糜子EST-SSR分子标记的开发及种质资源遗传多样性分析

doi:10.11983/CBB19037

植物学报 ›› 2019, Vol. 54 ›› Issue (6): 723-732.DOI: 10.11983/CBB19037

糜子EST-SSR分子标记的开发及种质资源遗传多样性分析

何杰丽¹,石甜甜²,陈凌³,王海岗³,高志军⁴,杨美红¹,王瑞云^2,^3,^*(),乔治军^3,^*()

1 山西农业大学文理学院, 太谷 030801
2 山西农业大学农学院, 太谷 030801
3 山西省农业科学院农作物品种资源研究所/农业部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室, 太原 030031
4 鄂尔多斯市农牧业科学研究院, 鄂尔多斯 017200

收稿日期:2019-02-24 接受日期:2019-06-18 出版日期:2019-11-01 发布日期:2020-07-09
通讯作者: 王瑞云,乔治军
基金资助:
国家现代农业产业技术体系建设专项(No.CARS-06-13.5-A16);国家自然科学基金(No.31271791);山西省回国留学人员科研资助项目(No.2016-066);山西省重点研发计划(No.201803D221008-5)

The Genetic Diversity of Common Millet (Panicum miliaceum) Germplasm Resources Based on the EST-SSR Markers

Jieli He¹,Tiantian Shi²,Ling Chen³,Haigang Wang³,Zhijun Gao⁴,Meihong Yang¹,Ruiyun Wang^2,^3,^*(),Zhijun Qiao^3,^*()

1 College of Arts and Science, Shanxi Agricultural University, Taigu 030801, China
2 College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
3 Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan 030031, China
4 Erdos Institute of Agriculture and Animal Husbandry, Erdos 017200, China

Received:2019-02-24 Accepted:2019-06-18 Online:2019-11-01 Published:2020-07-09
Contact: Ruiyun Wang,Zhijun Qiao

摘要/Abstract

摘要：

基于前期高通量测序结果设计EST-SSR引物, 用于评估国内外不同生态区144份糜子(Panicum miliaceum)种质资源的遗传差异。结果表明, 200对引物中80对呈多态性, 开发效率为40%; 引物分辨率(Rp)为0.67-4.67 (平均值为2.00), 扩增产物大小为50-500 bp。144份材料在80个位点共检测到206个等位变异, 每个位点为2-3个; 多样性指数(I)为0.659 3 (RYW108)-1.087 2 (RYW124), 平均为0.859 9; 多态性信息含量(PIC)为0.222 9 (RYW98)-0.717 2 (RYW124), 平均为0.457 3。基于UPGMA将144份资源划分为3个群组, 其中2个群组主要为北方春糜子区材料, 另一个群组主要为黄土高原春夏糜子区材料。基于Structure (K=4)将材料划分为4个类群, 即2个代表北方资源基因库以及代表黄土高原和国外资源基因库各1个。基于主成分分析将材料聚为7个类群, 划分结果与材料的地理来源一致。

关键词: 糜子, 遗传多样性, 主成分分析, SSR标记

Abstract:

The EST-SSR molecular markers of common millet (Panicum miliaceum) were developed by high-throughput sequencing. Using these markers, we assessed the genetic diversity in a panel of 144 common millet accessions collected from different ecotopic regions in China and abroad. It was shown that 80 pairs of these markers were polymorphic, with the efficiency of approximately 40%. The resolution power (Rp) was 0.67-4.67 (mean 2.00) and the amplified product sizes ranged from 50 to 500 bp. Among the examined 144 accessions, 206 allelic variations were identified in 80 loci, with 2-3 alleles at each locus. The Shannon’s diversity index (I) ranged from 0.659 3 (RYW108) to 1.087 2 (RYW124) with an average of 0.859 9. The range of polymorphism information content (PIC) was 0.222 9 (RYW98) -0.717 2 (RYW124) with an average of 0.457 3. Based on UPGMA, these 144 accessions were classified into 3 groups, two of which belonged to the the Northern China spring-sowing ecotopes and one group was mainly from the Loess Plateau spring-summer-sowing ecotopes. Based on Structure (K=4), all the accessions were divided into four groups, of which two groups represented the gene pool originated from the Northern China, whereas the other two groups from the Loess Plateau and abroad accessions. Based on principal component analysis (PCA), the accessions were clustered into seven groups, consistent with their geographic origins.

