苦荞全基因组SSR位点挖掘及遗传多样性分析

doi:10.13304/j.nykjdb.2021.0521

中国农业科技导报 ›› 2022, Vol. 24 ›› Issue (4): 38-51.DOI: 10.13304/j.nykjdb.2021.0521

苦荞全基因组SSR位点挖掘及遗传多样性分析

左茜茜¹^,²(), 宋英杰¹^,², 马心妍², 杨云卉¹^,², 王轶菲¹^,², 郭泽光², 朱雄智², 刘越¹^,²()

^1.中央民族大学民族地区生态环境国家民委重点实验室, 北京 100081
^2.中央民族大学生命与环境科学学院, 北京 100081

收稿日期:2021-06-26 接受日期:2021-11-30 出版日期:2022-04-15 发布日期:2022-04-19
通讯作者: 刘越
作者简介:左茜茜 E-mail： 609517510@qq.com；
基金资助:
生态环境部生物多样性调查评估项目(2019HJ2096001006);国家自然科学基金项目(81274185);国家民委中青年英才项目(2016-03-01);中央民族大学一流大学一流学科建设项目

Mining SSR Loci and Analysis the Genetic Diversity of Tartary Buckwheat Based on the Whole Genome Sequence

Xixi ZUO¹^,²(), Yingjie SONG¹^,², Xinyan MA², Yunhui YANG¹^,², Yifei WANG¹^,², Zeguang GUO², Xiongzhi ZHU², Yue LIU¹^,²()

^1.Key Laboratory of Ecology and Environment in Minority Areas of National Ethnic Affairs Commission，Minzu University of China，Beijing 100081，China
^2.College of Life and Environmental Sciences，Minzu University of China，Beijing 100081

Received:2021-06-26 Accepted:2021-11-30 Online:2022-04-15 Published:2022-04-19
Contact: Yue LIU

摘要/Abstract

摘要：

苦荞是一种重要的杂粮作物。利用GenBank数据库中苦荞的8条染色体基因组序列进行SSR标记挖掘，并基于Primer 3.0设计SSR引物，筛选多态性高的引物进行遗传多样性评价。共检测到51 485个SSR 位点，平均发生频率为114.07 Mb^-1，二核苷酸重复型最多（78.20%），其次为三核苷酸重复型（17.76%）。苦荞SSR中包含361种类型重复基元，具有碱基偏好性，优势基元为AT/TA （69.60%）、AAT/TTA （2.49 %）和AGA/TCT（2.10 %）。序列长度变化范围为12~228 bp，长度12~20 bp的占比57.93 %，长度大于20 bp 的占比42.07 %。SSR位点分布在每条染色体上的数量和种类特征较为一致，不同染色体能检出的SSR种类具有特异性。根据不同类型SSR位点设计并合成156对引物，筛选出17对多态性较高的引物用于遗传多样性分析，发现42份苦荞地方品种资源具有较高的多样性，美姑县的黑苦荞遗传多样性最高，布拖县的样品多数聚为同一分支，多样性显著低于美姑县和昭觉县的品种，西南种质库保存的野生苦荞与其他栽培品种明显分离。通过大量SSR的挖掘特别是染色体特异性SSR位点的挖掘，对苦荞种质资源的鉴定分析以及苦荞分子标记辅助育种有重要意义；遗传多样性检测也显示了SSR分子标记的可用性，以及黑苦荞的遗传多样性水平，对苦荞遗传多样性保护研究提供了新的途径。

关键词: 苦荞, 染色体, 简单重复序列（SSR）, 遗传多样性

Abstract:

