吉林省玉米种质资源SSR和SNP分子身份证的构建及应用

doi:10.3864/j.issn.0578-1752.2024.02.002

中国农业科学 ›› 2024, Vol. 57 ›› Issue (2): 236-249.doi: 10.3864/j.issn.0578-1752.2024.02.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

吉林省玉米种质资源SSR和SNP分子身份证的构建及应用

张茗起¹^,³(), 王蕊¹(), 张春宵², 孙擘¹^,³, 任洁¹, 李淑芳⁴, 王璐¹, 朱少喜¹, 张江斌¹, 施昕晨¹, 王海杰¹, 张云龙¹, 田红丽¹, 赵怡锟¹, 匡猛³, 王元东¹, 易红梅¹, 李晓辉²(), 王凤格¹()

¹ 北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室（部省共建）/玉米DNA指纹及分子育种北京市重点实验室，北京 100097
² 吉林省农业科学院玉米研究所，吉林公主岭 136100
³ 中国农业科学院棉花研究所/棉花生物学国家重点实验室，河南安阳 455000
⁴ 吉林省农业科学院作物资源研究所，吉林公主岭 136100

收稿日期:2023-06-05 接受日期:2023-08-01 出版日期:2024-01-16 发布日期:2024-01-19
通信作者:
王凤格，E-mail：gege0106@163.com。
李晓辉，E-mail：lixiaohui2002lix@163.com
联系方式: 张茗起，E-mail：mrzhangmq@foxmail.com。王蕊，E-mail：skywangr@126.com。张茗起和王蕊为同等贡献作者。
基金资助:
国家重点研发计划(2021YFD1201005); 北京市农林科学院科技创新能力建设专项(KJCX20230303); 北京市农林科学院科研创新平台建设专项(PT2023-34)

The Construction and Application of SSR and SNP Molecular ID for Maize Germplasm Resources of Jilin Province

ZHANG MingQi¹^,³(), WANG Rui¹(), ZHANG ChunXiao², SUN Bo¹^,³, REN Jie¹, LI ShuFang⁴, WANG Lu¹, ZHU ShaoXi¹, ZHANG JiangBin¹, SHI XinChen¹, WANG HaiJie¹, ZHANG YunLong¹, TIAN HongLi¹, ZHAO YiKun¹, KUANG Meng³, WANG YuanDong¹, YI HongMei¹, LI XiaoHui²(), WANG FengGe¹()

¹ Maize Research Institute, Beijing Academy of Agricultural and Forestry Sciences/Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing 100097
² Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin
³ Institute of Cotton Research of Chunese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang 455000, Henan
⁴ Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin

Received:2023-06-05 Accepted:2023-08-01 Published:2024-01-16 Online:2024-01-19

摘要/Abstract

摘要：

【目的】农作物种质资源具有重要的战略地位。吉林省玉米种质资源库主要存储具有北方春玉米区特色的种质资源。鉴于在传统农作物种质资源管理过程中难以获取真实身份信息的现状，利用分子标记技术构建种质资源分子身份证可以有效鉴定种质资源真实身份，强化种质资源的分类管理。通过深度发掘吉林省玉米种质资源库的优异资源，推动共享利用。【方法】以吉林省玉米种质资源库中的2 918份玉米种质资源为研究对象，采用玉米品种鉴定检测标准中推荐的40对SSR标记，以及61 214个SNP标记来构建其分子身份证。根据获得的分子身份证信息将种质资源划分为核心、同近源、异质和群体等类进行管理，并进一步针对核心种质进行遗传多样性分析。【结果】为2 918份种质资源构建了SSR分子身份证，为除异质性种质外的2 502份种质资源构建了SNP分子身份证。分别制定了玉米种质资源SSR和SNP分子身份证的建设规范。其中，SSR分子身份证由40个SSR位点指纹转化为三位数字和一位字母的编码组合构成，并以二维码形式存储；SNP分子身份证由61 214个SNP位点指纹转化为可视化的条形码。根据样品纯合度和指纹特异性等特征，将样品划分为1 561份核心类、705份同近源类、416份异质类及236份群体类种质资源。遗传多样性分析表明，以旅大红骨群、黄改群为代表的国内种质资源是该库的主要种质资源，占全部核心种质资源的64.38%。【结论】提出了玉米种质资源分子身份证构建流程，为吉林省玉米种质资源库2 918份种质资源构建了全部的SSR分子身份证和2 502份SNP分子身份证；建立了核心、同近源、异质、群体四类种质资源筛选方案，实现了种质资源的分类管理。

关键词: 玉米, 种质资源, 吉林, SSR, SNP, 分子身份证

Abstract:

