.15G266500 | AT1G79580 (SMB) | NAC (No Apical Meristem) domain transcriptional regulator superfamily protein (root cap development) | Cu 1, Cu 2 | |
LSEN_SDS_3 | Gm19_2913123_3603123 | AX-93886487_C_T | 6.8 | <0.01 | -0.01 | Glyma.19G027700 | AT5G39360 (EDL2) | EID1-like 2 (ABA signalling and stress respnse) | [84] | SIFC 1 |
LSEN_LDS_1 | Gm02_36400063_36730063 | AX-93981961_T_A | 6.6 | 0.14 | 0.54 | Glyma.02G192700 | AT5G04870 (CPK1) | Calcium dependent protein kinase 1 (ROS reduction and proline accumulation) | [85] | N/A |
Glyma.02G193000 | AT5G06410 | DNAJ heat shock N-terminal domain-containing protein (maintenance of seed shape and size at high ABA; AtDjA3) | [86] | N/A | ||||||
LSEN_LDS_2 | Gm16_25479906_26001906 | AX-93852357_C_A | 5.6 | 0.11 | -0.6 | N/A | N/A | N/A | N/A | N/A |
LSEN_LDS_3 | Gm16_29164663_29686663 | AX-93853705_G_C | 4 | <0.01 | -0.02 | N/A | N/A | N/A | N/A | PodShat 1, PodShat 2, qP16* |
LSEN_LDS_4a | Gm16_30272259_30794259 | AX-93854127_A_T | 4 | <0.01 | -0.14 | Glyma.16G145800 | AT3G54890 (LHCA1) | Photosystem I light harvesting complex 1 chlorophyll a/b binding protein (electron transport in photosynthesis) | [87] | eChl_T** |
LSEN_LDS_4b | Gm16_30395381_30917381 | AX-93650691_A_C | 4 | 0.01 | 0.08 | |||||
LSEN_LDS_5a | Gm18_48141658_48501658 | AX-94178903_C_G | 4 | 0.02 | -0.24 | Glyma.18G202900, Glyma.18G203500 | AT1G09950 (RAS1), AT3G51810 (EM1) | RESPONSE TO ABA AND SALT 1 (Salt and ABA sensitivity), Em-like protein GEA1 (stress induced ABA response through ABI5, ROS reduction) | SCN 2, Oil | |
LSEN_LDS_5b | Gm18_48144745_48504745 | AX-94178905_G_A | 4 | 0.02 | -0.24 | |||||
LSEN_LDS_5c | Gm18_48157192_48517192 | AX-93655968_A_C | 4 | 0.02 | -0.24 | |||||
LSEN_LDS_5d | Gm18_48205607_48565607 | AX-93655972_C_T | 4.1 | 0.02 | -0.21 | |||||
LSEN_LDS_5e | Gm18_48257716_48617716 | AX-93881368_A_C | 4.1 | 0.02 | -0.21 | |||||
LSEN_LDS_5f | Gm18_48277688_48637688 | AX-93952219_T_C | 4.7 | 0.02 | -0.24 | |||||
LSEN_LDS_5g | Gm18_48322720_48682720 | AX-93881396_G_T | 4.1 | 0.02 | -0.21 | |||||
LSEN_LDS_6 | Gm19_44805252_45495252 | AX-94195039_A_G | 7.2 | 0.12 | -0.49 | Glyma.19G191700 | AT5G03720 (HSFA3) | Heat shock transcription factor A3 (thermotolerance and drought tolerance in combination with DREB2A) | AMIN, Seedset 2, PH 5, Pods, LeafArea, LeafWidth, StemEnd, Internod, interbrach 1, DTM, DFTM, Lod, Nod, TotalSeed | |
AGRmax-Yr_SDS_1 | Gm05_31841551_32161551 | AX-93720346_T_C | 7.7 | 0.1 | 0.06 | Glyma.05G128000 | AT1G29930 (LHCB1.3) | Light harvesting chlorophyll a/b binding protein 1 (stomatal movement, drought response) | [93] | N/A |
AGRmax-Yr_SDS_2 | Gm06_19076651_19426651 | AX-93730252_G_T | 5.4 | 0.09 | 0.05 | Glyma.06G204100 | AT3G29575 (AFP3) | ABI5 binding protein 3 (negative regulator of ABA signalling) | [94] | WUE 4, WUE 5, interbrach 2, DTF |
Glyma.06G204400 | AT1G74160 | LONGIFOLIA protein (cellulose deposition) | N/A | |||||||
AGRmax-Yr_SDS_3 | Gm17_39250897_39530897 | AX-93866910_A_C | 7.1 | <0.01 | 0.01 | |||||
AGRmax-Yr_SDS_4 | Gm18_54299774_54659774 | AX-93883955_T_A | 4.6 | 0.09 | -0.04 | Glyma.18G259700 | AT5G15250 (FTSH6) | FtsH protease 6 (thylakoid membrane biogenesis, PSII repair mechanism) | [97] | SCN 3, Fe |
CH-Yr_LDS_1 | Gm06_18615861_18965861 | AX-93730063_A_G | 6.7 | 0.06 | -0.03 | Glyma.06G202200 | AT1G74310 (HSP101) | Heat shock protein 101 (tolerance to heat sterss) | [98] | PubC 1, PubC 4 |
CH-Yr_LDS_2 | Gm08_15065114_15385114 | AX-93754190_C_T | 5.1 | 0.16 | 0.06 | Glyma.08G191300 | AT4G33050 (EDA39) | Calmodulin-binding family protein (stomatal opening) | [99] | PUE, SIFC 2 |
CH-Yr_LDS_3 | Gm09_7236144_7576144 | AX-94060112_T_C | 4.2 | 0.16 | 0.05 | Glyma.09G071400 | AT1G19150 (LHCA6) | Photosystem I light harvesting chlorophyll a/b binding protein 6 (photosynthesis) | [100] | WUE 6 |
CH-Yr_LDS_4 | Gm16_32550790_33072790 | AX-93855040_G_A | 5.7 | 0.16 | 0.06 | N/A | N/A | N/A | N/A | BSR |