Tartary buckwheat （Fagopyrum tataricum） is an important minor crop. In this study， molecular markers of the simple sequence repeat （SSR） were mined from 8 chromosomes sequence of tartary buckwheat in GenBank database. SSR primers were designed by primer 3.0 software and those with high polymorphism were employed to evaluate the genetic diversity. A total of 51 485 SSR loci were screened with average frequency of 114.07 Mb^-1. Among these SSR motifs， dinucleotide repeat was the main type accounting for 78.20%， followed by trinucleotide repeat （17.76%）. There were 361 types of repeat motifs， while AT/AT （69.60 %）， AAT/TTA （2.49%） and AGA/TCT （2.10%） were the main repeat types. The SSRs length ranged from 12 to 228 bp， and the ratio of SSRs with length ranging from 12 to 20 bp was 57.93%， the ratio with length above 20 bp was 42.07%. It was found that the SSR types detected were specific to the chromosomes. Based on the type of SSR loci， 156 pairs of primers were designed and 17 pairs of primers were screened with high polymorphism to analyze the genetic diversity of the 42 local varieties of tartary buckwheat. The diversity of black tartary buckwheat samples in Meigu County was the highest. The diversity of samples in Butuo County was significantly lower than that in the other two counties. It was of great significance to identify and analyze tartary buckwheat germplasm resources and molecular marker-assisted breeding through a large number of SSR mining， especially the chromosome specific SSR loci mining. In this study， a large number of SSRs were mined， especially the chromosomal specific SSR sites were mined， which was of great significance for the identification and analysis of tartary buckwheat germplasm resources and the molecular marker-assisted breeding of tartary buckwheat. Genetic diversity analysis also revealed the availability of SSR markers and the level of genetic diversity of tartary buckwheat， which provided a new approach for the study of the conservation of genetic diversity of tartary buckwheat.

Key words: Fagopyrum tataricum, chromosome, simple repeat sequence （SSR）, genetic diversity

中图分类号:

S517

左茜茜, 宋英杰, 马心妍, 杨云卉, 王轶菲, 郭泽光, 朱雄智, 刘越. 苦荞全基因组SSR位点挖掘及遗传多样性分析[J]. 中国农业科技导报, 2022, 24(4): 38-51.

Xixi ZUO, Yingjie SONG, Xinyan MA, Yunhui YANG, Yifei WANG, Zeguang GUO, Xiongzhi ZHU, Yue LIU. Mining SSR Loci and Analysis the Genetic Diversity of Tartary Buckwheat Based on the Whole Genome Sequence[J]. Journal of Agricultural Science and Technology, 2022, 24(4): 38-51.

图/表 12

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采集地点 Sampling site	样品编号 Sample ID	来源 Source	数量 Amount
四川攀枝花 Panzhihua， Sichuan	XNZY-1	中国西南野生生物种质资源库 Germplasm Bank of Wild Species in Southwest China	3
西藏 Tibet	XNZY-2
河北 Hebei	XNZY-5
贵州 Guizhou	GZSF-1、GZSF-3、GZSF-4	贵州省荞麦工程技术研究中心 Guizhou Province Buckwheat Engineering Technology Research Center	4
湖南 Hunan	GZSF-2		4
山西 Shanxi	DTZX-1	云南省滇台特色农业产业化工程研究中心 Yunnan-Taiwan Engineering Research Center for Characteristic Agriculture Industrialization of Yunnan Province	3
云南 Yunnan	DTZX-2
重庆 Chongqing	DTZX-5
四川省昭觉县 Zhaojue， Sichuan	ZJJZ-1、ZJJZ-2、ZJLG、ZJSJ、ZJSY-1、ZJSY-2、ZJWQ-1、ZJWQ-2、ZJWQ-3、ZJWZ、ZJXY、EN-G-TU、CHU-G	本课题组采集 Sampled by this lab	13
四川省美姑县 Meigu， Sichuan	MG-48、MGLL、MGNY-1、MGNY-2、MGTZ、MGYD-1、MGYD-2、MGYS、EN-G-JIE、EN-G-WAZI	本课题组采集 Sampled by this lab	10
四川省布拖县 Butuo， Sichuan	BT-52、BTAE、BTDM、BTLC、BTLG、BTLJ、BTLK-1、BTLK-2、BTZE	本课题组采集 Sampled by this lab	9
总计Total			42