【Objective】 Crop germplasm resources hold a crucial strategic position. The Maize Germplasm Resources Bank in Jilin Province safeguards a collection of germplasm resources distinctively representative of the Northern Spring Maize Region. Traditional germplasm resource management faces challenges in ascertaining accurate identity information. To address this issue, molecular marker technology has been employed to establish a process for the construction and classification of molecular IDs for germplasm resources, thereby enabling precise identification and bolstering categorical management. Thorough exploration of the exceptional resources within Jilin Province's Maize Germplasm Resources Bank is intended to advance the shared utilization of these valuable germplasm resources. 【Method】 A total of 2 918 maize germplasm resources were utilized from the Jilin Provincial Maize Germplasm Resources Bank as subjects of the study, the molecular IDs were constructed by using 40 pairs of SSR markers and 61 214 SNP markers recommended in maize variety identification standards. Based on the molecular ID information, the germplasm resources were categorized into core, closely related, heterogeneous, and population groups for management purposes. Furthermore, the core germplasms were analyzed on genetic diversity. 【Result】 In this investigation, the SSR molecular IDs were constructed for 2 918 maize germplasm resources, while the SNP molecular IDs were constructed for 2 502 maize germplasm resources, excluding heterogeneous germplasm. The standards for the construction of SSR and SNP molecular IDs were established for maize germplasm resources. The SSR molecular ID is composed of a combination of three-digit numbers and one-letter code converted from 40 SSR loci fingerprints, stored in the form of a QR code. The SNP molecular ID converts the fingerprints of 61 214 SNP loci into visual barcodes. Based on the features of sample homozygosity and fingerprint specificity, the samples were categorized into 1 561 cores, 705 closely related, 416 heterogeneous, and 236 population types of germplasm resources. Genetic diversity analysis indicates that domestic germplasm resources, represented by Lüdahonggu and Huanggai groups, constituting the main germplasm resources in the Jilin Provincial Maize Germplasm Resources Bank, accounting for 64.38% of all core germplasm resources. 【Conclusion】 This research outlines a methodology for constructing molecular IDs for maize germplasm resources. The SSR molecular IDs were constructed for 2 918 accessions stored in the Jilin Provincial Maize Germplasm Resources Bank and the SNP molecular IDs were constructed for 2 502 among them. The germplasm resources were categorized into core, closely related, heterogeneous, and population types to achieve the classification management.

Key words: maize, germplasm resource, Jilin, SSR, SNP, molecular ID

张茗起, 王蕊, 张春宵, 孙擘, 任洁, 李淑芳, 王璐, 朱少喜, 张江斌, 施昕晨, 王海杰, 张云龙, 田红丽, 赵怡锟, 匡猛, 王元东, 易红梅, 李晓辉, 王凤格. 吉林省玉米种质资源SSR和SNP分子身份证的构建及应用[J]. 中国农业科学, 2024, 57(2): 236-249.

ZHANG MingQi, WANG Rui, ZHANG ChunXiao, SUN Bo, REN Jie, LI ShuFang, WANG Lu, ZHU ShaoXi, ZHANG JiangBin, SHI XinChen, WANG HaiJie, ZHANG YunLong, TIAN HongLi, ZHAO YiKun, KUANG Meng, WANG YuanDong, YI HongMei, LI XiaoHui, WANG FengGe. The Construction and Application of SSR and SNP Molecular ID for Maize Germplasm Resources of Jilin Province[J]. Scientia Agricultura Sinica, 2024, 57(2): 236-249.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2024.02.002

https://www.chinaagrisci.com/CN/Y2024/V57/I2/236

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玉米种质资源分类管理信息表（样表）"

