基于SV标记的猕猴桃种质资源遗传多样性分析及DNA分子身份证构建

doi:10.13560/j.cnki.biotech.bull.1985.2026-0397

摘要/Abstract

摘要：

目的猕猴桃作为重要的经济果树，其产业高质量发展长期受品种混乱、同物异名及侵权现象制约，亟需建立一套精准、高效的种质资源遗传鉴定技术体系。方法系统收集贵州、江西、重庆等地79份猕猴桃种质资源，包括野生种质36份和栽培品种43份。基于泛基因组及重测序数据，开发结构变异（structural variants, SV）分子标记，开展遗传聚类分析，并构建DNA指纹图谱与分子身份证。结果从50个SV位点对应的标记引物中，经初步筛选与扩大材料验证，获得5对高多态性核心SV引物。利用这5对引物组合，可有效区分77份供试种质，鉴别率达到97.47%。基于扩增基因型数据构建的二元（0/1）矩阵，绘制了供试材料的DNA指纹图谱，并进一步为每份种质生成了10位数字的专属分子身份证。UPGMA聚类分析显示，供试材料遗传多样性丰富，聚类结果与现有猕猴桃植物学分类基本一致。结论开发的SV标记可高效应用于猕猴桃种质资源遗传多样性分析与品种精准鉴定。

关键词: 猕猴桃, SV标记, 遗传多样性, DNA指纹图谱, 分子身份证

Abstract:

Objective Kiwifruit is an important economic fruit tree; however, the high-quality development of its industry has long been constrained by variety confusion, synonymy, and infringement. Hence, there is an urgent need to establish a precise and efficient genetic identification technology system for germplasm resources. Methods A total of 79 kiwifruit germplasm resources, including 36 wild accessions and 43 cultivated varieties, were systematically collected from Guizhou, Jiangxi, and Chongqing. Based on pan-genomic and resequencing data, SV (structural variants) molecular markers were developed, genetic cluster analysis was performed, and DNA fingerprints and molecular IDs were constructed. Results From the primer pairs corresponding to 50 SV loci, five core SV primer pairs with high polymorphism were obtained through preliminary screening and expanded validation. Using these five primer combinations, 77 tested germplasms could be effectively distinguished, achieving an identification rate of 97.47%. Based on the amplified genotype data, a binary (0/1) matrix was constructed to generate DNA fingerprints for the tested materials, and a unique 10-digit molecular ID was further assigned to each accession. UPGMA cluster analysis revealed rich genetic diversity among the tested materials, and the clustering results were generally consistent with the existing botanical classification of kiwifruit. Conclusion The developed SV markers can be efficiently applied to genetic diversity analysis and accurate identification of kiwifruit germplasm resources.

Key words: kiwifruit, SV markers, genetic diversity, DNA fingerprinting, molecular ID

耿远来, 张颖梓, 赵丹晨, 谭伟双, 陈晓妮, 王运生, 史斌斌, 唐冬梅, 李大志, 周嘉. 基于SV标记的猕猴桃种质资源遗传多样性分析及DNA分子身份证构建[J]. 生物技术通报, doi: 10.13560/j.cnki.biotech.bull.1985.2026-0397.

GENG Yuan-lai, ZHANG Ying-zi, ZHAO Dan-chen, TAN Wei-shuang, CHEN Xiao-ni, WANG Yun-sheng, SHI Bin-bin, TANG Dong-mei, LI Da-zhi, ZHOU Jia. Genetic Diversity Analysis and DNA Molecular ID Construction in Kiwifruit Germplasm Resources Based on SV Markers[J]. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2026-0397.

图/表 7

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染色体位置 Chromosomal location	标记编号 Marker ID	引物名称 Primer name	引物序列 Primer sequence （5'‒3'）
LG23	P1	Del_799-F	TTCAGTCAGAGTAAGCGCCC
LG23	P1	Del_799-R	CACCATATTCGCAAGCACGG
LG3	P2	Del_981-F	TTACATTGACCACCCCGAGG
LG3	P2	Del_981-R	TACACTGAACACCCCTGAGG
LG10	P3	Del_677-F	CATGCATGTCTTCTGCCACG
LG10	P3	Del_677-R	AGTCAGCAGAAGGGGAAGGA
LG12	P4	Del_441-F	ATGCCATGTTGGGAAGCTCA
LG12	P4	Del_441-R	TGCACCTAAGGACTCAATGGG
LG24	P5	Ins_622-F	CTGATATGTCGCGGCCCATA
LG24	P5	Ins_622-R	TGTCCTGGATTCCTTGGTGG

