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Table 2 Significant SNPs and predicted candidate genes associated with SCN HG Type 2.5.7 resistance in soybean

From: Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7

SNP Chr Position Model QTLs Gene Distance to SNP (Kbp) Functional description Expression pattern
rs35898587 7 35,898,587 FARMCPU - Glyma.07G190900 46.68 sphingosine kinase 1  
Glyma.07G191000 42.52 Vacuolar protein sorting-associated protein VPS28 family protein  
Glyma.07G191100 33.66 endonuclease 4  
Glyma.07G191200 29.08 alternative NAD(P)H dehydrogenase 2  
Glyma.07G191500 2.12 HAL2-like  
rs36423980 7 36,423,980 CMLM, ECMLM - Glyma.07G195400 28.22 RING/U-box superfamily protein  
Glyma.07G195500 12.78 transcription factor-related  
Glyma.07G196000 28.36 RING membrane-anchor 1  
Glyma.07G193900 174.20 Dof-type zinc finger DNA-binding family protein regulated by SCN
Glyma.07G196500 59.39 phosphate 2 regulated by SCN
Glyma.07G196800 85.03 lipoxygenase 3 regulated by SCN
rs7631207 8 7,631,207 CMLM, ECMLM Mattews et al. 1998 [40]; Yuan et al. 2002 [42]; Guo et al. 2006 [9]; Vuong et al. 2011 [41] Glyma.08G099400 24.52 CBL-interacting protein kinase 23  
rs7640250 8 7,640,250 CMLM, ECMLM Glyma.08G099700 32.06 Metallo-hydrolase/oxidoreductase superfamily protein  
rs7671170 8 7,671,170 CMLM, ECMLM, FARMCPU Glyma.08G100100 2.50 auxin response factor 8  
Glyma.08G100700 54.67 RING/U-box superfamily protein  
Glyma.08G100800 60.21 Leucine-rich repeat protein kinase family protein  
rs7662003 8 7,662,003 CMLM, ECMLM     
rs7664479 8 7,664,479 CMLM, ECMLM     
rs7622492 8 7,622,492 CMLM, ECMLM Glyma.08G097300 184.48 Aldolase-type TIM barrel family protein regulated by SCN
rs7661660 8 7,661,660 CMLM, ECMLM     
rs16268025 8 16,268,025 FARMCPU - Glyma.08G200800 21.21 protein kinase family protein / peptidoglycan-binding LysM domain-containing protein  
Glyma.08G201000 9.76 hydroxyproline-rich glycoprotein family protein  
Glyma.08G201100 1.89 HPT phosphotransmitter 4  
Glyma.08G200100 84.82 HAD superfamily, subfamily IIIB acid phosphatase regulated by SCN
Glyma.08G200200 80.21 HAD superfamily, subfamily IIIB acid phosphatase regulated both constitutively and by SCN
Glyma.08G202300 57.12 Integrase-type DNA-binding superfamily protein regulated by SCN
rs3853672 14 3,853,672 CMLM, ECMLM - Glyma.14G048600 74.83 disease resistance protein (TIR-NBS-LRR class), putative  
Glyma.14G049500 15.54 ethylene-forming enzyme  
Glyma.14G047900 179.55 Leucine-rich repeat receptor-like protein kinase family protein regulated by SCN
Glyma.14G051600 196.06 Copper transport protein family regulated by SCN
rs38522986 15 38,522,986 FARMCPU Kabelka et al. 2005 [43]     
rs46625879 18 46,625,879 CMLM, ECMLM, FARMCPU Winter et al. 2007 [12] Glyma.18G193200 65.89 laccase 7  
Glyma.18G193300 49.11 laccase 8  
Glyma.18G193400 3.01 Laccase/Diphenol oxidase family protein  
  1. Note: the expression pattern was according to Wan et al. BMC Genomics [39]