Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

Table 2 Measures of nucleotide diversity and Tajima's D

Gene	S_I^a	θ_w	π_T	π_sil	π_syn	π_nonosyn	π_nonsyn/π_syn	N° haplotypes	Haplotype diversity	Tajima's D
GO	0	0.0009	0.0004	0.0003	0	0.0005	-	3	0.205	-1.51
PGIP3	3	0.0013	0.0018	0.0050	0.0062	0	0	4	0.725	1.10
LZP	0	0	0	0	0	0	-	2	0.281^b	-
GLP	0	0	0	0	0	0	-	3	0.433^b	-
MADSB-TF3	5	0.0034	0.0025	0.0027	0.0159	0.0018	0.1141	9	0.801	-1.02
AALP	6	0.0119	0.0117	0.0203	0.0143	0	0	4	0.661	-0.08
LIM	5	0.0056	0.0076	0.0117	0.0092	0	0	4	0.579	1.13
RL41	1	0.0087	0.0071	0	0	0.0145	-	3	0.556	-0.50
ANT	9	0.0122	0.0225	0.0841	0.0888	0	0	2	0.526	2.93^***c
RS16	5	0.0047	0.0066	0.0206	0.0294	0	0	3	0.573	1.36
NsLTP	5	0.0068	0.0077	0.0084	0.0380	0.0057	0.1504	3	0.433	0.42
SEM	1	0.0038	0.0018	0.0027	0	0	-	3	0.205	-1.42
SAMC	7	0.0093	0.0084	0.0134	0.0357	0.0007	0.0204	5	0.684	-0.34
GCvT	2	0.0047	0.0064	0.0253	0.0270	0	0	3	0.579	0.95
SBP	6	0.0142	0.0137	0.0523	0.0550	0	0	5	0.760	-0.14
LHCP	8	0.0063	0.0079	0.0268	0.0313	0.0011	0.0341	3	0.602	0.8266
CPSI	2	0.0068	0.0041	0.0101	0.0059	0.0010	0.1616	2	0.298	-1.17
PSI-III-CAB	1	0.0004	0.0006	0.0010	0	0	-	2	0.409	0.79
CAB	7	0.0038	0.0059	0.0136	0.0203	0	0	3	0.485	1.91
CAM	18	0.0155	0.0137	0.0166	0.0217	0	0	6	0.801	-0.44
CHS	0	0	0	0	0	0	-	1	0.000	-
GAPDH	1	0.0008	0.0007	0.0017	0	0	-	3	0.485	-0.24
GIA	2	0.0008	0.0005	0.0011	0.0016	0	0	2	0.199	-0.73
GPX	0	0	0	0	0	0	-	2	0.256^b	-
GST	31	0.0204	0.0277	0.0464	0.0636	0.0080	0.1254	9	0.772	1.44
PGIC	13	0.0081	0.0055	0.0074	0.0021	0.0012	0.5673	4	0.298	-1.19
SCR1	3	0.0012	0.0018	0.0076	0.0079	0	0	3	0.649	1.39
SCR2	7	0.0040	0.0037	0.0126	0.0126	0.0009	0.0721	3	0.374	-0.26
Average	5.29	0.0056	0.0061	0.0140	0.0174	0.0013	0.0655	3.54	0.497

^aParsimony informative sites (S_I) used to measure nucleotide diversity.
^bThe number of haplotypes and haplotype diversity values was obtained by using indel polymorphisms.
^cTajima's D significant p < 0.001.

ISSN: 1471-2229