Genetic diversity and population structure of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, in South China

Figures & data

Fig. 1 The distribution of the 72 isolates of Rhizoctonia solani AG-1 IA collected from Guangdong, Guangxi and Hainan provinces.

Table 1. Details of the 72 isolates of Rhizoctonia solani AG-1 IA from Guangdong (GD), Guangxi (GX) and Hainan (HN).

Isolate code	Population & size	Subpopulation & size	Sampling date
GD01–GD06	GD, 24	Maoming, GD (MMGD), 6	July 9, 2007
GD07–GD12		Conghua, GD (CHGD), 6	July 13, 2007
GD13–GD18		Wuhua, GD (WHGD), 6	July 17, 2007
GD19–GD24		Lianzhou, GD (LZGD), 6	July 18, 2007
GX01–GX06	GX, 24	Bobai, GX (BBGX), 6	July 10, 2007
GX07–GX12		Zhaoping, GX (ZPGX), 6	July 11, 2007
GX13–GX18		Liuzhou, GX (LZGX), 6	July 21, 2007
GX19–GX24		Baise, GX (BSGX), 6	July 19, 2007
HN01–HN06	HN, 24	Ledong, HN (LDHN), 6	July 19, 2007
HN07–HN12		Dongfang, HN (DFHN), 6	July 19, 2007
HN13–HN18		Qiongzhong, HN (QZHN), 6	July 18, 2007
HN19–HN24		Wenchang, HN (WCHN), 6	July 21, 2007

Table 2. Sequences of arbitrary primers, annealing temperature, numbers of amplified and polymorphic bands resulting from ISSR analysis.

Primer	Sequence (5′ → 3′)	Nucleotide count	Annealing tem. (˚C)	Amplified band	Polymorphic band	Polymorphism (%)
EZ1	(AC)8 AG	18	55	10	10	100.00
EZ2	(AC)8 TG	18	55	12	12	100.00
EZ7	(AG)8 T	17	52	14	12	85.71
EZ9	(AG)8 G	17	52	11	9	81.81
EZ11	(AG)8 GG	18	54	13	11	84.62
EZ13	(AC)8 C	17	52	16	16	100.00
EZ18	(CA)8 G	17	54	16	16	100.00
EZ25	(AC)8 T	17	52	7	7	100.00
EZ27	(AC)8 G	17	54	17	17	100.00
Average				12.89	12.22	94.83
Total				116	110	94.83

Table 3. Genotype  diversity of Rhizoctonia solani AG-1 IA from the 12 subpopulations.

Subpopulation	h	I	NP	P (%)
MMGD	0.1838	0.2749	61	52.59
CHGD	0.1846	0.2766	61	52.59
WHGD	0.1879	0.2795	60	51.72
LZGD	0.1291	0.1985	48	41.38
BBGX	0.1892	0.2836	63	54.31
ZPGX	0.1836	0.2785	64	55.17
LZGX	0.2248	0.3405	77	66.38
BSGX	0.2237	0.3349	74	63.79
LDHN	0.1484	0.2269	54	46.55
DFHN	0.1759	0.2634	58	50.00
QZHN	0.1593	0.2445	58	50.00
WCHN	0.1826	0.2787	65	56.03
Average	0.1811	0.2734	61.92	53.38
Total	0.2034	0.3175	110	94.83

Notes: h: Nei’s gene diversity; I: Shannon’s diversity index; N_P, number of polymorphic loci; P, percentage of polymorphic loci.

Fig. 2 An example of the ISSR polymorphism of Rhizoctonia solani AG-1 IA isolates revealed by using ISSR primer EZ27. (Left to right: lane M, molecular weight marker DL5000 DNA ladder; lanes 1–16 represent the isolates).

Fig. 3 Dendrogram of the 72 isolates of Rhizoctonia solani AG-1 IA based on ISSR data using Nei and Li’s similarity coefficient and UPGMA clustering method. The scale bar at the bottom represents the Li’s genetic similarity coefficient.

Table 4. Comparisons of genetic diversity and gene differentiation in three populations of Rhizoctonia solani AG-1 IA from south China.

Population & size	HT	HS	GST	Nm
GD, 24	0.2086	0.1714	0.1783	2.3039
GX, 24	0.2381	0.2053	0.1377	3.1319
HN, 24	0.2028	0.1665	0.1789	2.2952
Average	0.2165	0.1811	0.1650	2.5770
Total	0.2372	0.2177	0.0822	5.5810

Table 5. Analysis of molecular variance (AMOVA).

Source of variation	df	SS	MS	Variance component	Percentage of variance component%	фST	P
Among populations	2	122.19	61.09	1.57	9.14	0.091	<0.002
Among subpopulations	9	209.91	23.32	1.53	8.92	0.098	<0.002
Within subpopulation	60	846.33	14.10	14.10	81.93	0.181	<0.002

Note: df, degree of freedom; SS, sum of square; MS, mean square; ф_ST, correlation within populations relative to the total.

Fig. 4 UPGMA dendrogram of the genetic relationships among 12 subpopulations of Rhizoctonia solani AG-1 IA inferred from a matrix of Nei’s genetic distances. The scale bar at the bottom represents the genetic distance.

Fig. 5 Correlation between ΦST values and geographical distances among 12 subpopulations of Rhizoctonia solani AG-1 IA.