序号 No.	样品条码号 Sample barcode number	样品名称 Sample name	SSR分子身份证 Molecular ID of SSR markers	SNP分子身份证 Molecular ID of SNP markers	种质库分类 Bank classification	纯合度 Homozygosity (%)	相同位点占比 Proportion of identical loci (%)	表型数据 Phenotypic data	入库来源 Collection source	首次扩繁号 The first propagation number	存储重量Storage weight (g)
1	NZ00556	大红袍137 Dahongpao137	有Yes	有Yes	核心Core	95.00	无No	有Yes	02725Y14G0195	12W1429	58
2	NZ01291	遗501 Yi501	有Yes	有Yes	核心Core	95.00	无No	有Yes	03458Y14G0928	13J1166	113
3	NZ01447	郑58（山东） Zheng58(Shandong)	有Yes	有Yes	核心Core	97.50	无No	有Yes	03621Y14G1091	13J1333	178
4	NZ00693	系14 Xi14	有Yes	有Yes	核心Core	90.00	无No	有Yes	02859Y14G0329	12W1568	30
5	NZ02361	43朝系43Chaoxi	有Yes	有Yes	核心Core	95.00	无No	有Yes	04550Y14G2020	13J1827	118
6	NZ02364	大器Daqi	有Yes	有Yes	核心Core	90.00	无No	有Yes	04555Y14G2025	100168	14
7	NZ02400	inbyed45	有Yes	有Yes	核心Core	90.00	无No	有Yes	04595Y14G2065	100217	144
8	NZ02519	大白棒Dabaibang	有Yes	有Yes	核心Core	92.50	无No	有Yes	04719Y14G2189	100370	55
9	NZ02526	秧Yang	有Yes	有Yes	核心Core	95.00	无No	有Yes	04727Y14G2197	100378	30
10	NZ00132	Mo17	有Yes	有Yes	核心Core	92.50	无No	有Yes	WG208NZ00132	18G3830	201
11	NZ01465	郑58（河南） Zheng58(Henan)	有Yes	有Yes	其它Others	100.00	无No	无No	03639Y14G1109	13J1351	106
12	NZ01555	K4H6003	有Yes	有Yes	群体Population	90.00	92.34	无No	03726Y14G1196	13W1201	101
13	NZ01556	K4H6004	有Yes	有Yes	群体Population	92.50	96.15	无No	03727Y14G1197	13W1202	197
14	NZ01557	K4H6005	有Yes	有Yes	群体Population	92.50	94.92	无No	03728Y14G1198	13W1203	179
15	NZ01559	K4H6002	有Yes	有Yes	群体Population	92.50	94.92	无No	03730Y14G1200	13W1205	139
16	NZ00942	MO17“c"cms	有Yes	有Yes	同近源 Closely related	92.50	98.90	有Yes	03107Y14G0577	13W0960	205
17	NZ00960	FRMO17 O2	有Yes	有Yes	同近源 Closely related	92.50	98.90	有Yes	03126Y14G0596	13W0980	102
18	NZ01377	系14 Xi14	有Yes	有Yes	同近源 Closely related	90.00	93.67	有Yes	03549Y14G1019	13J1260	130
19	NZ02308	FRM017Rfc	有Yes	有Yes	同近源 Closely related	90.00	98.70	有Yes	04496Y14G1966	13W1534	108
20	NZ02309	FRM017rhm	有Yes	有Yes	同近源 Closely related	92.50	98.50	有Yes	04497Y14G1967	13W1535	124
21	NZ02809	75-217	有Yes	有Yes	同近源 Closely related	90.00	99.98	有Yes	05027Y14G2497-2粉轴 05027Y14G2497-2 Pink cob	13J2310	78
22	NZ02810	75-217	有Yes	有Yes	同近源 Closely related	90.00	99.98	有Yes	05027Y14G2497-3圆粒 05027Y14G2497-3 Round grains	13J2310	100
23	NZ01899	K4H6001	有Yes	无No	异质性Heterogeneous	87.50	无No	无No	04055Y14G1525	13W1533	144
24	NZ00544	自16 Zi16	有Yes	无No	异质性Heterogeneous	85.00	无No	无No	02712Y14G0182	12W1416	99
25	NZ00570	大黄46 Dahuang46	有Yes	无No	异质性Heterogeneous	52.50	无No	无No	02740Y14G0210	12W1447	13
26	NZ00822	郑白1 Zhengbai1	有Yes	无No	异质性Heterogeneous	40.00	无No	无No	02985Y14G0455	12W0838	370
27	NZ01240	系14 Xi14	有Yes	无No	异质性Heterogeneous	77.50	无No	无No	03407Y14G0877	13J1114	71
28	NZ02719	MO17	有Yes	无No	异质性Heterogeneous	82.50	无No	无No	04930Y14G2400	13J2212	62
29	NZ02808	75-217	有Yes	无No	异质性Heterogeneous	55.00	无No	无No	05027Y14G2497-1红轴 05027Y14G2497-1 Red cob	13J2310	333

表2

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样品名 Sample name	分组 Classification	位点Loci
样品名 Sample name	分组 Classification	1	2	3	4	5	6	7	8	9	10
吉754 Ji754	Ⅰ组 Group Ⅰ	325Y	238Y	246Y	354Y	291Y	362Y	433Y	380Y	273Y	248Y
	Ⅱ组 Group Ⅱ	183Y	267Y	202Y	169Y	221Y	212Y	393Y	278Y	229Y	178Y
	Ⅲ组 Group Ⅲ	167Y	186Y	253Y	232Y	173Y	233Y	271Y	197Y	284Y	126Y
	Ⅳ组 Group Ⅳ	280Y	234Y	215Y	172Y	183Y	204Y	183Y	261Y	312Y	310Y
郑白1 Zhengbai1	Ⅰ组 Group Ⅰ	320N	252Y	248Y	359N	314N	343N	421Y	364N	275N	260Y
	Ⅱ组 Group Ⅱ	183Y	267N	202N	154Y	221N	212N	413N	284Y	222Y	185N
	Ⅲ组 Group Ⅲ	154Y	184N	253N	232N	175Y	233N	297N	197N	284N	134N
	Ⅳ组 Group Ⅳ	263N	000N	207Y	170Y	180N	215N	185N	261Y	304N	299Y

吉林省玉米种质资源SSR和SNP分子身份证的构建及应用

The Construction and Application of SSR and SNP Molecular ID for Maize Germplasm Resources of Jilin Province

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