采集地点 Sampling site	样品编号 Sample ID	来源 Source	数量 Amount
四川攀枝花 Panzhihua， Sichuan	XNZY-1	中国西南野生生物种质资源库 Germplasm Bank of Wild Species in Southwest China	3
西藏 Tibet	XNZY-2
河北 Hebei	XNZY-5
贵州 Guizhou	GZSF-1、GZSF-3、GZSF-4	贵州省荞麦工程技术研究中心 Guizhou Province Buckwheat Engineering Technology Research Center	4
湖南 Hunan	GZSF-2		4
山西 Shanxi	DTZX-1	云南省滇台特色农业产业化工程研究中心 Yunnan-Taiwan Engineering Research Center for Characteristic Agriculture Industrialization of Yunnan Province	3
云南 Yunnan	DTZX-2
重庆 Chongqing	DTZX-5
四川省昭觉县 Zhaojue， Sichuan	ZJJZ-1、ZJJZ-2、ZJLG、ZJSJ、ZJSY-1、ZJSY-2、ZJWQ-1、ZJWQ-2、ZJWQ-3、ZJWZ、ZJXY、EN-G-TU、CHU-G	本课题组采集 Sampled by this lab	13
四川省美姑县 Meigu， Sichuan	MG-48、MGLL、MGNY-1、MGNY-2、MGTZ、MGYD-1、MGYD-2、MGYS、EN-G-JIE、EN-G-WAZI	本课题组采集 Sampled by this lab	10
四川省布拖县 Butuo， Sichuan	BT-52、BTAE、BTDM、BTLC、BTLG、BTLJ、BTLK-1、BTLK-2、BTZE	本课题组采集 Sampled by this lab	9
总计Total			42

重复基元 Repeat motif	Chr.1	Chr.2	Chr.3	Chr.4	Chr.5	Chr.6	Chr.7	Chr.8	总计 Total	比例 Percentage/%
AT/TA	5 194	4 853	4 566	4 432	4 260	4 606	4 019	3 901	35 831	69.6
CT/GA	280	310	254	347	299	278	225	216	2 209	4.29
AG/TC	184	152	158	178	141	133	122	147	1 215	2.36
AC/TG	137	124	99	119	83	111	92	105	870	1.69
CA/GT	95	94	78	114	83	66	61	81	672	1.31
AAT/TTA	180	171	183	144	160	144	155	144	1 281	2.49
AGA/TCT	169	183	104	146	112	133	118	116	1 081	2.10
ATA/TAT	174	129	144	104	140	122	104	135	1 052	2.04
AAG/TTC	139	120	104	120	100	108	85	85	861	1.67
CTT/GAA	129	99	89	103	101	73	88	100	782	1.52
ATT/TAA	142	93	103	82	105	86	91	76	778	1.51
CAT/GTA	55	48	24	55	41	38	28	41	330	0.64
CAA/GTT	54	33	36	34	36	31	27	30	281	0.55
ACT/TGA	35	39	31	25	34	25	30	36	255	0.50
AAAT/TTTA	60	45	0	35	42	39	48	40	309	0.60
AATA/TTAT	27	23	35	33	20	19	26	20	203	0.39
AAGA/TTCT	26	17	17	23	20	30	17	13	163	0.32
ATAA/TATT	29	19	24	16	19	0	17	25	149	0.29
ATTT/TAAA	18	9	22	12	16	7	21	20	125	0.24
AAAAT/TTTTA	3	9	2	0	3	5	5	3	30	0.06
AGAAG/TCTTC	0	7	3	3	0	10	6	4	27	0.05
AAATA/TTTAT	7	0	0	0	0	0	3	3	13	0.03
AAAATA/TTTTAT	0	0	0	0	0	2	0	0	2	≈0.00
TCTACC	1	0	1	0	1	0	1	0	4	≈0.00
GTTCAG	1	1	0	1	1	0	0	0	4	≈0.00
总计Total	7 139	6 578	6 077	6 126	5 817	6 066	5 389	5 341	48 527	—

