利用荧光SSR分析中国糜子的遗传多样性和群体遗传结构

doi:10.3864/j.issn.0578-1752.2019.09.001

摘要/Abstract

摘要：

【目的】利用荧光SSR研究中国糜子的遗传多样性与群体遗传结构,为糜子品种改良、种质创新和资源利用提供依据。【方法】用不同地理来源且表型差异较大的6份糜子材料对SSR引物进行筛选,通过变性聚丙烯酰胺凝胶电泳获得条带清晰、稳定性好、多态性高的糜子SSR引物,对筛选出的引物5′末端进行6-FAM、HEX、ROX和TAMRA荧光标记,利用基因分析仪检测不同等位变异的扩增片段大小,并以此来分析131份糜子材料的遗传多样性和群体结构。【结果】从202对SSR引物中共筛选出22对扩增稳定、多态性好的SSR引物,能同时适用于传统变性PAGE胶电泳和荧光SSR标记-全自动分析检测技术。22对SSR引物共检测出128个主要等位变异,平均每个位点5.82个;基因多样性指数变化范围为0.3572—0.8132,平均0.6284;多态性信息含量为0.2934—0.8150,平均0.5874;Shannon多样性指数为0.5427—1.7681,平均1.2062。不同生态区糜子种质间遗传距离的变化范围为0.0764—0.7251,平均0.3121,遗传一致度的变化范围为0.4843—0.9265,平均0.7465。其中,北方春糜子区和黄土高原春夏糜子区的遗传距离最小,遗传一致度最高,亲缘关系较近。UPGMA聚类分析显示,北方春糜子区和黄土高原春夏糜子区的材料聚为一类,个体间聚类,东北春糜子区的育成品种和农家种聚类结果一致,黄土高原春夏糜子区的育成品种在多个组群中都有出现。通过绘制K与△K的关系图,K=4时,△K最大,据此将131份糜子材料划分为4个类群,类群Ⅰ代表北方春糜子区;类群Ⅱ主要来自东北春糜子区;类群Ⅲ主要是北方春糜子区,群组Ⅳ主要是黄土高原春夏糜子区。各群体中大部分品种亲缘关系单一,少数品种含有其他组群的遗传成分。基于遗传距离的聚类分析与群体遗传结构分析结果基本一致,表明糜子的遗传差异与地理来源相关。【结论】北方春糜子区和黄土高原春夏糜子区的遗传多样性比较丰富,东北春糜子区的育成品种主要以农家种为遗传背景选育而来,黄土高原春夏糜子区在育种过程中引种资源广泛,与其他生态区存在基因交流。

关键词: 糜子, SSR荧光标记, 遗传多样性, 群体结构

Abstract:

【Objective】Genetic diversity and population genetic structure of 131 broomcorn millet accessions in China were analyzed based on fluorescently labeled SSR markers for variety improvement and germplasm innovation as well as effective utilization of broomcorn millet germplasm.【Method】Six broomcorn millet accessions with phenotypical diversity from different geographical origins were used to select SSR markers with highly polymorphism by denaturing polyacrylamide gel electrophoresis. The polymorphic markers were labeled with four fluorescent dyes: 6-FAM, HEX, ROX and TAMRA at the 5' end of forward primers which used in subsequent analyses. The size of each allele locus was determined by DNA Analyzer to estimate the genetic diversity and genetic population structure of the tested accessions. 【Result】 Twenty-two polymorphic and stably amplifying markers were selected for both traditional denaturing PAGE electrophoresis detection and fluorescent SSR labeling-automatic analysis technology. A total of 128 alleles were detected with an average of 5.82 alleles per locus, the gene diversity index, polymorphism information content and Shannon's information index ranged from 0.3572 to 0.8132, 0.2934 to 0.8150 and 0.5427 to 1.7681, respectively, with an average of 0.6284, 0.5874 and 1.2062 respectively. Genetic distance and genetic identity of accessions from different ecotypes were 0.0764-0.7251 (average value is 0.3121) and 0.4843-0.9265 (average value is 0.7465), respectively, the smallest genetic distance was found between NSP ecotype and LPSS ecotype. UPGMA cluster analysis showed that NSP ecotype and LPSS ecotype were clustered into one group. The clustering result of the cultivars and landraces from NES ecotype was consistent, the cultivars from LPSS ecotype were divided into different groups. By plotting the relationship between K and ΔK, ΔK is the largest when K=4. Based on K and △K values, 131 broomcorn millet accessions were grouped four genotypes by the population genetic structure analysis. Group Ⅰ is composed of NSP ecotype. Group Ⅱ consist of NES ecotype. Most accessions of group Ⅲ are from NSP ecotype. Group Ⅳ mainly contain LPSS ecotype. Most of the accessions in same group have same genetic component while only a few accessions contained genetic component of other groups. The analysis result of population genetic structure was consistent with the UPGMA clustering, indicating that the genetic diversity is related to geographical region. 【Conclusion】 There have more abundant genetic diversity in NSP and LPSS ecotype than other regions. The cultivars of NES ecotype were bred mainly from the landraces. The cultivars of LPSS ecotype were introduced from a wide range of resources during the breeding process, harboring genetic exchanges with other ecological regions.

Key words: broomcorn millet, SSR fluorescently labeled markers, genetic diversity, population structure

寇淑君, 霍阿红, 付国庆, 纪军建, 王瑶, 左振兴, 刘敏轩, 陆平. 利用荧光SSR分析中国糜子的遗传多样性和群体遗传结构[J]. 中国农业科学, 2019, 52(9): 1475-1477.

