Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

doi:10.1016/S1672-6308(14)60293-6

Abstract

Abstract:

Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon’s diversity index (I) of 0.748 and the heterozygosity (He) of 0.434. In each regional population, I value varied widely. The widest range of I (0.228-0.489) was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea (0.168-0.270). The F-statistics of regional populations (Fis, Fit and Fst) also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea. All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.

Key words: weedy rice, simple sequence repeat, genetic diversity, population structure, weed control

Mao-bai Li, Hui Wang, Li-ming Cao. Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers[J]. Rice Science, 2015, 22(4): 180-188.

Figures/Tables 9

References 36

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36	(Managing Editor: Fang Hongmin)

Origin	Code for each material ^a	Year
Qingpu, Shanghai, China	Qp-1, Qp-2, Qp-3, Qp-4, Qp-5	2008
Jiading, Shanghai, China	Jd-1, Jd-2, Jd-3, Jd-4, Jd-5, Jd-6	2007
Nanhui, Shanghai, China	Nh-1, Nh-2, Nh-3, Nh-4	2010
Pudong, Shanghai, China	Pd-1, Pd-2, Pd-3, Pd-4, Pd-5	2009
Chongming, Shanghai, China	Cm-1, Cm-2, Cm-3, Cm-4, Cm-5	2008
Fengxian, Shanghai, China	Fx-1, Fx-2, Fx-3, Fx-4, Fx-5	2009
Taizhou, Jiangsu, China	Tz-1, Tz-2, Tz-3, Tz-4, Tz-5	2005
Shenyang, Liaoning, China	Sy-1, Sy-2, Sy-3, Sy-4, Sy-5	2000
Tieling, Liaoning, China	Tl-1, Tl-2, Tl-3, Tl-4, Tl-5	2004
Haicheng, Liaoning, China	Hc-1, Hc-2, Hc-3, Hc-4, Hc-5	2003
Dandong, Liaoning, China	Dd-1, Dd-2, Dd-3, Dd-4, Dd-5	2004
Gongzhuling, Jilin, China	Gz-1, Gz-2, Gz-3, Gz-4, Gz-5	2006
Jiamusi, Heilongjiang, China	Jm-1, Jm-2, Jm-3, Jm-4, Jm-5	2005
Yesan, Chungcheong, Korea	Ys-1, Ys-2, Ys-3, Ys-4, Ys-5	2000
Seosan, Chungcheong, Korea	Ss-1, Ss-2, Ss-3, Ss-4, Ss-5, Ss-6	2000
Qp, Qingpu; Jd, Jiading; Nh, Nanhui; Pd, Pudong; Cm, Chongming; Fx, Fengxian; Tz, Taizhou; Sy, Shenyang; Tl, Tieling; Hc, Haicheng; Dd, Dandong; Gz, Gongzhuling; Jm, Jiamusi; Ys, Yesan; Ss, Seosan. ^a The numbers represent weedy rice accessions from each location.

Origin	Code for each material ^a	Year
Qingpu, Shanghai, China	Qp-1, Qp-2, Qp-3, Qp-4, Qp-5	2008
Jiading, Shanghai, China	Jd-1, Jd-2, Jd-3, Jd-4, Jd-5, Jd-6	2007
Nanhui, Shanghai, China	Nh-1, Nh-2, Nh-3, Nh-4	2010
Pudong, Shanghai, China	Pd-1, Pd-2, Pd-3, Pd-4, Pd-5	2009
Chongming, Shanghai, China	Cm-1, Cm-2, Cm-3, Cm-4, Cm-5	2008
Fengxian, Shanghai, China	Fx-1, Fx-2, Fx-3, Fx-4, Fx-5	2009
Taizhou, Jiangsu, China	Tz-1, Tz-2, Tz-3, Tz-4, Tz-5	2005
Shenyang, Liaoning, China	Sy-1, Sy-2, Sy-3, Sy-4, Sy-5	2000
Tieling, Liaoning, China	Tl-1, Tl-2, Tl-3, Tl-4, Tl-5	2004
Haicheng, Liaoning, China	Hc-1, Hc-2, Hc-3, Hc-4, Hc-5	2003
Dandong, Liaoning, China	Dd-1, Dd-2, Dd-3, Dd-4, Dd-5	2004
Gongzhuling, Jilin, China	Gz-1, Gz-2, Gz-3, Gz-4, Gz-5	2006
Jiamusi, Heilongjiang, China	Jm-1, Jm-2, Jm-3, Jm-4, Jm-5	2005
Yesan, Chungcheong, Korea	Ys-1, Ys-2, Ys-3, Ys-4, Ys-5	2000
Seosan, Chungcheong, Korea	Ss-1, Ss-2, Ss-3, Ss-4, Ss-5, Ss-6	2000
Qp, Qingpu; Jd, Jiading; Nh, Nanhui; Pd, Pudong; Cm, Chongming; Fx, Fengxian; Tz, Taizhou; Sy, Shenyang; Tl, Tieling; Hc, Haicheng; Dd, Dandong; Gz, Gongzhuling; Jm, Jiamusi; Ys, Yesan; Ss, Seosan. ^a The numbers represent weedy rice accessions from each location.

