Genetic structure and diversity of Medicago lupulina populations in northern and central China based on EST-SSRs markers

doi:10.3724/SP.J.1003.2008.07362

Abstract

Abstract:

Abstract: Medicago lupulina is an annual or short-perennial and widespread herbaceous plant. It is generally considered a selfing species with a strong self-compatibility system, but a shift in mating system towards outcrossing or mix-mating has been reported. To estimate genetic variation, gene flow, mating system and genetic background of M. lupulina, we characterized 354 individuals from 17 wild populations from northern and central China using nine EST-SSRs markers. We found that: (1) EST-SSRs markers had a high percentage of polymorphic loci (PPL = 71.9%) and 4-11 alleles per loci. The Xinjiang-Nalati population had the highest level of genetic diversity (H_E= 0.388), whereas the Shaanxi-Xi’an population had the lowest (H_E= 0.042). Selfing rate was 93.8 %. (2) Genetic differentiation was high among populations (F_ST= 0.528; R_ST= 0.499). Of the total genetic variation, 59.02% was found among populations. (3) Mantel test revealed that genetic distance and geographic distance were positively correlated (r = 0.4141, P≤ 0.0003). Neighbor- joining trees based on Nei’s genetic distance (D_a) showed that neighboring populations clustered into the same clade, which was consistent with results of Mantel test. Our results indicated that the genetic structure of M. lupulina populations have been strongly affected by dispersal patterns and a strategy of inbreeding.

Key words: Medicago lupulina, EST-SSR, genetic diversity, genetic structure, selfing

Juan Yan, Haijia Chu, Hengchang Wang, Jianqiang Li. Genetic structure and diversity of Medicago lupulina populations in northern and central China based on EST-SSRs markers[J]. Biodiv Sci, 2008, 16(3): 263-270.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2008.07362

https://www.biodiversity-science.net/EN/Y2008/V16/I3/263

Figures/Tables 8

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居群 Population	经纬度 Locality	采样数目 Sample size
新疆 Xinjiang
1 喀什 Kashi	39.44° N, 75.988° E	23
2 伊犁 Yili	43.88° N, 81.305° E	20
3 那拉提 Nalati	43.45° N, 83.283° E	20
4 库尔勒 Korla	41.75° N, 86.128° E	17
5 奇台 Qitai	43.70° N, 89.604° E	23
6 巴里坤 Balikun	43.58° N, 93.008° E	20
内蒙古 Inner Mongolia
7 海拉尔 Hailar	48.90° N, 119.837° E	18
8 白音敖包 Baiyinaobao	43.53° N, 117.236° E	21
9 兴和 Xinghe	40.89° N, 113.885° E	21
北京 Beijing
10 东灵山 Dongling Mountain	39.96° N, 115.439° E	12
山西 Shanxi
11 偏关 Pianguan	39.44° N, 111.461° E	22
陕西 Shaanxi
12 鱼河 Yuhe	37.98° N, 109.853° E	23
13 南泥湾 Nanniwan	36.32° N, 109.651° E	20
14 西安 Xi’an	34.28° N, 108.958° E	27
甘肃 Gansu
15 朱岔 Zhucha	36.94° N, 102.589° E	21
16 兴隆山 Xinglong Mountain 湖北 Hubei	35.78° N, 104.048° E	20
17 武汉 Wuhan	30.55° N, 114.415° E	26
总计 Total		354

居群 Population	经纬度 Locality	采样数目 Sample size
新疆 Xinjiang
1 喀什 Kashi	39.44° N, 75.988° E	23
2 伊犁 Yili	43.88° N, 81.305° E	20
3 那拉提 Nalati	43.45° N, 83.283° E	20
4 库尔勒 Korla	41.75° N, 86.128° E	17
5 奇台 Qitai	43.70° N, 89.604° E	23
6 巴里坤 Balikun	43.58° N, 93.008° E	20
内蒙古 Inner Mongolia
7 海拉尔 Hailar	48.90° N, 119.837° E	18
8 白音敖包 Baiyinaobao	43.53° N, 117.236° E	21
9 兴和 Xinghe	40.89° N, 113.885° E	21
北京 Beijing
10 东灵山 Dongling Mountain	39.96° N, 115.439° E	12
山西 Shanxi
11 偏关 Pianguan	39.44° N, 111.461° E	22
陕西 Shaanxi
12 鱼河 Yuhe	37.98° N, 109.853° E	23
13 南泥湾 Nanniwan	36.32° N, 109.651° E	20
14 西安 Xi’an	34.28° N, 108.958° E	27
甘肃 Gansu
15 朱岔 Zhucha	36.94° N, 102.589° E	21
16 兴隆山 Xinglong Mountain 湖北 Hubei	35.78° N, 104.048° E	20
17 武汉 Wuhan	30.55° N, 114.415° E	26
总计 Total		354