染色体位置 Chromosomal location	标记编号 Marker ID	引物名称 Primer name	引物序列 Primer sequence （5'‒3'）
LG23	P1	Del_799-F	TTCAGTCAGAGTAAGCGCCC
LG23	P1	Del_799-R	CACCATATTCGCAAGCACGG
LG3	P2	Del_981-F	TTACATTGACCACCCCGAGG
LG3	P2	Del_981-R	TACACTGAACACCCCTGAGG
LG10	P3	Del_677-F	CATGCATGTCTTCTGCCACG
LG10	P3	Del_677-R	AGTCAGCAGAAGGGGAAGGA
LG12	P4	Del_441-F	ATGCCATGTTGGGAAGCTCA
LG12	P4	Del_441-R	TGCACCTAAGGACTCAATGGG
LG24	P5	Ins_622-F	CTGATATGTCGCGGCCCATA
LG24	P5	Ins_622-R	TGTCCTGGATTCCTTGGTGG

标记组合 Marker combination	可鉴别材料 Materials identified	小计 Subtotal	总计 Total
P3	11，19，26，36，40，58，72	7	7
P3+P2	3，4，6，7，10，13，14，16，18，20，21，22，23，25，27，30，32，33，35，37，39，41，44，46，48，49，50，51，52，53，55，56，57，59，60，61，65，66，67，68，70，71，73，75，76，77，78	47	54
P3+P2+P4	1，2，5，8，9，12，17，24，28，42，45，54，69，74，79	15	69
P3+P2+P4+P5	15，34，38，43，47，64	6	75
P3+P2+P4+P5+P1	29，31	2	77

标记组合 Marker combination	可鉴别材料 Materials identified	小计 Subtotal	总计 Total
P3	11，19，26，36，40，58，72	7	7
P3+P2	3，4，6，7，10，13，14，16，18，20，21，22，23，25，27，30，32，33，35，37，39，41，44，46，48，49，50，51，52，53，55，56，57，59，60，61，65，66，67，68，70，71，73，75，76，77，78	47	54
P3+P2+P4	1，2，5，8，9，12，17，24，28，42，45，54，69，74，79	15	69
P3+P2+P4+P5	15，34，38，43，47，64	6	75
P3+P2+P4+P5+P1	29，31	2	77

序号 Code	品种名 Name	分子身份证 Molecular ID	序号 Code	品种名 Name	分子身份证 Molecular ID
1	魁蜜	0117061211	40	贵猕2号	0813090511
2	魁绿	0222030104	41	1807	1333040109
3	A10	0206140405	42	贵丰	1431060511
4	丰绿	0323030404	43	2024033	0817060511
5	恒优1号	0322030204	44	1826	1525140405
6	紫玉	0415030104	45	江口梵之语	0828060605
7	红宝石星	0236030203	46	23259	0817120515
8	龙城2号	0522030404	47	金丰	0817060513
9	徐香	0601010105	48	G3	0804010507
10	华特	0128030305	49	黔雄1号	0128121515
11	翠香	0102081604	50	金艳	1431140711
12	1813	0701140305	51	金阳	1612011512
13	翠玉	0103030803	52	XWZYP大籽	1530010207
14	金怡	0801030705	53	中砧1号	1711140405
15	楚红	0801010705	54	中猕1号	0131061209
16	贵长	0120030804	55	红阳	1808061311
17	哑特	0801011408	56	东红	1407061313
18	G9	0801060711	57	米良1号	1935121516
19	金硕	0119130911	58	金圆	0128151511
20	金桃	0117140102	59	花叶水杨桃	1616140405
21	金魁	0122120914	60	2024001	0129060308
22	磨山3号	0126021515	61	2024002	0110140506
23	武植3号	0117101413	64	翡翠香果	0801010707
24	金霞	0817011311	65	建香	0833061511
25	华优	0903021511	66	朝晖	0833121504
26	大山10号	0133111515	67	金什	0828061511
27	2023002	0122140107	68	2024007	0805140202
28	2023004	0122030804	69	2024010	0817010504
29	2023006	0101140101	70	2024011	2009141104
30	2023010	0119140102	71	瑞玉	1432121315
31	2023015	1001140101	72	2024014	0832150715
32	2023017	0119100108	73	2024017	0827010202
33	2023022	0803140208	74	2024018	0828010604
34	2023201	0809140108	75	2024023	0834060504
35	2023224	1114040109	76	2024027	0828140310
36	2023245	1214050408	77	2024034	0818011004
37	2023244	1201070615	78	2024042	0824060604
38	2023246	0809140107	79	2024051	0828010504
39	中猕2号	0821070509