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

Chu-Ying Chiou; Huei-Chuan Shih; Chi-Chu Tsai; Xiao-Lei Jin; Ya-Zhu Ko; Junaldo A Mantiquilla; I-Szu Weng; Yu-Chung Chiang

doi:10.1016/j.heliyon.2020.e05078

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

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

Authors

Chu-Ying Chiou¹, Huei-Chuan Shih², Chi-Chu Tsai^{1

3}, Xiao-Lei Jin⁴, Ya-Zhu Ko⁴, Junaldo A Mantiquilla^{4

5}, I-Szu Weng¹, Yu-Chung Chiang^{4

6}

Affiliations

¹ Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan.
² Department of Nursing, Meiho University, Pingtung 912, Taiwan.
³ National Pingtung University of Science and Technology, Pingtung 912, Taiwan.
⁴ Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
⁵ Department of Biological Sciences and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Mintal, Davao City 8022, Philippines.
⁶ Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.

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.