Key words: Panicum miliaceum, genetic diversity, PCA, EST-SSR markers

何杰丽,石甜甜,陈凌,王海岗,高志军,杨美红,王瑞云,乔治军. 糜子EST-SSR分子标记的开发及种质资源遗传多样性分析. 植物学报, 2019, 54(6): 723-732.

Jieli He,Tiantian Shi,Ling Chen,Haigang Wang,Zhijun Gao,Meihong Yang,Ruiyun Wang,Zhijun Qiao. The Genetic Diversity of Common Millet (Panicum miliaceum) Germplasm Resources Based on the EST-SSR Markers. Chinese Bulletin of Botany, 2019, 54(6): 723-732.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB19037

https://www.chinbullbotany.com/CN/Y2019/V54/I6/723

图/表 11

参考文献 40

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Ecotope/abroad	Origin	Number of accession	Total
Northwest spring and summer-sowing ecotope (NWSS)	Xinjiang	4	4
Northern spring-sowing ecotope (NSP)	Qinghai	13	48
	Gansu	11
	Inner Mongolia	14
	Shanxi	10
Loess Plateau spring and summer-sowing ecotope (LPSS)	Shanxi	18	37
	Shaanxi	8
	Ningxia	11
Northeast spring-sowing ecotope (NES)	Heilongjiang	5	9
	Jilin	3
	Liaoning	1
Northern summer-sowing ecotope (NSU)	Hebei	9	13
	Shandong	2
	Anhui	1
	Henan	1
Southern autumn and winter-sowing ecotope (SAW)	Hainan	2	2
Abroad	Former Soviet Union	2	31
	Poland	2
	India	27
Total		144

Ecotope/abroad	Origin	Number of accession	Total
Northwest spring and summer-sowing ecotope (NWSS)	Xinjiang	4	4
Northern spring-sowing ecotope (NSP)	Qinghai	13	48
	Gansu	11
	Inner Mongolia	14
	Shanxi	10
Loess Plateau spring and summer-sowing ecotope (LPSS)	Shanxi	18	37
	Shaanxi	8
	Ningxia	11
Northeast spring-sowing ecotope (NES)	Heilongjiang	5	9
	Jilin	3
	Liaoning	1
Northern summer-sowing ecotope (NSU)	Hebei	9	13
	Shandong	2
	Anhui	1
	Henan	1
Southern autumn and winter-sowing ecotope (SAW)	Hainan	2	2
Abroad	Former Soviet Union	2	31
	Poland	2
	India	27
Total		144

Number	Unicode	Accession name	Origin
1	00000177	Hongmizi	Ningan, Heilongjiang
2	00000750	Baimizi	Shawan, Xinjiang
3	00006653	Jinshu	Hainan
4	00007238	Dahongmizi	Bameng, Inner Mongolia
5	00007478	Baigedami	Huangzhong, Qinghai
6	No unicode	Hongshuzi	Anyang, Henan

Number	Unicode	Accession name	Origin
1	00000177	Hongmizi	Ningan, Heilongjiang
2	00000750	Baimizi	Shawan, Xinjiang
3	00006653	Jinshu	Hainan
4	00007238	Dahongmizi	Bameng, Inner Mongolia
5	00007478	Baigedami	Huangzhong, Qinghai
6	No unicode	Hongshuzi	Anyang, Henan

