Genetic diversity and ecological differentiation of Chinese annual wild soybean (Glycine soja)

doi:10.3724/SP.J.1003.2008.07286

Abstract

Abstract:

The annual wild soybean (Glycine soja), known as the ancestor of the cultivated soybean (G. max), is endemic to East Asia with most of its range in China. It is believed that the wild soybean holds a reservoir of genetic variation potentially useful for improvement of cultivated soybeans. Our study combined molecular techniques with evaluation of botanical traits to investigate genetic diversity and genetic specificity caused by geographic differentiation in wild soybean populations in China. A total of 196 wild accessions from three distinct geographic regions (Northeast China, Huang-Huai-Hai Valleys and South China, abbreviated as NEC, HHH and SOC, respectively) were genotyped using 52 SSR markers and phenotyped using 10 botanical traits. The average allelic richness (NA) of the entire wild population and Simpson diversity index (H) were 16.1 and 0.852, respectively; higher than those of cultivated populations (NA = 11.4, H = 0.773). Among the three geographic populations, the SOC population had the highest genetic diversity (NA = 12.9, H = 0.842), the NEC population the next highest (NA = 12.4 and H = 0.834), and the HHH population the lowest (NA = 11.4, H = 0.805). Population-specific alleles existed on a number of loci (including AW132402 (Linkage group A2), Satt522 (F), satt150 (M), Sat_332 (D1a), Satt046 (K), sct_190 (K), thus indicating the existence of genetic differentiation among, and ecological specificity of geographic populations. Analysis of botanical traits revealed high variation, diversity (H= 0.710) and geographic differentiation, especially in growth period traits. These differences in botanical traits indicate the significance of natural selection due to geographic variation in day-length and temperature. Analysis of molecular data and botanical traits indicated that the geographic differentiation observed in botanical traits was based on genetic differentiation, and that genetic diversity of the SOC population was higher than the other two populations.

Key words: Glycine soja, SSR marker, botanical traits, genetic diversity, genetic differentiation

Yanlai Ding, Tuanjie Zhao, Junyi Gai. Genetic diversity and ecological differentiation of Chinese annual wild soybean (Glycine soja)[J]. Biodiv Sci, 2008, 16(2): 133-142.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2008.07286

https://www.biodiversity-science.net/EN/Y2008/V16/I2/133

Figures/Tables 6

References 34

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引物(连锁群) Primer (LG)	全国 National		东北 NEC		黄淮海 HHH		南方 SOC		引物(连锁群) Primer (LG)	全国National		东北 NEC		黄淮海HHH		南方 SOC
引物(连锁群) Primer (LG)	NA	H	NA	H	NA	H	NA	H	引物(连锁群) Primer (LG)	NA	H	NA	H	NA	H	NA	H
Sat_385 (A1)	13	0.886	10	0.864	13	0.886	11	0.859	BE806387 (F)	10	0.843	8	0.810	9	0.846	8	0.784
Satt225 (A1)	11	0.825	9	0.784	7	0.776	10	0.819	Satt659 (F)	25	0.914	22	0.930	15	0.853	15	0.896
BE820148 (A2)	19	0.901	16	0.911	11	0.782	18	0.911	Satt522 (F)	22	0.861	16	0.878	14	0.834	14	0.796
AW132402(A2)	33	0.948	20	0.939	19	0.906	30	0.939	Satt163 (G)	9	0.317	5	0.286	5	0.301	7	0.354
Satt209 (A2)	7	0.531	6	0.311	7	0.524	7	0.644	Satt324 (G)	11	0.813	10	0.813	7	0.727	7	0.801
Satt509 (B1)	18	0.904	13	0.884	14	0.875	15	0.909	AF162283 (G)	12	0.837	8	0.797	6	0.617	13	0.899
Satt665 (B1)	15	0.866	12	0.877	9	0.809	13	0.854	Satt442 (H)	26	0.930	19	0.908	18	0.906	22	0.932
Satt168 (B2)	13	0.870	10	0.762	10	0.857	12	0.876	Satt302 (H)	12	0.854	9	0.821	9	0.774	9	0.860
Satt020 (B2)	22	0.919	19	0.918	17	0.902	15	0.871	Satt239 (I)	18	0.915	13	0.884	17	0.901	14	0.868
Sat_337 (C1)	15	0.896	13	0.887	11	0.871	13	0.891	Sat_299 (I)	21	0.909	14	0.884	15	0.865	15	0.896
Sct_191 (C1)	12	0.871	11	0.872	10	0.841	9	0.845	AW310961(J)	19	0.927	18	0.920	16	0.912	15	0.904
Satt291 (C2)	15	0.856	11	0.859	11	0.845	10	0.801	Satt244 (J)	24	0.914	16	0.892	15	0.863	19	0.922
Satt286 (C2)	20	0.848	14	0.886	10	0.671	17	0.847	Satt046 (K)	17	0.892	12	0.883	15	0.876	14	0.866
Satt277 (C2)	20	0.914	16	0.904	16	0.828	16	0.908	Sct_190 (K)	13	0.828	9	0.812	7	0.798	11	0.772
Satt307 (C2)	19	0.885	14	0.889	14	0.887	11	0.834	Sat_293 (K)	16	0.895	12	0.878	13	0.859	14	0.880
Satt316 (C2)	15	0.879	12	0.891	12	0.856	10	0.840	Satt284 (L)	10	0.832	9	0.810	9	0.764	9	0.853
Sat_332 (D1a)	14	0.856	13	0.850	11	0.779	10	0.788	Satt373 (L)	11	0.826	9	0.800	8	0.818	10	0.827
Satt436 (D1a)	12	0.807	9	0.756	7	0.741	11	0.852	Satt150 (M)	19	0.908	14	0.862	14	0.879	13	0.847
Satt147 (D1a)	15	0.820	9	0.718	8	0.809	14	0.861	Satt567 (M)	13	0.803	11	0.793	10	0.757	10	0.818
BE475343(D1b)	17	0.886	15	0.881	12	0.804	14	0.910	Satt210 (M)	16	0.875	12	0.834	10	0.818	15	0.898
Satt005 (D1b)	25	0.924	19	0.926	19	0.899	18	0.915	Satt683 (N)	27	0.909	21	0.911	18	0.871	23	0.889
Sat_289 (D1b)	12	0.880	11	0.842	11	0.857	11	0.862	Satt234 (N)	9	0.796	9	0.800	7	0.727	7	0.744
Satt443 (D2)	9	0.753	6	0.733	6	0.681	8	0.750	Satt347 (O)	11	0.736	9	0.796	8	0.688	7	0.692
Satt311 (D2)	17	0.899	11	0.858	12	0.875	14	0.898	Satt592 (O)	16	0.813	12	0.855	6	0.655	12	0.800
Satt186 (D2)	13	0.879	12	0.880	9	0.836	12	0.886	最大值 Max.	33	0.948	22	0.939	19	0.912	30	0.939
Satt720 (E)	12	0.865	12	0.861	10	0.848	10	0.824	最小值 Min.	7	0.317	5	0.286	5	0.301	7	0.354
Satt606 (E)	19	0.879	15	0.868	13	0.842	15	0.880	总计 Total	837		651		594		672
Satt269 (F)	18	0.910	16	0.886	14	0.858	15	0.906	平均 Average	16.1	0.852	12.5	0.834	11.4	0.805	12.9	0.842

