Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

BMC Genomics

Table 3 SNP allele, map position, and segregation ratio of markers polymorphic in the Ogle1040 × TAM O-301 (OT) mapping population

SNP	Allele		OT LG^a	SR^b
	Ogle1040	TAM O-301
C51_1	T	C	OT_4	0.90
C51_2	C	T	OT_4	0.81
C104_1	G	A	OT_30	0.49
C250_1	A	G	OT_20_29	2.00
c318_1	G	C	OT_34	1.61
c540_1	A	G	Frag_14	1.08
c841_2	T	G	OT_32_33	0.71
c841_3	T	G	OT_32_33	0.68
c876_1a	T	G	OT_16	0.89
c876_1b	A	T	OT_10	1.32
c1196_1	A	T	OT_6	1.30
c1361_1	C	A	OT_32_33	0.91
c1579_1	G	C	OT_20_29	1.08
c2043_1	C	G	OT_31	0.91
c2106_2	-	-	OT_32_33	0.96
c2391_1	C	T	OT_32_33	0.68
c2391_2	C	T	OT_30	0.82
c2391_4	C	G	OT_34	1.01
c2391_5	G	T	OT_34	1.09
c2539_1	-	-	Unlinked	1.60
c2680_1	T	C	OT_24	0.94
c3212_1	A	G	OT_24	1.48
c3768_1	G	A	OT_24	1.03
c4096_1	-	-	OT_13	0.86
c5153_1	G	A	OT_27	0.79
c5252_1	G	A	OT_11	0.94
c5469_1	A	G	OT_1	1.05
c7461_1	G	A	OT_2	1.08
c10486_1	T	G	Unlinked	0.92
c11164_1	A	G	OT_11	1.16
c11164_2	C	T	OT_6	1.21
c12344_1	C	G	Unlinked	0.79
c12516_1	T	A	OT_27	0.82
c12516_2	G	A	OT_34	1.08
c14852_2	C	A	OT_2	0.78
c15098_1	C	T	OT_34	1.00
c16908_1	C	A	OT_10	0.73
c22314_1	G	T	OT_11	0.94
c23257_1	A	C	OT_13	0.96
lrc14030_1	T	A	OT_27	0.79
lrc16053_1	A	G	OT_8	1.13
lrc16053_2	C	T	OT_32_33	0.67
lrc16053_3	T	C	OT_32_33	0.89
lrc27472_2	A	C	OT_32_33	0.68
lrc34490_1	C	A	OT_15	0.92
lrc38531_1	C	A	OT_34	0.94
lrc38531_2	-	-	OT_8	0.75
lrc40347_1	G	C	Unlinked	0.81

^a Linkage group assignment is based on appending new SSR loci to the existing OT linkage map [Ref. [35]] using Map Manager QTX.
^b SR = Segregation ratio, calculated as the quotient of O/T allele frequencies within the population.

ISSN: 1471-2164