Origin	Code	Accession name
Shanghai, China	C-Sh	Jinfeng, Youfeng, Hanfeng, Qiufeng
Jiangsu, China	C-Js	Xiushui 7, Xiushui 9, Xiushui 61, Xiushui 110, Wuyunjing 7, Wuyunjing 3, Zhendao 88
Liaoning, China	C-Ln	Liaojing 9, Liaojing 294, Liaojing 371, Liaoxing 15, Shendao 7
Chungcheong, Korea	C-Cc	Ilpum, Singeumo, Gopum, Dongjin 2, Yeon 308

Origin	Code	Accession name
Shanghai, China	C-Sh	Jinfeng, Youfeng, Hanfeng, Qiufeng
Jiangsu, China	C-Js	Xiushui 7, Xiushui 9, Xiushui 61, Xiushui 110, Wuyunjing 7, Wuyunjing 3, Zhendao 88
Liaoning, China	C-Ln	Liaojing 9, Liaojing 294, Liaojing 371, Liaoxing 15, Shendao 7
Chungcheong, Korea	C-Cc	Ilpum, Singeumo, Gopum, Dongjin 2, Yeon 308

Primer	Chr	SSR motif	Forward sequence	Reverse sequence	EPS	Na	Ne	I
RM1	1	(GA)₂₆	GCGAAAACACAATGCAAAAA	GCGTTGGTTGGACCTGAC	113	6	2.721	1.250
RM9	1	(GA)₁₅GT(GA)₂	GGTGCCATTGTCGTCCTC	ACGGCCCTCATCACCTTC	136	3	1.236	0.398
RM14	1	(GA)₁₈	CCGAGGAGAGGAGTTCGAC	GTGCCAATTTCCTCGAAAAA	191	4	2.416	1.041
RM23	1	(GA)₁₅	CATTGGAGTGGAGGCTGG	GTCAGGCTTCTGCCATTCTC	145	3	1.903	0.733
RM212	1	(CT)₂₄	CCACTTTCAGCTACTACCAG	CACCCATTTGTCTCTCATTATG	136	2	1.403	0.462
RM237	1	(CT)₁₈	CAAATCCCGACTGCTGTCC	TGGGAAGAGAGCACTACAGC	130	2	1.492	0.512
RM110	2	(GA)₁₅	TCGAAGCCATCCACCAACGAAG	TCCGTACGCCGACGAGGTCGAG	156	2	1.280	0.377
RM425	2	(CGG)₉	CCAACGAAGATTCGAAGCTC	CAGCACCATGAAGTCGCC	126	3	2.103	0.814
RM525	2	(AAG)₁₂	GGCCCGTCCAAGAAATATTG	CGGTGAGACAGAATCCTTACG	131	4	3.034	1.179
RM1178	2	(AG)₁₃	CAGTGGGCGAGCATAGGAG	ATCCTTTTCTCCCTCTCTCG	112	3	2.998	1.098
RM156	3	(CGG)₈	GCCGCACCCTCACTCCCTCCTC	TCTTGCCGGAGCGCTTGAGGTG	160	3	2.090	0.879
RM218	3	(TC)₂₄ACT₅(GT)₁₁	TGGTCAAACCAAGGTCCTTC	GACATACATTCTACCCCCGG	148	3	1.943	0.766
RM489	3	(ATA)₈	ACTTGAGACGATCGGACACC	TCACCCATGGATGTTGTCAG	271	4	2.175	0.893
RM8209	3	(AG)₁₅	AGGAGAAGAGGAATCTTTGC	CGATCGAGAGCTACTATTGC	188	3	1.043	0.117
RM241	4	(CT)₃₁	GAGCCAAATAAGATCGCTGA	TGCAAGCAGCAGATTTAGTG	138	2	1.729	0.613
RM470	4	(CTT)₁₄	TCCTCATCGGCTTCTTCTTC	AGAACCCGTTCTACGTCACG	83	4	3.406	1.297
RM567	4	(GA)₂₁	ATCAGGGAAATCCTGAAGGG	GGAAGGAGCAATCACCACTG	261	1	1.000	0.000
RM5473	4	(TC)₂₀	ACACGGAGATCCGAGACACGAG	CGAGATTAACGTCGTCCTC	105	5	4.117	1.493
RM31	5	(GA)₁₅	GATCACGATCCACTGGAGCT	AAGTCCATTACTCTCCTCCC	140	6	2.737	1.266
RM188	5	(CA)₈	TCCGCCTCTCCTCTCGCTTCCC	GCAACGCACAACCGAACCGAGC	210	3	2.283	0.924
