Genetic Diversity and Fingerprinting of 231 Mango Germplasm Using Genome SSR Markers

Abstract

Mango (Mangifera indica L.) (2n = 40) is an important perennial fruit tree in tropical and subtropical regions. The lack of information on genetic diversity at the molecular level hinders efforts in mango genetic improvement and molecular marker-assisted breeding. In this study, a genome-wide screening was conducted to develop simple sequence repeat (SSR) markers using the Alphonso reference genome. A total of 187 SSR primer pairs were designed based on SSR loci with consisting of tri- to hexa-nucleotide motifs, and 34 highly polymorphic primer pairs were selected to analyze the diversity of 231 germplasm resources. These primers amplified 219 alleles (Na) across 231 accessions, averaging of 6.441 alleles for per marker. The polymorphic information content (PIC) values ranged from 0.509 to 0.757 with a mean of 0.620. Genetic diversity varied among populations, with Southeast Asia showing the highest diversity, and Australia the lowest. Population structure analysis, divided the accessions into two groups, Group I (India) and Group II (Southeast Asia), containing 104 and 127 accessions, respectively, consistent with results from phylogenetic analysis and principal component analysis (PCA). Sixteen SSR primer pairs capable of distinguishing all tested accessions, were selected as core primers for constructing fingerprints of 229 mango accessions. These findings offer valuable resources for enhancing the utilization of mango germplasm in breeding programs.

Keywords: finger-printing; genetic diversity; genomic SSR; mango (Mangifera indica L.).

Figure 1

Proportions of different types of SSR units in the mango genome. Each pie chart represents the SSR loci with different repeat units in the genome.

Figure 2

Polymorphism of 12 mango varieties by primer G1134, G1342, G1382, and G1097 based on PAGE. 6~123 represent the mango varieties Jinhuang, Tainong No. 1, Renong No. 1, GeDong, Keitt, Sri Lank No. 811, Nam Dok Mai Sitong, Dashehari, Zill, Haden, Guire No. 82, and Neelum, respectively.

Figure 3

Different genotype of six mango varieties by primer G573 based on capillary electrophoresis. (A–F) represent the mango varieties Ono, Sri Lank No. 811, Glenn, Irwin, Renong No. 1, and Guifei, respectively.

Figure 4

LnP(D) and ΔK evaluations of the 231 mango accessions.

Figure 5

Genetic structure of 231 mango accessions. (A) Population structure analysis of the 231 mango accessions (K = 2 and K = 5). (B) UPGMA tree of 231 mango accessions based on Nei’s genetic distances. (C) The principal component analysis of the 231 mango accessions. All the results showed that the samples could be divided into two clusters: Red—Group I; Blue—Group II.

Figure 5

Genetic structure of 231 mango accessions. (A) Population structure analysis of the 231 mango accessions (K = 2 and K = 5). (B) UPGMA tree of 231 mango accessions based on Nei’s genetic distances. (C) The principal component analysis of the 231 mango accessions. All the results showed that the samples could be divided into two clusters: Red—Group I; Blue—Group II.

Figure 6

Fingerprinting of 2D barcode from part mango varieties. (A–F) represent the mango varieties Irwin, Apple, NamDocMai, Chishu, Arumanis B, and JinHuang, respectively.