CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops.

ABSTRACT:

Background

DNA marker profiles play a crucial role in the identification and registration of germplasm, as well as in the distinctness, uniformity, and stability (DUS) testing of new plant variety protection. However, selecting minimal marker sets from large-scale SNP dataset can be challenging to distinguish a maximum number of samples.

Results

Here, we developed the CoreSNP pipeline using a "divide and conquer" strategy and a "greedy" algorithm. The pipeline offers adjustable parameters to guarantee the distinction of each sample pair with at least two markers. Additionally, it allows datasets with missing loci as input. The pipeline was tested in barley, soybean, wheat, rice and maize. A few dozen of core SNPs were efficiently selected in different crops with SNP array, G

SUBMITTER: Dou T 

PROVIDER: S-EPMC10662547 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature