Development and application of whole genome SNP markers in mango

Mango (Mangifera indica L.) is a globally significant fruit over the world. The precise identification of germplasm resources is of great significance for the breeding of new mango cultivars. Traditional methods based on phenotypic characterization are time-consuming, labor-intensive, and often lack accuracy in distinguishing and identifying accessions. In contrast, DNA fingerprinting utilizing single nucleotide polymorphism (SNP) markers offers an efficient and accurate alternative for germplasm identification and variety protection. However, applications of such SNP-based systems remain relatively limited in mango research.

In this study, 438,322 SNP sites of SNP-InDel information were obtained by GATK software filtering. After filtered by minimum allele frequency (MAF) > 0.4; mismatch rate < 0.25; heterozygosity rate < 0.5; no other mutations within 70 bp on either side of the SNP site, 272 high-quality SNP sites was identified. Then 85 novel PARMS-SNP markers were developed. Based on the 85 novel PARMS-SNP markers, 145 mango germplasm accessions were grouped to three major categories. Based on the polymorphism results, 16 SNP markers were selected as the core markers to construct the DNA fingerprints of 145 mango germplasms. The results showed that 145 mango germplasms had unique genotyping and strong identification ability, indicating that there was no misidentification in the germplasm. At the same time, it provided a basis for the accurate identification of mango germplasm resources and the breeding of new varieties. In addition, 85 SNP markers were screened and 3 specific SNP markers of "Keitt" (KT) × "Renong No.1" (RN) were mined, which could effectively distinguish parents and control materials. The most important thing was to realize the rapid identification of mango parent-child relationship.

To the best of our knowledge, this represents the first attempt to establish SNP markers in genomic wide. The objective is to conduct genetic diversity analysis and construct DNA fingerprint of mango germplasm resources, thereby providing a foundation for germplasm utilization and molecular marker-assisted breeding.