Isolation and Characterization of Microsatellite Markers and Analysis of Genetic Diversity in Chinese Jujube (Ziziphus jujuba Mill.)

Abstract

Chinese jujube (Ziziphus jujuba Mill, 2n = 2× = 24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba ‘Dongzao’ using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for ‘Dongzao’. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars.

Genetic Diversity and Population Structure of Toona Ciliata Roem. Based on Sequence-Related Amplified Polymorphism (SRAP) Markers

“…The PPB was 77.10% in this study, indicating a certain degree of genetic variation among populations. For the PIC, when the PIC > 0.5, 0.25 < PIC < 0.5, or the value < 0.25, loci polymorphism could be classified as high, medium, or low, respectively [31][32][33]. In this study, Me35Em32 was the most informative primer combination for genetic diversity studies among T. ciliata.…”

“…The highest PIC value, 0.45, was obtained for Me35Em32 combination, followed by 0.44 for Me23Em22 and Me27Em7, and 0.43 for Me31Em24, Me32Em17, Me39Em32 and Me43Em19. The primer combinations with the higher PIC values could be used to develop a rapid detection method [31][32][33]. The primer combination Me17Em27 had the lowest PIC value of 0.32.…”

Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers

“…Shannon's information index can indicate the level of genetic diversity; a higher value indicates greater genetic diversity (Wang et al, 2014b). For the 94 oil palm lines, the average I was 0.6565, indicating various levels of genetic diversity.…”

Molecular markers and their application for DNA fingerprinting and genetic diversity studies in Coffea species Marka molekuler dan penerapannya untuk studi sidik jari DNA dan keragaman genetik pada spesies Coffea

“…Moreover, they are valuable genetic markers because of their multi-allelic nature, and they are abundant, variable, and easy to genotype. Compared with RFLP, SSR markers are easier to handle, cheaper to use, suitable for automation, and high reproducible (Wang et al, 2014). Therefore SSR could be used for high throughput genotyping.…”