KOU ShuJun, HUO AHong, FU GuoQing, JI JunJian, WANG Yao, ZUO ZhenXing, LIU MinXuan, LU Ping. Genetic Diversity and Population Structure of Broomcorn Millet in China Based on Fluorescently Labeled SSR[J]. Scientia Agricultura Sinica, 2019, 52(9): 1475-1477.

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位点 Locus	等位基因数目 Allele number	主要等位基因 Major allele		稀有基因数 Rare gene number	基因多样性指数 H	多态性信息含量 PIC	Shannon信息指数 I
位点 Locus	等位基因数目 Allele number	片段大小 Size (bp)	频率 Frequency	稀有基因数 Rare gene number	基因多样性指数 H	多态性信息含量 PIC	Shannon信息指数 I
BM552	7	240	0.4427	5	0.7403	0.7124	1.4924
BM637	5	167	0.3382	1	0.7373	0.6897	1.3527
BM787	5	290	0.6908	1	0.4874	0.4530	0.8807
BM2654	7	206	0.3015	1	0.7835	0.7525	1.6300
BM2715	6	227	0.3893	4	0.7324	0.6914	1.3745
BM2717	7	284	0.5916	5	0.6109	0.5825	1.2828
BM2729	4	122	0.6107	4	0.5593	0.5064	0.9212
BM2766	5	194	0.6450	1	0.5285	0.4817	1.0270
BM2792	5	132	0.4084	1	0.6626	0.5991	1.1651
BM6414	7	270	0.4618	5	0.7149	0.6814	1.3771
BM6573	2	118	0.7672	2	0.3572	0.2934	0.5427
BM6598	6	210	0.6450	1	0.5364	0.4964	1.0300
LMX503	5	226	0.6336	1	0.5489	0.5081	1.0867
LMX780	5	229	0.5076	1	0.6278	0.5659	1.1080
LMX836	8	224	0.4275	1	0.7562	0.7310	1.6617
LMX1553	6	192	0.7061	4	0.4788	0.4560	0.8776
LMX1959	5	266	0.4847	3	0.6584	0.6043	1.1549
LMX2019	8	250	0.3321	2	0.8132	0.7918	1.7681
LMX2068	8	289	0.7405	1	0.4411	0.4294	0.9994
LMX2281	5	248	0.6718	0	0.5140	0.4818	0.9819
LMX2382	8	195	0.2710	6	0.8350	0.8150	1.7779
LMX2734	4	210	0.4733	1	0.6826	0.6351	1.2678
合计Total	128			51
平均Average	5.8		0.5189	2.3	0.6284	0.5874	1.2062

生态区 Ecotype	类型 Type	资源数 Accessions	等位基因数 Allele number	基因多样性指数 H	多态性信息含量 PIC	Shannon信息指数 I
东北春糜子区 NES	育成品种 Cultivars	20	3.8636	0.5474	0.4953	0.9848
	农家种 Landraces	11	3.3636	0.5373	0.4901	0.9225
	材料数 Number	31	4.3182	0.5732	0.5291	1.0562
华北夏糜子区 NSU	育成品种 Cultivars	0
	农家种 Landraces	3	2.0455	0.3838	0.3197	0.4402
	材料数 Number	3	2.0455	0.3838	0.3197	0.4402
北方春糜子区 NSP	育成品种 Cultivars	32	4.4091	0.5521	0.5042	1.1074
	农家种 Landraces	26	4.5455	0.6221	0.5725	1.1114
	材料数 Number	58	5.0455	0.6083	0.5607	1.1283
黄土高原春夏糜子区 LPSS	育成品种 Cultivars	20	4.3636	0.5808	0.5337	1.0379
	农家种 Landraces	16	4.0000	0.5250	0.4993	0.9290
	材料数 Number	36	5.1364	0.6020	0.5576	1.1222
西北春夏糜子区 NWSS	育成品种 Cultivars	0
	农家种 Landraces	3	2.1818	0.4621	0.3811	0.5001
	材料数 Number	3	2.1818	0.4621	0.3811	0.5001

生态区 Ecotype	东北春糜子区 NES	北方春糜子区 NSP	华北夏糜子区 NSU	西北春夏糜子区 NWSS	黄土高原春夏糜子区 LPSS
东北春糜子区 NES	—	0.8548	0.6408	0.7078	0.8814
北方春糜子区 NSP	0.1569	—	0.5993	0.8552	0.9265
华北夏糜子区 NSU	0.4451	0.5120	—	0.4843	0.6463
西北春夏糜子区 NWSS	0.3456	0.1564	0.7251	—	0.8684
黄土高原春夏糜子区 LPSS	0.1263	0.0764	0.4364	0.1411	—

省份 Province	红色 Red	绿色 Green	蓝色 Blue	黄色 Yellow
山西省Shanxi	3	3	15	6
甘肃省Gansu	8	2		2
内蒙古自治区Inner Mongolia	7		9	1
青海省Qinghai	7		1
宁夏回族自治区Ningxia	6	1	4	4
黑龙江省Heilongjiang	3	10	2	1
陕西省Shaanxi	1	1	2	5
辽宁省 Liaoning		1	2	1
吉林省 Jilin		3	1	6
河北省 Hebei			6	3
新疆维吾尔自治区 Xinjiang			1	2
山东省 Shandong				1
合计 Total	35	21	43	32