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. 2020 Oct 2;6(10):e05078.
doi: 10.1016/j.heliyon.2020.e05078. eCollection 2020 Oct.

The genetic relationships of Indian jujube (Ziziphus mauritiana Lam.) cultivars using SSR markers

Chu-Ying Chiou  1 , Huei-Chuan Shih  2 , Chi-Chu Tsai  1   3 , Xiao-Lei Jin  4 , Ya-Zhu Ko  4 , Junaldo A Mantiquilla  4   5 , I-Szu Weng  1 , Yu-Chung Chiang  4   6
Affiliations

The genetic relationships of Indian jujube (Ziziphus mauritiana Lam.) cultivars using SSR markers

Chu-Ying Chiou et al. Heliyon. .

Abstract

The genetic relationships among 24 Indian jujube cultivars (Ziziphus mauritiana Lam.) were evaluated by genotyping the microsatellite loci using simple sequence repeat (SSR) markers. The SSR loci were scored by fluorescent labelling and automated detection systems for the high-throughput capillary electrophoresis and high-resolution gel electrophoresis. Out of the 29 newly characterized SSR loci, 26 were considered as polymorphic with a total of 181 alleles obtained. The number of alleles ranged from 2-12, while the polymorphism information content ranged from 0.08-0.83, and the expected and observed heterozygosity were 0.04-0.83 and 0.04-0.82, respectively. The allele pattern of Indian jujube for all SSR loci confirmed its karyotype as tetraploid. Similarity coefficients and UPGMA dendrogram revealed that the Taiwanese cultivars consisted of a large 'A' clade, which is further divided into 'A1' and 'A2' groups, and the 'B' clade where both are rooted by the wild accession, 'Chad native'. These four genetic clusters were supported by the results of PCoA and the assignment test. The excess of heterozygotes based on F-statistics was attributed to its mating system as outcrossing and self-incompatible, and the introgression of the presumed mutation-derived cultivars with genetic admixture. Based on this study, SSR markers offer valuable information on the genetic relationship of this tropical fruit tree which is basically in agreement with the genealogy of its breeding history.

Keywords: Biodiversity; Crop breeding; DNA barcoding; Genetic diversity; Genetic structure; Horticulture; Microsatellite DNA; Plant biology; Plant genetics; Ziziphus mauritiana.

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Figures

Figure 1
Figure 1
J181 SSR locus analysis of polymorphism in 24 Indian jujube cultivars. M: DNA marker. Lanes 1–24 represent different cultivars (see Table 1).
Figure 2
Figure 2
J58 SSR locus analysis of polymorphism in 24 Indian jujube cultivars. M: DNA marker. Lanes 1–24 represent different cultivars (see Table 1).
Figure 3
Figure 3
Dendrogram showing the genetic relationships among 24 Indian jujube cultivars using SSR markers. Scale bar represents the genetic distance.
Figure 4
Figure 4
The PCoA analysis performed by POLYSAT based on 29 microsatellite loci from 24 strains of Ziziphus mauritiana Lam. (A) The PCoA plot with the Chad-native strain. (B) The PCoA plot without the Chad-native strain.
Figure 5
Figure 5
Plots of (A) the log likelihood and ΔK and (B) the best clustering at K = 4 estimated by the program Structure analysis of the full data set of 24 strains of Ziziphus mauritiana Lam. The vertical lines represent the 24 strains.
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