Genetic Diversity of Pineapple (Ananas comosus) Germplasm in Malaysia Using Simple Sequence Repeat (SSR) Markers

Abstract

Assessments of genetic diversity have been claimed to be significantly efficient in utilising and managing resources of genetic for breeding programme. In this study, variations in genetic were observed in 65 pineapple accessions gathered from germplasm available at Malaysian Agriculture Research and Development Institute (MARDI) located in Pontian, Johor via 15 markers of simple sequence repeat (SSR). The results showed that 59 alleles appeared to range from 2.0 to 6.0 alleles with a mean of 3.9 alleles per locus, thus displaying polymorphism for all samples at a moderate level. Furthermore, the values of polymorphic information content (PIC) had been found to range between 0.104 (TsuAC035) and 0.697 (Acom_9.9), thus averaging at the value of 0.433. In addition, the expected and the observed heterozygosity of each locus seemed to vary within the ranges of 0.033 to 0.712, and from 0.033 to 0.885, along with the average values of 0.437 and 0.511, respectively. The population structure analysis via method of delta K (ΔK), along with mean of L (K) method, revealed that individuals from the germplasm could be divided into two major clusters based on genetics (K = 2), namely Group 1 and Group 2. As such, five accessions (Yankee, SRK Chalok, SCK Giant India, SC KEW5 India and SC1 Thailand) were clustered in Group 1, while the rest were clustered in Group 2. These outcomes were also supported by the dendrogram, which had been generated through the technique of unweighted pair group with arithmetic mean (UPGMA). These analyses appear to be helpful amongst breeders to maintain and to manage their collections of germplasm. Besides, the data gathered in this study can be useful for breeders to exploit the area of genetic diversity in estimating the level of heterosis.

Keywords: Co-dominant; Germplasm Characterisation; Molecular Marker; Simple Sequence Repeat (SSR).

Figure 1

Scatter plot to determine true K value using log probability (ΔK) method; the highest value of ΔK represents the optimum K value (K = 2) (Evanno et al. 2005).

Figure 2

Determination of K value using mean of Ln P (K) method; Ln P (K) plateaus and the variation between runs increases when approaching an optimum K value (Pritchard et al. 2000; Evanno et al. 2005). K = 2 shows the first plateau with the highest variations.

Figure 3

Bar plot structure of K = 2 obtained by STRUCTURE software version 2.3.4. The plot shows two major clusters separated by a straight line (Group 1 and Group 2).

Figure 4

UPGMA cluster dendrogram showing the relationships of 65 pineapple accessions based on 15 polymorphic SSR markers. Two major clusters can be observed (Group 1 and Group 2).