重复基元 Repeat motif	Chr.1	Chr.2	Chr.3	Chr.4	Chr.5	Chr.6	Chr.7	Chr.8	总计 Total	比例 Percentage/%
AT/TA	5 194	4 853	4 566	4 432	4 260	4 606	4 019	3 901	35 831	69.6
CT/GA	280	310	254	347	299	278	225	216	2 209	4.29
AG/TC	184	152	158	178	141	133	122	147	1 215	2.36
AC/TG	137	124	99	119	83	111	92	105	870	1.69
CA/GT	95	94	78	114	83	66	61	81	672	1.31
AAT/TTA	180	171	183	144	160	144	155	144	1 281	2.49
AGA/TCT	169	183	104	146	112	133	118	116	1 081	2.10
ATA/TAT	174	129	144	104	140	122	104	135	1 052	2.04
AAG/TTC	139	120	104	120	100	108	85	85	861	1.67
CTT/GAA	129	99	89	103	101	73	88	100	782	1.52
ATT/TAA	142	93	103	82	105	86	91	76	778	1.51
CAT/GTA	55	48	24	55	41	38	28	41	330	0.64
CAA/GTT	54	33	36	34	36	31	27	30	281	0.55
ACT/TGA	35	39	31	25	34	25	30	36	255	0.50
AAAT/TTTA	60	45	0	35	42	39	48	40	309	0.60
AATA/TTAT	27	23	35	33	20	19	26	20	203	0.39
AAGA/TTCT	26	17	17	23	20	30	17	13	163	0.32
ATAA/TATT	29	19	24	16	19	0	17	25	149	0.29
ATTT/TAAA	18	9	22	12	16	7	21	20	125	0.24
AAAAT/TTTTA	3	9	2	0	3	5	5	3	30	0.06
AGAAG/TCTTC	0	7	3	3	0	10	6	4	27	0.05
AAATA/TTTAT	7	0	0	0	0	0	3	3	13	0.03
AAAATA/TTTTAT	0	0	0	0	0	2	0	0	2	≈0.00
TCTACC	1	0	1	0	1	0	1	0	4	≈0.00
GTTCAG	1	1	0	1	1	0	0	0	4	≈0.00
总计Total	7 139	6 578	6 077	6 126	5 817	6 066	5 389	5 341	48 527	—

SSR引物类型 SSR primer type	总引物数量 Total primers number	有效引物数量 Effective primers number	多态性引物数量 Polymorphic primers number	基序长度 Sequence length /bp
复合型 Compound	3	3	2	55、66
二核苷酸 Dinucleotide	119	86	11	14~66
三核苷酸 Trinucleotide	26	23	4	15、27、48、63
四核苷酸Tetranucleotide	7	7	—	—
五核苷酸Pentanucleotide	1	1	—	—
总计Total	156	120	—	—

苦荞全基因组SSR位点挖掘及遗传多样性分析

Mining SSR Loci and Analysis the Genetic Diversity of Tartary Buckwheat Based on the Whole Genome Sequence

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重复类型 Repeat type		Chr.1	Chr.2	Chr.3	Chr.4	Chr.5	Chr.6	Chr.7	Chr.8
四核苷酸重复 Tetranucleotide	基元类型 Motif type	31	28	28	34	26	31	29	26
四核苷酸重复 Tetranucleotide	特异类型 Specific motif type	4	3	4	7	6	4	5	2
五核苷酸重复 Pentanucleotide	基元类型 Motif type	38	38	34	28	33	30	28	29
五核苷酸重复 Pentanucleotide	特异类型 Specific motif type	9	14	13	9	8	9	9	7
六核苷酸重复 Hexanucleotide	基元类型 Motif type	23	24	18	18	14	19	18	10
六核苷酸重复 Hexanucleotide	特异类型 Specific motif type	17	17	11	14	9	13	14	9

