Comparison of Individual- and Bulked-Samples-Based Approaches Using RAPD and ISSR Markers for Identifying Genetic Relationships in <i>Brassica</i> Cultivars

Abstract

Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) variation among 24 cultivars of four Brassica species (B. rapa, B. juncea, B. napus, and B. oleracea) was examined using individual-and bulked-samples-based approaches. In both the approaches, eight plants were sampled for each cultivar, and were amplified individually and as bulked DNA, respectively. In total, 305 and 422 bands were scored in the individual-and bulked-samples-based approaches, respectively, and almost all the bands (99.8-100%) were polymorphic. Based on the individual-samples dataset, the within cultivar variation was smaller than the among cultivars variation, leading to a distribution reflecting genome compositions of each cultivar with principal coordinates analysis (PCoA) and unweighted pair-group method with arithmetic average (UPGMA) analysis. Although PCoA and UPGMA analysis based on bulked-samples data clustered the cultivars into groups with more emphasized variance among species than the results obtained by the individual-based approach, both PCoA plots and dendrograms of the individual-and bulked-samples-based approaches, respectively, were highly correlated with each other. These findings indicate that the number of individuals used to profile each cultivar can be reduced to eight per cultivar for analysis of the genetic variability in Brassica using RAPD and ISSR polymorphism, and the bulked-samples-based approach can be used to describe the genetic relationship among Brassica cultivars.

Genetic diversity analysis of some species in Brassicaceae family with ISSR markers

“…Likewise, the high value of expected heterozygosity is desirable for high genetic variation in the population. In previous studies, the mean value of expected heterozygosity was recorded as 0.088 (Takahashi et al, 2019) and 0.2883 (Wang et al, 2017). In the current study, the mean value of expected heterozygosity is higher than or similar to former studies which could be because of the substantial genetic diversity in the population.…”

“…ISSR markers have been used for genetic diversity analysis and molecular characterization of different plants like bread wheat (El-Sherbeny et al, 2020), taramira (Zafar-Pashanezhad et al, 2019), ginger (Baruah et al, 2019), kewda (Nasim et al, 2020), cassava (Afonso et al, 2019), flax (Ahmed et al, 2019), asparagus (Chen et al, 2020), and anise (Akçali-Giachino, 2020). Besides, ISSR markers were used for genetic diversity analysis and molecular characterization of Brassica by different researchers (Kalia et al, 2017;Kaur et al, 2014;Koch et al, 2017;Kong et al, 2011;Mohammadin et al, 2017;Takahashi et al, 2019;Verma et al, 2016).…”