Genetic diversity and structure analysis of Croatian garlic collection assessed by SSR markers

Abstract

This study examines genetic diversity and structure of a Croatian garlic germplasm collection using 13 simple sequence repeat (SSR) markers. A total of 71 alleles were observed across 64 accessions representing 3 Croatian regions (Istria, Dalmatia and continental Croatia) and 16 foreign landraces, with an average of 5.46 alleles per locus. Among the 80 accessions analysed, 61 distinct multilocus genotypes (MLG) were identified, of which 51 represented unique genotypes and the remaining accessions were divided into 10 MLG groups, comprising potential duplicates or redundant genotypes. Model-based Bayesian and hierarchical UPGMA clustering approaches revealed five major groups within the collection which partially correlated with geographical origin. The analysis of molecular variance (AMOVA) showed that the majority (87.71%) of the total molecular diversity is within the Croatian groups of accessions, even though a significant share (12.29%) of diversity derived from genetic diversity among groups. These results support regional structuring, as well as the existence of significant diversity within local populations. This study is the first comprehensive report on an extensive evaluation of genetic resources of garlic maintained by Croatia with the aim of setting the course for future preservation strategies with particular emphasis on the value of diversity in the context of climate change both on macro and micro levels.

Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation

“…SSRs are considered ideal DNA markers due to their stability and reproducibility [26]; thus, they have been widely used to assess genetic diversity in local garlic collections [2,15,17,26,35,[43][44][45]. The SSR markers used in this study revealed a mean PIC value of 0.471, which is lower than the PIC values reported by Cuhna et al [43,44], which were 0.518 and 0.500, respectively.…”

“…He) and expected heterozygosity (Exp. He), Shannon's Information index (I), number of alleles per locus (Na), and effective number of alleles (Ne) (Table 4), reflected comparative levels of genetic variation between ours and other previously characterized garlic germplasm collections, e.g., [15,31,44]. It should also be noted that the values of Obs.…”

“…On the other hand, garlic exhibits wide phenotypic diversity in different ecological areas of cultivation due to naturally occurring mutations and also soil type, environmental parameters, and cultural techniques, which eventually lead to a great number of cultivars [21]. This discrepancy between phenotypic and genetic data may arise because either the farmers tend to exchange their garlic varieties and thus generate confusion in garlic nomenclature through naming the same local variety/landrace with different names or vice versa [17,39], or it could be due to epigenetic phenomena which also cause significant phenotypic variation in garlic lines cultivated in the same region for an extended period [15,65,66].…”

“…In Greece, garlic is cultivated in approximately 780 ha with a total production of 8230 tons (http://fao.org/faostat/, accessed on 28 April 2023). tion, such as amplified fragment length polymorphisms (AFLPs) [16,[37][38][39], random amplified polymorphic DNA (RAPD) [14,40,41], sequence-related amplified polymorphisms (SRAPs) [5,42], insertions-deletions (InDels) [39], inter-simple sequence repeats (ISSRs) [1,18,22], and simple sequence repeats (SSRs) [2,15,17,35,[43][44][45]. Among these types of markers, SSRs became very popular since they are typically codominant, reproducible, highly polymorphic, and cross-species transferable [17,26], while ISSRs are broadly used in genetic studies as they are informative, reliable, and efficient in laboratory usage [18,28].…”

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

“…Furthermore, AMOVA revealed that the variation among E. stauntonii populations (18.53%) was higher than that of many other plant species, such as Origanum vulgare subsp. hirtum (8%) ( Alekseeva et al, 2021 ) and Allium sativum L. (12.29%) ( Poljuha et al, 2021 ), suggesting that disruption of gene flow between the populations played a role in determining the genetic differentiation of populations. Similarly, the results of the Mantel test ( r = 0.56, p < 0.001) showed that increase in geographic distance reduced gene flow.…”