Plant Gene and Trait 2025, Vol.16, No.4, 182-193 http://genbreedpublisher.com/index.php/pgt 185 3 Analysis of Genetic Diversity of Pitaya Germplasm Resources 3.1 Application of molecular marker technology in genetic diversity research In studying the genetic diversity of pitaya, scientists have used many molecular marker methods. Among them, SSR markers (also called simple sequence repeat markers) are the earliest and most widely used. Shah et al. (2023) first established the SSR marker system for pitaya, and they analyzed the genetic relationship between 46 pitaya materials. They found a total of 183 different allele variations. On average, 2 to 3 different alleles can be detected at each locus. Later, researchers used SSR markers to study pitaya varieties from different places. Japanese researchers developed 16 new pairs of SSR primers to analyze pitaya collected in Okinawa. They used these primers to “fingerprint” different varieties and also saw the diversity between different varieties. Some primers showed great differences between varieties. In addition to SSR, there are some easier-to-operate methods, such as RAPD and ISSR. These are also used to study the genetic differences of pitaya. In a study in Bangladesh, scientists used 43 RAPD primers to analyze 15 dragon fruit materials. They found that 86.05% of the loci in these materials showed polymorphism, and the Nei's genetic diversity index was 0.327. According to the results of UPGMA clustering, these materials were divided into 3 groups, which were almost consistent with their geographical origins. In Colombia, researchers used ISSR markers to analyze 76 yellow-skinned pitaya (S. megalanthus) samples. The average heterozygosity was 0.34, showing high genetic diversity and clear genetic differentiation (Morillo et al., 2022). In California, USA, AFLP methods were used to perform cluster analysis of several pitaya varieties, mainly to help identify cultivars. 3.2 Integration of genetic diversity assessment based on meta-analysis Pitaya grown in Asia (mainly H. undatus and its red-fleshed type) is generally at a medium or low level in terms of genetic diversity. Let’s look at a commonly used indicator - Nei’s genetic diversity index (He). In China and Southeast Asia, the He of pitaya is mostly between 0.1 and 0.3. For example, Rifat et al. (2019) mentioned that the average He of pitaya varieties introduced in China is about 0.25. In contrast, the He of 15 varieties introduced in Bangladesh is 0.327, which is slightly higher. Pitaya germplasm in Latin America shows greater genetic diversity. In Colombia, the yellow-skinned pitaya population had an He value of 0.34. In Mexico, red-skinned pitaya had lower overall diversity, with He ranging from about 0.07 to 0.13 (depending on the region). However, genetic differences between regions were still clear. Particularly, the populations in central-western and southeastern Mexico belonged to two distinct genetic groups. Compared to many outcrossing fruit trees like mango and citrus, pitaya has fewer alleles and lower genetic diversity. However, it has higher diversity than completely self-pollinating crops. Introducing wild species such as S. setaceus and crossing them with cultivated varieties may bring in new allelic variations. In such hybrid populations, He can exceed 0.20. The results obtained by different molecular markers like SSR and ISSR are also relatively consistent. In these studies, the average percentage of polymorphic loci was usually between 50% and 85% (Morillo et al., 2022). 3.3 Genetic differentiation and population structure characteristics After AMOVA analysis of yellow-skinned pitaya from three production areas in Colombia, it was found that the genetic differences within the population accounted for 75%, and the differences between the populations accounted for 25%. The genetic differentiation coefficient F_st is about 0.26 (Morillo et al., 2022). In the pitaya grown in Maya family gardens in Mexico, structural analysis divided the populations in 9 regions into two main genetic groups (K=2), but the materials from different places in each group were still mixed together (Shah et al., 2023). Their F_st value is about 0.15, indicating that the degree of genetic differentiation is not high. Asian pitaya varieties have a complicated history of introduction and propagation, so the population structure is also relatively complex. Some studies have used structural analysis methods to group varieties from multiple countries and found that some patterns can be seen according to the color of the flesh, such as white flesh varieties
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