CN-122012785-A - Method for constructing kelp core germplasm and identifying germplasm based on SNP molecular markers

Abstract

The invention provides a method for constructing kelp core germplasm and identifying germplasm based on SNP molecular markers. The method comprises the steps of collecting kelp gametophyte germplasm with complete and accurate source information, detecting and screening SNP loci, determining an optimal core germplasm population by utilizing an EN-MR/CE model and combining genetic diversity comparison, further screening to obtain 130 SNP markers which are uniformly distributed on chromosomes and are rich in polymorphism, and realizing accurate identification of 91 core germplasm. Meanwhile, the core SNP markers can be used for effectively distinguishing germplasm materials from different kelp culture strains. The method can truly reflect the genetic diversity background of the kelp germplasm library, efficiently screen core germplasm and identify germplasm materials, and provides technical support for improving the preservation and utilization efficiency of kelp germplasm.

Inventors

• ZHANG LINAN
• Gai Zihan
• CHEN SHUXIU
• LI YAN
• LI XIAOJIE
• WANG WEIWEI

Assignees

• 青岛农业大学
• 山东东方海洋科技股份有限公司

Dates

Publication Date

20260512

Application Date

20260310

Priority Date

20250416

Claims (10)

1. 1. A SNP marker derived from kelp in whole genome scale is characterized in that the SNP marker is positioned at the 50 th position of any sequence in SEQ ID NO. 1-130.
2. 2. The use of the SNP marker according to claim 1 for the germplasm identification of kelp.
3. 3. A method for identifying a kelp core germplasm sample, characterized in that the method is to use any one or several of the SNP markers of claim 1 for identification.
4. 4. The method of claim 3, wherein the kelp core germplasm samples are 91 core sample sets constructed based on genetic diversity and germplasm resource background information.
5. 5. A method according to claim 3, wherein the sites of all samples are analysed differently in pairs, ensuring that the sites of difference between two pairs are ≡2.
6. 6. A method for identifying a kelp strain, characterized in that the identification is performed using 12 of the SNP markers of claim 1.
7. 7. The method of claim 6, wherein the kelp population is a cultivar JLH of kelp and long kelp cross.
8. 8. The method of claim 6, wherein the SNP marker comprises any one or more of the following SNP loci: 1) SNP site located at 50 th position of nucleic acid fragment with sequence of SEQ ID NO. 2; 2) SNP site located at 50 th position of nucleic acid fragment with sequence of SEQ ID NO. 6; 3) SNP site located at 50 th position of nucleic acid fragment with sequence of SEQ ID NO. 7; 4) SNP site located at 50 th position of nucleic acid fragment of SEQ ID NO. 19; 5) SNP site located at 50 th position of nucleic acid fragment of SEQ ID NO. 81; 6) A SNP site located at position 50 of the nucleic acid fragment having the sequence of SEQ ID NO. 92; 7) SNP site located at 50 th position of nucleic acid fragment with sequence of SEQ ID NO. 94; 8) SNP site located at 50 th position of nucleic acid fragment with sequence of SEQ ID NO. 102; 9) SNP site located at 50 th position of nucleic acid fragment with sequence of SEQ ID NO. 103; 10 SNP site located at position 50 of the nucleic acid fragment having the sequence of SEQ ID NO. 104; 11 SNP site located at position 50 of the nucleic acid fragment having the sequence of SEQ ID NO. 107; 12 SNP site at position 50 of a nucleic acid fragment having the sequence SEQ ID NO. 108.
9. 9. The method for constructing the kelp core germplasm based on SNP molecular markers is characterized by comprising the following steps: 1) Obtaining kelp gametophyte germplasm resource samples with complete and accurate information sources, extracting genome DNA of all samples, detecting DNA samples, establishing libraries, carrying out whole genome re-sequencing and controlling quality, and obtaining high-quality sequencing data; 2) Comparing the resequencing data obtained in the step 1) to a reference genome to detect SNP loci, and detecting and filtering out high-quality SNP data sets; 3) Constructing Core germplasm sets with different proportions by using the high-quality SNP data set obtained in the step 2) as genetic information data and Core Hunter3 software; 4) Aiming at the core germplasm collection with different proportions in the step 3), analyzing genetic diversity parameters and combining germplasm resource background information to finally determine kelp core germplasm; 5) Extracting all SNP loci of a sample by using the core germplasm set obtained in the step 4), and constructing a core SNP marker set by filtering and screening loci with high polymorphism.
10. 10. The method according to claim 8, wherein the SNP marker set is the SNP marker according to claim 1.