引物(连锁群) Primer (LG)	全国 National		东北 NEC		黄淮海 HHH		南方 SOC		引物(连锁群) Primer (LG)	全国National		东北 NEC		黄淮海HHH		南方 SOC
引物(连锁群) Primer (LG)	NA	H	NA	H	NA	H	NA	H	引物(连锁群) Primer (LG)	NA	H	NA	H	NA	H	NA	H
Sat_385 (A1)	13	0.886	10	0.864	13	0.886	11	0.859	BE806387 (F)	10	0.843	8	0.810	9	0.846	8	0.784
Satt225 (A1)	11	0.825	9	0.784	7	0.776	10	0.819	Satt659 (F)	25	0.914	22	0.930	15	0.853	15	0.896
BE820148 (A2)	19	0.901	16	0.911	11	0.782	18	0.911	Satt522 (F)	22	0.861	16	0.878	14	0.834	14	0.796
AW132402(A2)	33	0.948	20	0.939	19	0.906	30	0.939	Satt163 (G)	9	0.317	5	0.286	5	0.301	7	0.354
Satt209 (A2)	7	0.531	6	0.311	7	0.524	7	0.644	Satt324 (G)	11	0.813	10	0.813	7	0.727	7	0.801
Satt509 (B1)	18	0.904	13	0.884	14	0.875	15	0.909	AF162283 (G)	12	0.837	8	0.797	6	0.617	13	0.899
Satt665 (B1)	15	0.866	12	0.877	9	0.809	13	0.854	Satt442 (H)	26	0.930	19	0.908	18	0.906	22	0.932
Satt168 (B2)	13	0.870	10	0.762	10	0.857	12	0.876	Satt302 (H)	12	0.854	9	0.821	9	0.774	9	0.860
Satt020 (B2)	22	0.919	19	0.918	17	0.902	15	0.871	Satt239 (I)	18	0.915	13	0.884	17	0.901	14	0.868
Sat_337 (C1)	15	0.896	13	0.887	11	0.871	13	0.891	Sat_299 (I)	21	0.909	14	0.884	15	0.865	15	0.896
Sct_191 (C1)	12	0.871	11	0.872	10	0.841	9	0.845	AW310961(J)	19	0.927	18	0.920	16	0.912	15	0.904
Satt291 (C2)	15	0.856	11	0.859	11	0.845	10	0.801	Satt244 (J)	24	0.914	16	0.892	15	0.863	19	0.922
Satt286 (C2)	20	0.848	14	0.886	10	0.671	17	0.847	Satt046 (K)	17	0.892	12	0.883	15	0.876	14	0.866
Satt277 (C2)	20	0.914	16	0.904	16	0.828	16	0.908	Sct_190 (K)	13	0.828	9	0.812	7	0.798	11	0.772
Satt307 (C2)	19	0.885	14	0.889	14	0.887	11	0.834	Sat_293 (K)	16	0.895	12	0.878	13	0.859	14	0.880
Satt316 (C2)	15	0.879	12	0.891	12	0.856	10	0.840	Satt284 (L)	10	0.832	9	0.810	9	0.764	9	0.853
Sat_332 (D1a)	14	0.856	13	0.850	11	0.779	10	0.788	Satt373 (L)	11	0.826	9	0.800	8	0.818	10	0.827
Satt436 (D1a)	12	0.807	9	0.756	7	0.741	11	0.852	Satt150 (M)	19	0.908	14	0.862	14	0.879	13	0.847
Satt147 (D1a)	15	0.820	9	0.718	8	0.809	14	0.861	Satt567 (M)	13	0.803	11	0.793	10	0.757	10	0.818
BE475343(D1b)	17	0.886	15	0.881	12	0.804	14	0.910	Satt210 (M)	16	0.875	12	0.834	10	0.818	15	0.898
Satt005 (D1b)	25	0.924	19	0.926	19	0.899	18	0.915	Satt683 (N)	27	0.909	21	0.911	18	0.871	23	0.889
Sat_289 (D1b)	12	0.880	11	0.842	11	0.857	11	0.862	Satt234 (N)	9	0.796	9	0.800	7	0.727	7	0.744
Satt443 (D2)	9	0.753	6	0.733	6	0.681	8	0.750	Satt347 (O)	11	0.736	9	0.796	8	0.688	7	0.692
Satt311 (D2)	17	0.899	11	0.858	12	0.875	14	0.898	Satt592 (O)	16	0.813	12	0.855	6	0.655	12	0.800
Satt186 (D2)	13	0.879	12	0.880	9	0.836	12	0.886	最大值 Max.	33	0.948	22	0.939	19	0.912	30	0.939
Satt720 (E)	12	0.865	12	0.861	10	0.848	10	0.824	最小值 Min.	7	0.317	5	0.286	5	0.301	7	0.354
Satt606 (E)	19	0.879	15	0.868	13	0.842	15	0.880	总计 Total	837		651		594		672
Satt269 (F)	18	0.910	16	0.886	14	0.858	15	0.906	平均 Average	16.1	0.852	12.5	0.834	11.4	0.805	12.9	0.842

