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CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops
Tingyu Dou1, Chunchao Wang1, Yanling Ma1
1Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China.
BMC Plant Biology
|November 21, 2023
Summary
The CoreSNP pipeline efficiently selects minimal single nucleotide polymorphism (SNP) marker sets from large crop datasets. This aids in distinguishing plant varieties for germplasm identification and intellectual property protection.
Area of Science:
- Agricultural Science
- Genetics
- Bioinformatics
Background:
- DNA marker profiles are vital for germplasm identification, registration, and Distinctness, Uniformity, and Stability (DUS) testing.
- Selecting optimal marker sets from large single nucleotide polymorphism (SNP) datasets for maximum sample differentiation is challenging.
Purpose of the Study:
- To develop an efficient pipeline, CoreSNP, for selecting minimal marker sets from genome-wide SNP data.
- To ensure selected markers can reliably distinguish individual samples.
Main Methods:
- Developed the CoreSNP pipeline employing a "divide and conquer" strategy and a "greedy" algorithm.
- Incorporated adjustable parameters for sample distinction and handling datasets with missing loci.
- Tested the pipeline on diverse crop datasets including barley, soybean, wheat, rice, and maize.
Main Results:
- Efficiently selected a few dozen core SNPs from various crops (SNP array, GBS, WGS datasets) capable of differentiating thousands of samples.
- Core SNPs showed lower linkage disequilibrium (LD) and higher polymorphism information content (PIC) and minor allele frequencies (MAF), distributed across chromosomes.
- Identified that population genetic diversity and dataset characteristics influence core marker numbers and that core SNPs capture population structure.
Conclusions:
- CoreSNP provides an efficient method for selecting core marker sets from genome-wide SNP data in crops.
- This approach, combined with low-density SNP chips or genotyping technologies, offers a cost-effective solution for evaluating genetic resources and differentiating crop varieties.
- CoreSNP is expected to significantly benefit germplasm comparison and intellectual property protection for new varieties.
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