Description

Method for constructing kelp core germplasm and identifying germplasm based on SNP molecular markers Technical Field The invention relates to the technical fields of molecular biology, genomics and germplasm resources, in particular to a method for constructing kelp core germplasm and identifying germplasm based on SNP molecular markers. Background Kelp SACCHARINA JAPONICA is a large-scale marine brown algae with important economic value and ecological function. Algin, mannitol, iodine and the like produced by using kelp as a raw material are widely applied to various fields such as cosmetics, chemical industry, medicine, biological energy and the like. Meanwhile, the kelp is taken as an important component in the marine ecological environment, and the formed seaweed forest can provide habitat, food and shelter for organisms, so that the kelp has the effects of improving offshore diversity and regulating the ecological environment of offshore areas. Kelp is the biggest large algae with the longest culture history and the highest yield in China. The species was found to be wild species locally at the end of the 30 s of the 20 th century after the unexpected introduction of our national company from the north sea road in japan since the 20 th century. In the 40 s of the 20 th century, japanese algae expert Yoshiro Otuki and other Japanese farmers have introduced kelp into the Dalian. In 1949, the Shandong tobacco stand adopts a floating raft cultivation technology and an artificial seedling cultivation technology to realize large-scale kelp cultivation, and is gradually popularized to Qingdao. Along with the implementation of the strategy of 'south transplanting cultivation', the kelp cultivation technology is introduced into Zhejiang Zhoushan from Qingdao in 1956, and further promoted to Fujian Lianjiang in 1957, so as to promote China to become a global kelp cultivation and production core area. Through the research of kelp breeding for decades, more than 40 new varieties of kelp are cultivated in China successively, wherein 12 new varieties are examined by the national committee for fine variety of aquatic products, and an important support is provided for the sustainable development of the kelp industry. Germplasm resources are the core biological capital that supports genetic breeding and industry sustainability. As a representative species of the large brown algae group, kelp germplasm resource preservation is not only concerned with the potential of variety improvement, but also a strategic reserve for coping with climate change, disease outbreak and marine environment fluctuation. The kelp life history has typical abnormal generation alternation characteristics, and the kelp gametophyte cloning technology is established, so that the long-term living preservation of kelp gametophyte materials is realized, and the kelp gametophyte becomes a main carrier for the current kelp germplasm preservation. At present, sea tangle gametophyte germplasm libraries are established by high and new technical enterprises such as China academy of sciences, china university of ocean, china institute of aquatic products, yellow sea institute of aquatic products, shandong eastern ocean technology and stock, and the like, so that a foundation is laid for germplasm resource preservation and utilization. However, the existing kelp germplasm pool in China still has a plurality of problems in management and utilization, namely (1) kelp is not naturally distributed in China, so that kelp germplasm resources in China are limited, the genetic diversity level is low, and wild genetic germplasm resources which can be excavated are limited. (2) The method comprises the steps of (1) storing a large amount of kelp gametophytes from the same variety (line) in a germplasm library, easily causing redundancy of germplasm materials, increasing consumption of manpower, material resources and space resources for daily storage and management, (3) partially storing gametophyte germplasm material source information incompletely or inaccurately, for example, partially obtaining gametophytes through donation, communication and other ways, deleting background information, mixing different varieties due to common reasons of a seedling workshop or a breeding area in a seedling raising and breeding stage, further causing distortion of gametophyte germplasm information of subsequent separation and storage, and (4) lacking an efficient kelp germplasm identification method in the prior art system, and being difficult to meet the requirement of accurate recognition of germplasm resources. Disclosure of Invention Aiming at the problems of lack of gametophyte germplasm genetic information and low germplasm resource preservation and utilization efficiency existing in the prior kelp germplasm resource preservation, the invention aims to provide a method for constructing kelp core germplasm and germplasm identification based on SNP molecular markers, which lays