Ecotope/ abroad	Accessions	Na	Ne	I	Ho	He	PIC
NWSS	4	2.3375±0.5017	2.1517±0.4194	0.7644±0.2178	0.8042±0.2688	0.5944±0.1193	0.3551
NSP	48	2.5750±0.4975	2.3106±0.3211	0.8604±0.1576	0.8228±0.1308	0.5655±0.0604	0.4536
LPSS	37	2.5750±0.4975	2.2803±0.3110	0.8506±0.1534	0.8384±0.1166	0.5615±0.0595	0.4203
NES	9	2.5125±0.5030	2.2435±0.3929	0.8289±0.1823	0.7937±0.1732	0.5737±0.0909	0.4212
NSU	13	2.5625±0.4992	2.2815±0.3527	0.8496±0.1632	0.7946±0.1608	0.5712±0.0667	0.4304
SAW	2	2.2375±0.5092	2.0608±0.4387	0.7347±0.2316	0.7812±0.3265	0.6813±0.2006	0.2156
Domestic	113	2.5750 ±0.4975	2.3122±0.3086	0.8628±0.1554	0.8200±0.1188	0.5625±0.0584	0.4651
Abroad	31	2.5750±0.4975	2.2464±0.2909	0.8387±0.1449	0.8540±0.1193	0.5571±0.0561	0.3896

糜子EST-SSR分子标记的开发及种质资源遗传多样性分析

The Genetic Diversity of Common Millet (Panicum miliaceum) Germplasm Resources Based on the EST-SSR Markers

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Population	NWSS	NSP	LPSS	NES	NSU	SAW	Abroad
NWSS		0.9560	0.9614	0.9487	0.9380	0.8694	0.9477
NSP	0.0449		0.9884	0.9678	0.9794	0.9110	0.9864
LPSS	0.0394	0.0117		0.9716	0.9830	0.9116	0.9865
NES	0.0527	0.0327	0.0288		0.9675	0.8974	0.9587
NSU	0.0640	0.0208	0.0171	0.0331		0.9023	0.9762
SAW	0.1400	0.0932	0.0926	0.1083	0.1029		0.9102
Abroad	0.0537	0.0137	0.0136	0.0422	0.0240	0.0941

Group	Accessions	Na	Ne	I	Ho	He	PIC
A	33	2.5750±0.4975	2.3226±0.3374	0.8654±0.1620	0.8055±0.1417	0.5696±0.0636	0.4716
B	15	2.5125±0.5030	2.2471±0.3383	0.8330±0.1627	0.8153±0.1530	0.5651±0.0686	0.3993
C	96	2.5750±0.4975	2.2922±0.2894	0.8571±0.1495	0.8363±0.1111	0.5599±0.0553	0.4380
C1	70	2.5750±0.4975	2.3136±0.3098	0.8635±0.1551	0.8291±0.1199	0.5643±0.0584	0.4531
C2	26	2.5625±0.4992	2.1912±0.2797	0.8163±0.1391	0.8555 ±0.1212	0.5477±0.0558	0.3420
C11	37	2.5750±0.4975	2.3014±0.3143	0.8589±0.1561	0.8332±0.1182	0.5664±0.0603	0.4382
C12	33	2.5750±0.4975	2.3028±0.3224	0.8583±0.1571	0.8255±0.1383	0.5654±0.0610	0.4348

Cluster		Accessions	Na	Ne	I	Ho	He	PIC
K=2	Red	68	2.5750±0.4975	2.2446±0.2626	0.8407±0.1403	0.8602±0.1056	0.5528±0.0520	0.3773
K=2	Green	76	2.5750±0.4975	2.3396±0.3329	0.8711±0.1620	0.7975±0.1315	0.5679±0.0619	0.5031
K=4	Red	47	2.5750± 0.4975	2.3496±0.3944	0.8745±0.1768	0.7439±0.1668	0.5785±0.0743	0.5296
	Green	31	2.5750± 0.4975	2.2844±0.3202	0.8516± 0.1549	0.8225±0.1399	0.5635±0.0607	0.4414
	Blue	19	2.5750±0.4975	2.2973±0.3199	0.8575±0.1568	0.8190±0.1311	0.5628±0.0608	0.4450
	Yellow	47	2.5750±0.4975	2.2238±0.2723	0.8312±0.1387	0.3634±0.2702	0.4984±0.1050	0.3543

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