Identification of quantitative trait loci associated with leaf rust resistance in rye by precision mapping

BMC Plant Biology

Table 4 Translational effect of single-nucleotide polymorphisms (SNPs) located in the genes from “common 21 pool”

SNP-DArT marker^a	Consequence	Impact	cDNA position	CDS position	Protein position	Amino acids	Codons	Strand
7467766\|F\|0–6:T > G	missense variant	mod	59	59	20	Y/S	tAc/tCc	-1
3730018\|F\|0–57:A > G	intron variant	mof	-	-	-	-	-	1
3362858\|F\|0–20:G > C	synonymous variant	low	522	522	174	G	ggC/ggG	-1
5203314\|F\|0–14:C > T	synonymous variant	low	390	390	130	A	gcC/gcT	1
3603211\|F\|0–20:C > G	missense variant	mod	384	384	128	E/D	gaG/gaC	-1
3597912\|F\|0–20:C > T	missense variant	mod	856	856	286	V/M	Gtg/Atg	-1
3596033\|F\|0–14:T > C	synonymous variant	low	2232	2232	744	T	acA/acG	-1
3596652\|F\|0–30:A > G	synonymous variant	low	1017	1017	339	S	tcT/tcC	-1
3591362\|F\|0–11:A > C	synonymous variant	low	420	420	140	A	gcT/gcG	-1
3345552\|F\|0–36:A > G	missense variant	mod	701	701	234	M/T	aTg/aCg	-1
5034809\|F\|0–32:G > C	missense variant	mod	177	177	59	E/D	gaG/gaC	1
3594357\|F\|0–29:A > C	stop lost	high	553	553	185	*/E	Tag/Gag	-1
3587847\|F\|0–44:C > A	missense variant	mod	681	681	227	E/D	gaG/gaT	-1
3349900\|F\|0–20:T > C	synonymous variant	low	1551	1551	517	N	aaT/aaC	1
3344187\|F\|0–12:G > C	missense variant	mod	1580	1580	527	S/T	aGc/aCc	1
3899895\|F\|0–56:G > A	intron variant	mof	-	-	-	-	-	1
75511600\|F\|0–32:T > G	synonymous variant	low	495	495	165	A	gcT/gcG	1
5503350\|F\|0–5:G > A	synonymous variant	low	228	228	76	H	caC/caT	-1
3353307\|F\|0–11:T > C	synonymous variant	low	2286	2286	762	L	ctT/ctC	1
3360254\|F\|0–23:C > T	intron variant	mof	-	-	-	-	-	-1
3596868\|F\|0–24:T > C	synonymous variant	low	1368	1368	456	V	gtA/gtG	-1

^aFirst, reference allele; second, alternative allele. mod, referred to moderate impact; mof referred to modifier impact; L referred to low impact. Marker location and gene ID are given in Table 3

ISSN: 1471-2229