引物Primer	序列Sequence（5’-3’）	Na	Ne	I	Ho	He	PIC
P1	F：TGATTATATTCAATTGACCGATCTT R：CTGTGATTGTTTTCGTCAGAGG	9	3.773	1.684	0.905	0.095	0.708
P2	F：TTCTTGGAATGCACCAATGA R：GCAGTTTTGGGGCAACTTTA	3	1.243	0.397	0.976	0.024	0.183
P5	F：TTTGCATTGGGATCTCCTCT R：CCTCCTGCATTTACCCAAAA	6	3.500	1.382	0.048	0.952	0.664
P24	F：GCCAGCTTGTCCGTGTTTAC R：CCAGACCAGACCCACTTGTT	8	1.823	1.056	1.000	0.000	0.434
P40	F：GGCAACCAATCCCTCTACAA R：CCATTCTCAAGCCACCAAAT	9	4.698	1.772	0.952	0.048	0.759
P41	F：GCCTTCTTCACGTGTCCTGT R：GCCCAGCCCTAATATTCGAT	11	4.813	1.939	0.976	0.024	0.774
P72	F：TTTGGAAGTTGGTTCGAAGG R：TCAGCATTAAGGTCAGCACG	5	1.377	0.627	1.000	0.000	0.264
P79	F：TTTTTATCAGAGGCGCACAA R：AGTTGGCAGGGATTTTCCTT	6	2.365	1.066	0.810	0.191	0.502
P82	F：GTCGCGGAGGTTATCCACTA R：TGGACCACAGTCACAGGCTA	6	2.852	1.261	0.929	0.071	0.587
P89	F：GCGCGATTTACTCCTTCATA R：TCCCCTCAATCTTGTATTTTCA	2	1.214	0.320	0.951	0.049	0.161
P90	F：CGATCCTTCTCGCGTTTTAC R：ATGACGTATCTCCCGACGTG	14	4.246	2.004	0.905	0.095	0.751
P91	F：ATTCCATTGTCGAGCAAACC R：GTGCAGTCCCGCGTATTTAT	13	5.188	2.101	0.905	0.095	0.794
P102	F：CTGGAAAGAAGCAAAGGCTG R：ATGCAAACATTGCCCACATA	3	1.519	0.635	0.976	0.024	0.313
P115	F：TCATGAGGCAGATGAAGGTG R：CGACAACACAAATCAACGAAA	6	2.495	1.211	0.881	0.119	0.557
P126	F：GCAAAATCTTTTAACAACATTAAGGA R：TTTGCTAGAAAACATTGCACTTTC	4	1.709	0.824	0.929	0.071	0.389
P128	F：CGGTCATCATCGAAGTCAAA R：CTGGACCAACACTCCTGGAT	5	1.279	0.495	0.952	0.048	0.209
P132	F：CTTGCTTAATCATGGCGGAT R：CAGCCCTCCATTCTTCTCTG	4	2.114	0.859	0.881	0.119	0.431
总计Total		114	—	—	—	—	—
平均Average		6.706	2.718	1.155	0.881	0.119	0.499

群体 Group	Na	Ne	I	Ho	He	Nei
B群体（布拖县） Group B （Butuo County）	2.647	1.563	0.520	0.830	0.170	0.278
C群体（CHU-GE） Group C（CHU-GE）	1.063	1.063	0.043	0.938	0.063	0.031
D群体（云南滇台中心） Group D （Yunnan-Taiwan Engineering Research Center）	2.000	1.892	0.580	0.941	0.059	0.376
E群体（EN-G系列黄苦荞） Group E （EN-G series yellow Tartary buckwheat）	2.235	1.992	0.642	0.824	0.177	0.395
G群体（贵州师范大学） Group G （Guizhou Normal University）	2.294	2.151	0.664	0.927	0.074	0.401
M群体（美姑县） Group M （Meigu County）	3.353	2.406	0.899	0.890	0.110	0.484
X群体（中国西南野生生物种质资源库） Group X （Germplasm Bank of Wild Species in Southwest China）	2.529	2.308	0.803	0.824	0.177	0.497
Z群体（昭觉县） Group Z （Zhaojue County）	3.471	2.272	0.887	0.909	0.091	0.475
平均值Average	2.449	1.956	0.630	0.885	0.115	0.367

群体 Group	C	D	E	G	M	X	Z
B	0.340 3	0.807 2	0.746 8	0.790 4	0.908 2	0.386 7	0.791 5
C		0.474 3	0.528 2	0.412 8	0.513	0.303 9	0.576 5
D			0.816 6	0.787 5	0.862 9	0.454 8	0.832 2
E				0.726 8	0.853 7	0.453 2	0.864 6
G					0.828 9	0.546 7	0.783 5
M						0.462 2	0.897 8
X							0.487 3

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