SNP marker set for identifying upland cotton varieties and application thereof

By constructing a marker set through screening 1553 SNP loci, the high cost and redundancy of existing commercial chips in upland cotton variety identification are solved, realizing efficient and low-cost upland cotton variety identification, which is suitable for large-scale sample screening and small-to-medium-scale variety identification.

CN122279098APending Publication Date: 2026-06-26JIANGSU ACAD OF AGRI SCI
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Patent Information

Authority / Receiving Office
CN · China
Patent Type
Applications(China)
Current Assignee / Owner
JIANGSU ACAD OF AGRI SCI
Filing Date
2026-05-29
Publication Date
2026-06-26

AI Technical Summary

Technical Problem

Existing commercial SNP chips are costly in cotton variety identification and contain redundant markers, making it difficult to effectively distinguish upland cotton varieties and failing to meet the needs of variety identification and variety rights protection.

Method used

1553 SNP loci were screened out, and a set of SNP markers suitable for upland cotton variety identification was constructed through linkage disequilibrium analysis and genomic uniform distribution. Combined with genetic distance criteria, the authenticity of the varieties was established.

Benefits of technology

It enables efficient and low-cost identification of upland cotton varieties, improves analytical efficiency, reduces genotype testing costs, is suitable for large-scale sample screening, has high discriminative power and flexibility, and is suitable for small and medium-sized variety identification.

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Abstract

This application relates to the fields of molecular genetics and biotechnology, particularly to SNP marker sets and their applications for upland cotton variety identification. Through analysis of 10K SNP microarray data from 1205 upland cotton varieties (1194 species), this application identified a core marker set containing 1553 SNP loci. These markers exhibit high polymorphism, low linkage disequilibrium, and uniform chromosome distribution among upland cotton varieties, enabling efficient and accurate identification. This application is the first to determine a genetic distance threshold of 0.3 for identifying the authenticity of upland cotton varieties using this 1553 SNP marker set. This marker set demonstrates strong identification capabilities and high cost-effectiveness, and can be widely applied in areas such as intellectual property protection, breeding, and variety management of upland cotton varieties.
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Claims

1. A set of SNP markers for identifying upland cotton varieties, characterized in that, The SNP marker set consists of SNP sites as shown in Table 1 of the specification.

2. The application of the SNP marker set as described in claim 1 in the identification of upland cotton varieties.

3. The application as described in claim 2, characterized in that, The specific steps are as follows: Calculate the genetic distance between the upland cotton variety to be tested and the control variety using the SNP marker set. When the genetic distance is >0.3, the variety to be tested and the control variety are determined to be "different varieties". When the genetic distance is ≤0.3, the variety to be tested is determined to be a "suspected similar variety" of the control variety. Then, conduct field adjacent planting identification to obtain the final identification result.