基于51K液相探针构建国外松良种的DNA指纹图谱

doi:10.11707/j.1001-7488.LYKX20240401

摘要/Abstract

摘要：

目的: 由于国外松在苗期的形态特征十分相似，区分这些良种具有一定的挑战性。本研究旨在构建一套针对国外松良种的DNA指纹图谱，为国外松种质资源管理、良种知识产权保护等提供技术支持。方法: 本研究以38份国外松本种及其杂种松良种为材料，利用湿地松和火炬松的51K液相探针芯片进行SNPs捕获，获得38个国外松改良品种的基因型数据。通过次要等位基因频率、缺失率、杂合率和多态性信息含量等遗传参数筛选能够高效识别国外松种质资源的核心SNPs；根据PIC值进一步简化SNP标记的数量，达到较少数量的SNPs能高效识样本的目的。结果: 通过SNP位点捕获和基因分型，共得到560,567个SNPs位点，筛选得到344个核心SNPs，并利用PIC值进一步精简为20个SNPs，能够高效区分湿地松、火炬松、加勒比松及其杂交松，成功建立了38个松树良种的DNA指纹图谱。结论: 开发了一套针对国外松良种的DNA指纹图谱，建立了指纹图谱鉴定国外松及其良种的方法，可为良种知识产权保护、种质管理和系谱分析提供技术支持。

关键词: DNA指纹图谱, 品种鉴别, 湿地松, 火炬松

Abstract:

Objective: Slash pine (Pinus elliottii), loblolly pine (P. taeda), Caribbean pine (P. caribaea) and their interspecific hybrids are the main timber species introduced and domesticated from North America in China. In recent years, dozens of elite varieties of foreign pines have been approved. As the morphological characteristics of exotic pines are very similar at seedling stage, it is a challenge to distinguish these elite varieties. The purpose of this study is to construct a set of DNA fingerprints for foreign pine varieties, which can be used for the identification of different foreign pine species, and provide technical support for the management of germplasm resources and intellectual property protection of exotic pine varieties. Method: The 51K liquid phase probe microarray of slash pine and loblolly pine was used to capture SNPs of 38 elite varieties of exotic pines and their hybrids, and obtained their genotype data. The core SNPs in exotic pine germplasm resources were able to be efficiently identified through screening genetic parameters, such as minor allele frequency, deletion rate, heterozygosity and polymorphism information content. The number of SNP markers was further simplified based on PIC values to achieve the goal of efficiently identifying samples with a smaller number of SNPs. Result: A total of 60 567 SNPs loci were obtained by SNP locus capture and genotyping. Through strict control of minor allele frequency, deletion rate, heterozygosity and other parameters, 344 core SNPs were screened. The PIC value was further reduced to 20 SNPs, with which slash pine, loblolly pine, Caribbean pine and their hybrids were able to be efficiently distinguished. This approach was used to successfully establish DNA fingerprint profiles for 38 elite pine varieties. Conclusion: In this study, a DNA fingerprinting system for elite exotic pine varieties has been developed, and a method for identifying exotic pines and their elite varieties has been established. The research results can provide technical support for the protection of intellectual property rights, germplasm management, and pedigree analysis of elite varieties.

Key words: DNA fingerprinting, pine varieties identification, Pinus elliottii, P. taeda

中图分类号:

S722.5

吴亚荻,刁姝,丁显印,黄琴韵,栾启福. 基于51K液相探针构建国外松良种的DNA指纹图谱[J]. 林业科学, 2025, 61(6): 109-119.

Yadi Wu,Shu Diao,Xianyin Ding,Qinyun Huang,Qifu Luan. Construction of a DNA Fingerprinting of Elite Varieties of Introduced Exotic Pines in China Based on 51K Liquid-Phased Probes[J]. Scientia Silvae Sinicae, 2025, 61(6): 109-119.

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树种 Species	样本数量 Number of samples	优良性状 Superior traits
PEE	25	速生 Fast-growing
PEE	4	高产脂 High resin yield
PTA	2	速生丰产 Fast-growing and high-yielding
PAC	5	速生丰产 Fast-growing and high-yielding
PEC	2	速生丰产 Fast-growing and high-yielding

筛选步骤 Screening steps	筛选条件 Screening criteria	剩余SNP的数量 Number of remaining SNPs
原始数据 Raw data	—	183 849
第1步 Step 1	次要等位基因频率大于0.3，缺失率为0 MAF >0.3，miss rate=0	22 593
第2步 Step 2	符合哈迪-温伯格平衡 HWE <1E-4	13 931
第3步 Step 3	连锁不平衡大于0.2 LD >0.2	8 502
第4步 Step 4	多态信息含量大于0.35 PIC >0.35	8 502
第5步 Step 5	杂合度小于0.25 He <0.25	344

序号 No.	SNP名称 SNP ID	染色体 Chromosome	等位基因A Alley gene A	等位基因B Alley gene B	次要等位基因频率 Minor allele frequency （MAF）	多态信息含量 Polymorphic information content（PIC）
1	super2776.88036	10	G	A	0.500 0	0.500 0
2	scaffold121890.3772	6	T	C	0.500 0	0.500 0
3	scaffold124124.14341	11	C	T	0.500 0	0.500 0
4	scaffold156626.9213	6	A	G	0.500 0	0.500 0
5	Gene.280112.80	12	C	T	0.500 0	0.500 0
6	super3477.582311	3	G	A	0.486 8	0.499 7
7	super3658.67227	12	G	C	0.486 8	0.499 7
8	super3673.196162	1	G	C	0.486 8	0.499 7
9	scaffold4919.104166	11	C	T	0.486 8	0.499 7
10	scaffold8912.56207	2	C	T	0.486 8	0.499 7
11	scaffold18745.243173	7	G	C	0.486 8	0.499 7
12	scaffold28210.166698	4	C	T	0.486 8	0.499 7
13	scaffold45863.102243	8	A	C	0.486 8	0.499 7
14	scaffold71374.123891	1	G	T	0.486 8	0.499 7
15	scaffold120395.63994	12	C	A	0.486 8	0.499 7
16	scaffold127392.228550	9	A	C	0.486 8	0.499 7
17	scaffold144338.102562	10	A	G	0.486 8	0.499 7
18	scaffold146854.112944	5	A	T	0.486 8	0.499 7
19	Gene.117474.537	7	T	C	0.486 8	0.499 7
20	super2715.43005	9	C	T	0.460 5	0.496 9

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