Genetic Diversity of Main Inbred Indica Rice Varieties Applied in Guangdong Province as Revealed by Molecular Marker

doi:10.1016/S1672-6308(14)60275-4

Abstract

Abstract:

Genetic diversity of 299 inbred indica rice varieties, including 33 introduced varieties, applied in Guangdong Province of China were assessed using 20 ILP (intron length polymorphism) and 34 SSR (simple sequence repeat) markers. Totally, 154 loci were screened for the 299 varieties, with the average number of alleles (Na), rare alleles (Nr), and polymorphism information content (PIC) scored at 3.4, 0.7 and 0.32, respectively. The Nei’s genetic distance (GD) was estimated ranging from 0 to 0.7529 with an average of 0.4797. There was no significant difference of Na, Nr, PIC or GDs between the introduced and local varieties. Neighbor-joining (NJ) analysis showed that the 299 varieties failed into three main distinct groups, and the 33 introduced varieties were distributed over all the groups or subgroups. Model-based cluster analysis demonstrated that only 73 (24.4%) of the 299 varieties and 7 (21.2%) of the 33 introduced varieties could be distinctly classified into the three groups. Analysis of molecular variance showed that within the groups divided by NJ analysis, the genetic variations revealed by ILP, SSR and these two combined were 7.7%, 5.6% and 6.6%, and within the groups divided by region (Guangdong local and the introduced varieties), the genetic variables were 2.1%, 4.6%, 5.4%, respectively. These results suggested that the genetic diversity of the 299 inbred rice varieties in Guangdong Province was low, simultaneously relationship among varieties was poor and close in all kind of groups. Hence, it is very necessary to extend the genetic diversity during the breeding and selection practical procedure.

Key words: cluster analysis, genetic diversity, molecular marker, rice, population structure

Ming Huang, Ya-hui Wu, Xing-xing Tao, Yong-zhu Liu, Gui-li Yang, Zhi-qiang Chen. Genetic Diversity of Main Inbred Indica Rice Varieties Applied in Guangdong Province as Revealed by Molecular Marker[J]. Rice Science, 2015, 22(1): 1-8.

Figures/Tables 6

References 54

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Marker	Chr	Na	Nr	PIC	Marker	Chr	Na	Nr	PIC
ILP marker					RM212	2	3	1	0.46
RI02341	1	2	0	0.5	RM489	3	2	1	0.05
RI04587	1	2	1	0.01	RM279	3	3	1	0.25
RI00945	2	2	1	0.06	RM240	3	3	2	0.07
RI00301	3	3	0	0.47	RM251	3	3	0	0.3
RI05751	3	2	0	0.35	RM168	4	3	0	0.49
RI01085	4	2	0	0.49	RM401	4	3	0	0.53
RI01614	5	2	0	0.5	RM437	4	3	2	0.1
RI02821	5	2	1	0.03	RM584	4	3	0	0.64
RI04246	6	2	0	0.36	RM564	5	3	0	0.42
RI03949	6	2	1	0.09	RM214	5	3	2	0.03
RI05815	7	2	1	0.01	RM321	5	3	1	0.45
RI04107	7	2	1	0.01	RM21	6	3	0	0.47
RI03187	8	2	1	0.01	RM224	6	3	0	0.2
RI00213	8	2	1	0.04	RM1337	7	3	1	0.53
RI02123	10	2	1	0.02	RM499	7	4	2	0.09
RI01540	10	2	0	0.38	RM246	8	4	0	0.66
RI05818	11	2	0	0.5	RM341	8	4	1	0.58
RI05618	11	2	1	0.01	RM280	9	4	1	0.34
RI05373	12	2	1	0.01	RM481	9	4	0	0.67
RI03123	12	4	2	0.49	RM248	9	4	1	0.54
SSR marker					RM531	10	4	0	0.68
RM1395	1	2	0	0.24	RM566	10	4	0	0.45
RM274	1	2	0	0.27	RM3808	11	4	0	0.41
RM30	1	2	0	0.22	RM474	11	4	1	0.39
RM271	1	2	1	0.03	RM80	12	5	1	0.63
RM277	2	2	1	0.04	RM518	12	5	2	0.65
RM5479	2	2	0	0.5	RM440	12	5	1	0.6
Average of ILPs							2.2	0.7	0.22
										Average of SSRs	3.3	0.7	0.38
										Average of ILP and SSR combinations	3.4	0.7	0.32

