Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne

Xing, Yongzhong; Frei, Uschi; Schejbel, Britt; Asp, Torben; Lübberstedt, Thomas

doi:10.1186/1471-2229-7-43

BMC Plant Biology

Table 4 Summary of DNA polymorphism and diversity estimates in the about 1000 bp of 11 candidate genes

From: Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne

Parameters	Entire region	Non-coding	Coding regions
			All sites	Synonymous	Non-synonymous
EST1 (bp)	949	33	916
Indels (sites)	57	12	45
SNP sites	107	0	107	25	82
Polymorphic sites in %^a	12.0	0	12.3	12.0	12.6
θ/bp^b	0.0297	0	0.0301
Tajima's D^b	-0.0676^ns	-	-0.0676^ns
EST6 (bp)	936	95	841
Indels (sites)	67	0	67
SNP sites	247	17	230	71^c	137^c
Polymorphic sites in %	28.4	17.9	29.7	40.3	22.0
θ/bp	0.0793	0.0553	0.0829
Tajima's D	-0.4662^ns	0.0302^ns	-0.5024^ns
EST7 (bp)	1036	0	1036
Indels (sites)	13		13
SNP sites	277		277	57^c	183^c
Polymorphic sites in %	27.1		27.1	27.1	22.9
θ/bp	0.0791		0.0791
Tajima's D	-0.3672^ns		-0.3672^ns
EST26 (bp)	1030	0	1030
Indels (sites)	0		0
SNP sites	16		16	6	10
Polymorphic sites in %	1.6		1.6	2.6	1.3
θ/bp	0.00365		0.00365	0.0060	0.0030
Tajima's D	0.0986^ns		0.0986^ns
EST31 (bp)	943	0	943
Indels (sites)	0		0
SNP sites	20		20	0	20
Polymorphic sites in %	2.1		2.1	0	2.7
θ/bp	0.0050		0.0050	0	0.0064
Tajima's D	1.1385^ns		1.1385^ns
EST45 (bp)	1056	309	747
Indels (sites)	87	0	87
SNP sites	258	91	167	32^c	107^c
Polymorphic sites in %	26.6	29.4	22.4	21.8	21.7
θ/bp	0.0756	0.0896	0.0691
Tajima's D	-0.4209^ns	-0.3269^ns	-0.4715^ns
EST13 (bp)	959	326	633
Indels (sites)	9	5	4
SNP sites	9	2	7	3	4
Polymorphic sites in %	0.9	6.2	1.1	2.2	0.8
θ/bp	0.0022	0.0015	0.0026	0.0051	0.0020
Tajima's D	0.8068^ns	1.0927^ns	0.5250^ns
EST24 (bp)	985	385	600
Indels (sites)	11	7	4
SNP sites	37	25	12	8	4
Polymorphic sites in %	3.8	6.6	2.0	6.1	0.9
θ/bp	0.0089	0.0160	0.0047	0.0144	0.0020
Tajima's D	1.1897^ns	1.1556^ns	1.0406^ns
EST28 (bp)	1019	398	621
Indels (sites)	58	58	0
SNP sites	63	33	30	20	10
Polymorphic sites in %	6.6	9.7	4.8	14.8	2.1
θ/bp	0.0154	0.0228	0.0114	0.0347	0.0049
Tajima's D	0.8363^ns	1.3632^ns	0.1900^ns
EST39 (bp)	977	257	720
Indels (sites)	28	23	5
SNP sites	52	13	39	24^c	10^c
Polymorphic sites in %	5.5	5.4	5.5	12.8	1.9
θ/bp	0.0130	0.0138	0.0138
Tajima's D	2.1562*	0.9752^ns	2.4360*
EST40 (bp)	1085	371	712
Indels (sites)	2	0	2
SNP sites	9	2	7	1	6
Polymorphic sites in %	0.8	0.5	1.0	0.6	1.1
θ/bp	0.0020	0.0013	0.0023	0.0013	0.0027
Tajima's D	-0.1300^ns	1.2987^ns	-0.7024^ns

^a Polymorphic sites in percentage measured as polymorphic sites in the target region divided by the total nucleotides in the region excluding indels. Synonymous (non-synonymous) polymorphic sites in percentage measured as synonymous (non-synonymous) mutation sites divided by synonymous (non-synonymous) sites.
^b θ Watterson's estimator; π nucleotide diversity per site; D Tajimas's D: *, ** significant at P = 0.05 and 0.01 level; ns non-significant.
^c A number of synonymous and non-synonymous mutations were not included due to some codons with multiple and complex evolutionary path.

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