RM430	5	(GA)₂₅	AAACAACGACGTCCCTGATC	GTGCCTCCGTGGTTATGAAC	173	5	2.922	1.217
RM193	6	(GCT)₅	CGCCTCTTCTTCCTCGCCTCCG	CGGGTCCATCCCCCCTCTCCTC	189	1	1.000	0.000
RM276	6	(AG)₈A₃(GA)₃₃	CTCAACGTTGACACCTCGTG	TCCTCCATCGAGCAGTATCA	149	4	2.113	0.960
RM402	6	(ATA)₇	GAGCCATGGAAAGATGCATG	TCAGCTGGCCTATGACAATG	133	3	1.321	0.487
RM469	6	(AG)₁₅	AGCTGAACAAGCCCTGAAAG	GACTTGGGCAGTGTGACATG	105	2	1.465	0.498
RM557	6	(AC)₁₃	GTGGCGAGATCTATGTGGTG	GCTTTGTGTGTGTGTGTGTG	211	1	1.000	0.000
RM234	7	(CT)₂₅	ACAGTATCCAAGGCCCTGG	CACGTGAGACAAAGACGGAG	156	2	1.729	0.613
RM346	7	(CTT)₁₈	CGAGAGAGCCCATAACTACG	ACAAGACGACGAGGAGGGAC	175	3	2.132	0.867
RM429	7	(TG)₁₀	TCCCTCCAGCAATGTCTTTC	CCTTCATCTTGCTTTCCACC	159	3	1.876	0.744
RM500	7	(AAG)₉	GAGCTTGCCAGAGTGGAAAG	GTTACACCGAGAGCCAGCTC	259	1	1.000	0.000
RM256	8	(CT)₂₁	GACAGGGAGTGATTGAAGGC	GTTGATTTCGCCAAGGGC	127	2	1.021	0.058
RM264	8	GA)₂₇	GTTGCGTCCTACTGCTACTTC	GATCCGTGTCGATGATTAGC	178	5	2.586	1.149
RM281	8	(GA)₂₁	ACCAAGCATCCAGTGACCAG	GTTCTTCATACAGTCCACATG	138	3	2.073	0.799
RM408	8	(CT)₁₃	CAACGAGCTAACTTCCGTCC	ACTGCTACTTGGGTAGCTGACC	128	3	2.014	0.783
RM515	8	(GA)₁₁	TAGGACGACCAAAGGGTGAG	TGGCCTGCTCTCTCTCTCTC	211	4	2.419	1.005
RM201	9	(CT)₁₇	CTCGTTTATTACCTACAGTACC	CTACCTCCTTTCTAGACCGATA	158	2	1.741	0.617
RM242	9	(CT)₂₆	GGCCAACGTGTGTATGTCTC	TATATGCCAAGACGGATGGG	225	3	1.916	0.807
RM257	9	(CT)₂₄	CAGTTCCGAGCAAGAGTACTC	GGATCGGACGTGGCATATG	147	4	3.504	1.314
RM566	9	(AG)₁₅	ACCCAACTACGATCAGCTCG	CTCCAGGAACACGCTCTTTC	239	3	1.879	0.802
RM216	10	(CT)₁₈	GCATGGCCGATGGTAAAG	TGTATAAAACCACACGGCCA	146	3	1.291	0.436
RM228	10	(CA)₆(GA)₃₆	CTGGCCATTAGTCCTTGG	GCTTGCGGCTCTGCTTAC	154	7	4.632	1.693
RM484	10	(AT)₉	TCTCCCTCCTCACCATTGTC	TGCTGCCCTCTCTCTCTCTC	299	1	1.000	0.000
RM224	11	(AAG)₈(AG)₁₃	ATCGATCGATCTTCACGAGG	TGCTATAAAAGGCATTCGGG	157	4	2.390	1.070
RM286	11	(GA)₁₆	GGCTTCATCTTTGGCGAC	CCGGATTCACGAGATAAACTC	110	4	2.484	1.066
RM17	12	(GA)₂₁	TGCCCTGTTATTTTCTTCTCTC	GGTGATCCTTTCCCATTTCA	184	3	1.349	0.495
RM101	12	(CT)₃₇	GTGAATGGTCAAGTGACTTAGGTGGC	ACACAACATGTTCCCTCCCATGC	324	3	2.563	1.001
RM277	12	(GA)₁₁	CGGTCAAATCATCACCTGAC	CAAGGCTTGCAAGGGAAG	124	2	1.929	0.675
RM1103	12	(AG)₁₂	CAGCTGCTGCTACTACACCG	CTACTCCACGTCCATGCATG	216	2	1.792	0.634
Chr, Chromosome; EPS, Expected PCR product size; Na, Observed number of alleles; Ne, Effective number of alleles; I, Shannon’s information index.