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

Abstract

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

CLC Number:

S722.5

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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Construction of a DNA Fingerprinting of Elite Varieties of Introduced Exotic Pines in China Based on 51K Liquid-Phased Probes

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染色体 Chromosome	核心SNPs标记数量 Number of core SNPs
01	22
02	23
03	34
04	30
05	33
06	26
07	23
08	30
09	31
10	33
11	20
12	30