Marker	Chr	Na	Nr	PIC	Marker	Chr	Na	Nr	PIC
ILP marker					RM212	2	3	1	0.46
RI02341	1	2	0	0.5	RM489	3	2	1	0.05
RI04587	1	2	1	0.01	RM279	3	3	1	0.25
RI00945	2	2	1	0.06	RM240	3	3	2	0.07
RI00301	3	3	0	0.47	RM251	3	3	0	0.3
RI05751	3	2	0	0.35	RM168	4	3	0	0.49
RI01085	4	2	0	0.49	RM401	4	3	0	0.53
RI01614	5	2	0	0.5	RM437	4	3	2	0.1
RI02821	5	2	1	0.03	RM584	4	3	0	0.64
RI04246	6	2	0	0.36	RM564	5	3	0	0.42
RI03949	6	2	1	0.09	RM214	5	3	2	0.03
RI05815	7	2	1	0.01	RM321	5	3	1	0.45
RI04107	7	2	1	0.01	RM21	6	3	0	0.47
RI03187	8	2	1	0.01	RM224	6	3	0	0.2
RI00213	8	2	1	0.04	RM1337	7	3	1	0.53
RI02123	10	2	1	0.02	RM499	7	4	2	0.09
RI01540	10	2	0	0.38	RM246	8	4	0	0.66
RI05818	11	2	0	0.5	RM341	8	4	1	0.58
RI05618	11	2	1	0.01	RM280	9	4	1	0.34
RI05373	12	2	1	0.01	RM481	9	4	0	0.67
RI03123	12	4	2	0.49	RM248	9	4	1	0.54
SSR marker					RM531	10	4	0	0.68
RM1395	1	2	0	0.24	RM566	10	4	0	0.45
RM274	1	2	0	0.27	RM3808	11	4	0	0.41
RM30	1	2	0	0.22	RM474	11	4	1	0.39
RM271	1	2	1	0.03	RM80	12	5	1	0.63
RM277	2	2	1	0.04	RM518	12	5	2	0.65
RM5479	2	2	0	0.5	RM440	12	5	1	0.6
Average of ILPs							2.2	0.7	0.22
										Average of SSRs	3.3	0.7	0.38
										Average of ILP and SSR combinations	3.4	0.7	0.32

Region /	No. of varieties	Na	Ne	He
Group	No. of varieties	Na	Ne	He
Introduced	33	1.67 ± 0.06	1.34 ± 0.03	0.21 ± 0.01
Local	266	1.92 ± 0.03	1.33 ± 0.03	0.21 ± 0.01
Group I	15	1.35 ± 0.07	1.27 ± 0.03	0.16 ± 0.01
Group II	131	1.84 ± 0.04	1.34 ± 0.03	0.21 ± 0.01
Group III	153	1.84 ± 0.04	1.32 ± 0.03	0.20 ± 0.01
Total	299	1.93 ± 0.03	1.34 ± 0.03	0.21 ± 0.01

Region /	No. of varieties	Na	Ne	He
Group	No. of varieties	Na	Ne	He
Introduced	33	1.67 ± 0.06	1.34 ± 0.03	0.21 ± 0.01
Local	266	1.92 ± 0.03	1.33 ± 0.03	0.21 ± 0.01
Group I	15	1.35 ± 0.07	1.27 ± 0.03	0.16 ± 0.01
Group II	131	1.84 ± 0.04	1.34 ± 0.03	0.21 ± 0.01
Group III	153	1.84 ± 0.04	1.32 ± 0.03	0.20 ± 0.01
Total	299	1.93 ± 0.03	1.34 ± 0.03	0.21 ± 0.01

Source of variation^a	df	SS	MS	Estimated variance	Variance (%)	P-
Source of variation^a	df	SS	MS	Estimated variance	Variance (%)	value
ILP
Among Regions	1	27.048	27.048	0.385	2.1	0.001
Among Pops	2	83.027	41.514	0.458	7.7
Within Pops	295	1233.959	4.183	4.049	90.2
Total	298	1344.033		4.893	100
SSR
Among Regions	1	54.904	54.904	0.692	4.6	0.001
Among Pops	2	163.565	81.782	0.834	5.6
Within Pops	295	4077.531	13.822	14.456	89.7
Total	298	4296		15.982	100
ILP + SSR
Among Regions	1	81.951	81.951	1.077	5.4	0.001
Among Pops	2	246.592	123.296	1.293	6.6
Within Pops	295	5311.49	18.005	18.403	89.5
Total	298	5640.033		20.772	100