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

Zhao, Xue; Teng, Weili; Li, Yinghui; Liu, Dongyuan; Cao, Guanglu; Li, Dongmei; Qiu, Lijuan; Zheng, Hongkun; Han, Yingpeng; Li, Wenbin

doi:10.1186/s12864-017-3843-y

BMC Genomics

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

Note: the expression pattern was according to Wan et al. BMC Genomics [39]

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ISSN: 1471-2164

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