	遗传丰富度 Allele richness (NA)				遗传离散度 Simpson diversity index (H)
	全国National	东北 NEC	黄淮海HHH	南方 SOC	全国National	东北 NEC	黄淮海HHH	南方 SOC
最大值 Maximum	21	9	13	18	0.905	0.860	0.878	0.915
最小值 Minimum	4	2	3	4	0.408	0.292	0.479	0.392
极差 Range	17	7	10	14	0.497	0.568	0.398	0.524
平均值 Mean	11.4	5.6	6.9	9.6	0.773	0.729	0.737	0.748

	遗传丰富度 Allele richness (NA)				遗传离散度 Simpson diversity index (H)
	全国National	东北 NEC	黄淮海HHH	南方 SOC	全国National	东北 NEC	黄淮海HHH	南方 SOC
最大值 Maximum	21	9	13	18	0.905	0.860	0.878	0.915
最小值 Minimum	4	2	3	4	0.408	0.292	0.479	0.392
极差 Range	17	7	10	14	0.497	0.568	0.398	0.524
平均值 Mean	11.4	5.6	6.9	9.6	0.773	0.729	0.737	0.748

连锁群 LG	引物 Primer	等位基因 Allele (bp)	全国 National (%)	东北 NEC (%)	黄淮海 HHH (%)	南方 SOC (%)	连锁群LG	引物 Primer	等位基因 Allele (bp)	全国 National (%)	东北 NEC (%)	黄淮海 HHH (%)	南方 SOC (%)
A2	BE820148	177	11.9	8.3	4.9	20.5	D1a	Sat_332	233	12.1	9.5	27.1	2.6
	AW132402	348	1.1	0.0	0.0	2.9			230	9.6	27.0	3.4	0.0
		340	0.5	0.0	0.0	1.4	D2	Satt443	244	12.8	3.2	5.0	27.4
		336	0.5	0.0	0.0	1.4	F	Satt269	378	14.2	17.2	24.6	2.8
		272	0.5	0.0	0.0	1.4			374	12.7	20.3	9.8	8.3
		244	0.5	0.0	0.0	1.4		Satt522	281	4.2	13.8	0.0	0.0
		236	0.5	0.0	0.0	1.4			251	11.0	1.7	5.0	23.3
		188	6.3	3.3	13.3	2.9	I	Satt239	197	9.1	4.8	19.7	4.1
		144	11.1	8.3	20.0	5.8			149	10.2	3.2	8.2	17.8
		140	9.0	6.7	3.3	15.9	K	Satt046	183	7.0	0.0	3.2	16.0
	Satt209	174	14.9	3.2	11.5	27.3		Sct_190	218	8.7	25.8	0.0	1.4
B2	Satt168	247	10.5	3.2	8.2	18.2	M	Satt150	196	12.0	1.7	1.7	28.4
		208	18.5	40.3	13.1	5.2			169	5.7	19.0	0.0	0.0