Comparative analysis of genetic variation in kava (Piper methysticum) assessed by SSR and DArT reveals zygotic foundation and clonal diversification

Abstract

Kava (Piper methysticum) is a major cash crop in the Pacific. The aim of this study was to assess genetic variation among 103 accessions of kava using SSRs and DArTs. Genetic structure was determined using clustering analyses (WPGMA) and principal coordinate analyses (PCA). Thirteen SSR primers and 75 DArT markers were found polymorphic, and the two types of markers generated similar clustering patterns. Genetic distances ranged from 0 to 0.65 with an average of 0.24 using SSRs and from 0 to 0.64 with an average of 0.24 using DArT. Eleven genotypes were identified with SSR while 28 genotypes were identified with DArT markers. By combining the two sets of markers, a total of only 30 distinct genotypes were observed. In the Vanuatu archipelago, noble cultivars originating from different islands clustered together within a very narrow genetic base despite their diversity of morphotypes. SSR and DArT fingerprints allowed the identification of kava cultivars unsuitable for consumption, so called two-days, and clearly differentiated the wild types classified as P. methysticum var. wichmannii from the cultivars as var. methysticum. Molecular data reveals that all noble cultivars evolved by the predominance of clonal selection. Although they are represented by clearly distinct morphotypes, these cultivars are genetically vulnerable and their potential to adapt to forthcoming changes is limited. These newly developed markers provide high resolution and will be useful for kava diversity analyses and quality assessment.

Kavalactones and Flavokavins Profiles Contribute to Quality Assessment of Kava (Piper methysticum G. Forst.), the Traditional Beverage of the Pacific

“…The results presented here indicate that DHK is significantly higher in two-day (33.8), and DHM is significantly higher in wichmannii (29.4). DNA analysis of kava varieties using SSR and DArT markers has shown that they correspond to three distinct genotypes with somatic mutants within each group [6]. The PCA and PCAmix results ( Figure 3) are in agreement with the three genetic groups.…”

“…All plants were clones of local varieties collected throughout the major islands of Vanuatu and were grown in a common field to minimize variation due to environmental factors. Following a previous DNA classification done using SSR and DArT markers [6], accessions were grouped in three genotype clusters): noble (N), two-day (TD) and wichmannii (W) varieties. After harvest, roots and peeled rhizomes were washed by hand under cold running water and cut into small pieces with a knife.…”

“…As the data was not following a normal distribution after being tested with Shapiro-Wilk, Anderson-Darling, Lilliefors, and Jarque-Bora tests (p < 0.0001), non-parametric tests were applied to test the variance (Kruskal-Wallis and Friedman tests for k samples). The quantitative peak areas for nine compounds (variables, 6KLs + 3FKs) were combined with a qualitative variable corresponding to the genotype group defined using DNA markers: N = nobles, TD = two-day, W = wichmannii [6] and the mixed data matrix was analyzed with ExcelStat™ using the factorial analysis of mixed data called PCAmix. This analysis can be seen as a mixture of PCA (Principal Component analysis) and MCA (Multiple Correspondence Analysis) which allows the study of qualitative variables.…”

“…wichmannii) and "two-day" varieties, known for their lasting effect causing nausea and hangover, are illegal [5]. DNA markers studies have shown that these varieties correspond to three distinct groups of genotypes [6].…”

Dynamic quantification of canopy structure to characterize early plant vigour in wheat genotypes

“…The traditional phenotyping technologies are time-consuming and expensive with anthropogenic interference ( Richards and Lukacs, 2002 ; Bertin et al , 2010 ). Breeders have to select new genotypes more efficiently for target population environments to secure food requirement in the future as it takes 7–15 years for a breeding cycle ( Chapman et al , 2012 ; Zheng et al , 2013 ), and crop production must double by 2050 to meet the global population demand ( Chilcoat, 2015 ). Consequently, there is now greater interest in developing rapid and non-destructive technologies for high-throughput phenotyping (e.g.…”