Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

Bahri, Bochra A.; Daverdin, Guillaume; Xu, Xiangyang; Cheng, Jan-Fang; Barry, Kerrie W.; Brummer, E. Charles; Devos, Katrien M.

doi:10.1186/s12862-018-1193-2

Table 2 Characteristics of non-synonymous mutations in biomass genes and corresponding amino acid changes

From: Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.)

						Amino Acid				Allele frequencies %			SNP characteristics
Gene	Contig	Chromosome	Amino Acid position in Setaria Reference sequence	SNP region	Setaria italica reference sequence	Ref	Alt1	Alt2	Setaria italica	Wild-type allele	Mutant 1	Mutant 2	Conservative (Con) vs. non conservative (Non Con)
GI	contig15400	Chr05K	155	Exon7	Si000107m	E	K		E	91.59	8.41		Con
GI	contig15400	Chr05K	175	Exon7	Si000107m	S	Y		S	80.32	19.68		Non Con
GI	contig15400	Chr05K	177	Exon7	Si000107m	G	D		D	32.80	67.20		Non Con
GI	contig15400	Chr05K	180	Exon7	Si000107m	G	R		G	92.79	7.21		Non Con
GI	contig15400	Chr05K	234	Exon9	Si000107m	C	F	Y	C	79.82	19.59	0.58	Non Con
GI	contig01489	Chr05N	63	Exon5	Si000107m	W	S		S	37.50	62.50		Non Con
GI	contig01489	Chr05N	185	Exon7	Si000107m	R	Q		R	65.84	34.16		Con
GI	contig01489	Chr05N	960	Exon14	Si000107m	F	L		L	35.83	64.17		Non Con
PHYB	contig13571	Chr09N	661	Exon2	Si033968m	S	C		S	63.64	36.36		Non Con
PHYB	contig13571	Chr09N	702	Exon2	Si033968m	V	I		V	79.13	20.87		Con
PHYB	contig13571	Chr09N	713	Exon2	Si033968m	Y	D		D	50.30	49.70		Non Con
HD1	contig03275	Chr04K	11	Exon1	Seita.4G122700.1	E	M		E	85.98	14.02		Non Con
HD1	contig03275	Chr04K	32	Exon1	Seita.4G122700.1	A	T		A	94.56	5.44		Non Con
HD1	contig03275	Chr04K	35	Exon1	Seita.4G122700.1	G	S		S	60.63	39.37		Non Con
PGM	contig17299	Chr09K	351	Exon6	Si034948m	A	V		A	73.21	26.79		Non Con
TB1	contig06045	Chr09K	57	Exon1	Si038692m	G	D		G	91.61	8.39		Non Con
TB1	contig06045	Chr09K	213	Exon1	Si038692m	G	D		G	89.76	10.24		Non Con
TB1	contig06045	Chr09K	337	Exon1	Si038692m	I	V		L	56.64	43.36		Con
TB1	contig76312	Chr09N	51	Exon1	Si038692m	H	Y		H	88.06	11.94		Con
TB1	contig76312	Chr09N	89	Exon1	Si038692m	A	P		A	92.42	7.58		Non Con
TB1	contig76312	Chr09N	137	Exon1	Si038692m	S	P		S	92.77	7.23		Non Con
TB1	contig76312	Chr09N	193	Exon1	Si038692m	I	V		V	60.26	39.74		Con
TB1	contig76312	Chr09N	321	Exon1	Si038692m	N	S		N	91.87	8.13		Con
PHYC	contig03093	Chr09N	422	Exon1	Si034030m	V	L		L	45.71	54.29		Con
PHYC	contig03093	Chr09N	966	Exon3	Si034030m	E	V		V	42.90	57.10		Non Con
PHYC	contig03093	Chr09N	1029	Exon3	Si034030m	P	A		P	81.03	18.97		Non Con
PHYC	contig03093	Chr09N	1031	Exon3	Si034030m	K	E		K	76.66	23.34		Con
PHYC	contig03093	Chr09N	1041	Exon3	Si034030m	K	N		K	83.44	16.56		Non Con
PHYC	contig03093	Chr09N	1069	Exon1	Si034030m	L	W		L	94.26	5.74		Non Con
PHYC	contig03093	Chr09N	1104	Exon1	Si034030m	L	H		L	67.70	32.30		Non Con
VRN3	contig07490	Chr03N	238	Exon2	Si021330m	E	D		E	89.78	10.22		Con
VRN3	contig07490	Chr03N	286	Exon3	Si021330m	L	M		L	93.11	6.89		Con
VRN3	contig07490	Chr03N	295	Exon3	Si021330m	T	A		T	90.10	9.90		Non Con
VRN3	contig07490	Chr03N	412	Exon4	Si021330m	P	R		P	91.53	8.47		Non Con
VRN3	contig07490	Chr03N	493	Exon4	Si021330m	L	S		S	84.26	15.74		Non Con
VRN3	contig07490	Chr03N	511	Exon4	Si021330m	N	K		N	93.63	6.37		Non Con
VRN3	contig07490	Chr03N	600	Exon4	Si021330m	G	V		E	88.59	11.41		Non Con
VRN3	contig16433	Chr03K	144	Exon2	Si021330m	P	A		P	90.45	9.55		Non Con
VRN3	contig16433	Chr03K	398	Exon4	Si021330m	V	I		A	93.98	6.02		Con
VRN3	contig16433	Chr03K	409	Exon4	Si021330m	S	N		S	89.42	10.58		Con
VRN3	contig16433	Chr03K	450	Exon4	Si021330m	D	G		G	43.61	56.39		Non Con
VRN3	contig16433	Chr03K	569	Exon4	Si021330m	Q	E		R	88.36	11.64		Con
VRN3	contig16433	Chr03K	682	Exon4	Si021330m	L	Q		Q	28.61	71.39		Non Con
DW3	contig26301	Chr06K	672	Exon3	Si013123m	E	G		E	94.29	5.71		Non Con
DW3	contig26301	Chr06K	751	Exon3	Si013123m	M	V		M	21.22	78.78		Con
DW3	contig117938	Chr06N	713	Exon3	Si013123m	I	M		M	87.84	12.16		Con
DW3	contig26301	Chr06N	897	Exon3	Si013123m	I	V		V	82.96	17.04		Con
DW3	contig117938	Chr06N	872	Exon3	Si013123m	T	A	S	A	78.04	21.96	0.30	Non Con
FLD	contig01920	Chr07N	511	Exon1	Si009376m	S	G		G	76.70	23.30		Non Con

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ISSN: 2730-7182

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