位点 Locus	等位基因数 A	预期杂合度 H_E	观察杂合度 H_O	遗传分化系数 F_ST	基因流 N_m	遗传分化系数R_ST
MTIC189	10	0.256	0.017	0.555	0.201	0.478
MTIC432	5	0.177	0.034	0.643	0.139	0.58
MTIC339	4	0.039	0.000	0.058	4.038	-0.004
MTIC345	8	0.320	0.085	0.463	0.290	0.447
MTIC210	10	0.267	0.005	0.564	0.193	0.636
MTIC14	6	0.180	0.000	0.604	0.164	0.703
MTIC188	11	0.247	0.014	0.612	0.159	0.619
MAA660870	5	0.157	0.003	0.605	0.163	0.508
MtSSRNFAL05	7	0.266	0.017	0.649	0.135	0.528
平均 Mean	7.333	0.212	0.020	0.528	0.224	0.499

位点 Locus	等位基因数 A	预期杂合度 H_E	观察杂合度 H_O	遗传分化系数 F_ST	基因流 N_m	遗传分化系数R_ST
MTIC189	10	0.256	0.017	0.555	0.201	0.478
MTIC432	5	0.177	0.034	0.643	0.139	0.58
MTIC339	4	0.039	0.000	0.058	4.038	-0.004
MTIC345	8	0.320	0.085	0.463	0.290	0.447
MTIC210	10	0.267	0.005	0.564	0.193	0.636
MTIC14	6	0.180	0.000	0.604	0.164	0.703
MTIC188	11	0.247	0.014	0.612	0.159	0.619
MAA660870	5	0.157	0.003	0.605	0.163	0.508
MtSSRNFAL05	7	0.266	0.017	0.649	0.135	0.528
平均 Mean	7.333	0.212	0.020	0.528	0.224	0.499

居群 Population	平均等位基因数n_a	有效等位基因数n_e	观察杂合度 H_o	预期杂合度 H_E	近交系数 F	自交率 s	多态率 PPL (%)	私有基因数 Private alleles
1 喀什 Kashi	2.444	1.746	0.019	0.346	0.947	0.973	66.7	0
2 伊犁 Yili	3.556	1.717	0.056	0.342	0.845	0.916	100	5
3 那拉提 Nalati	2.667	1.868	0.028	0.388	0.932	0.965	88.9	1
4 库尔勒 Korla	2.222	1.779	0.007	0.348	0.982	0.991	77.8	1
5 奇台 Qitai	2.111	1.380	0.000	0.214	1.000	1.000	77.8	0
6 巴里坤 Balikun	1.667	1.196	0.034	0.118	0.725	0.841	33.3	0
7 海拉尔 Hailar	2.111	1.137	0.025	0.107	0.781	0.877	66.7	1
8 白音敖包 Baiyinaobao	1.778	1.196	0.011	0.145	0.93	0.964	66.7	0
9 兴和 Xinghe	1.889	1.223	0.011	0.153	0.931	0.964	77.8	0
10 东灵山 Dongling Mountain	2.111	1.467	0.009	0.270	0.968	0.984	77.8	0
11 偏关 Pianguan	2.000	1.183	0.035	0.137	0.752	0.858	88.9	0
12 鱼河 Yuhe	2.333	1.294	0.034	0.188	0.824	0.904	66.7	1
13 南泥湾 Nanniwan	1.667	1.246	0.000	0.152	1.000	1.000	55.6	1
14 西安 Xi’an	1.444	1.049	0.012	0.042	0.716	0.835	33.3	0
15 朱岔 Zhucha	3.556	1.448	0.042	0.252	0.840	0.913	77.8	8
16 兴隆山 Xinglongshan	2.333	1.576	0.000	0.302	1.000	1.000	66.7	0
17 武汉 Wuhan	2.333	1.122	0.009	0.104	0.921	0.959	100	3
平均 Mean	2.248	1.390	0.020	0.212	0.888	0.938	71.9	1