Abstract
BackgroundQinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. In order to provide basic data for selection and optimization of molecular markers of tea plants. 118 markers, including 40 EST-SSR, 40 SRAP and 38 SCoT markers were used to evaluate the genetic diversity of 50 tea plant (Camellia sinensis.) samples collected from Qinb. tea germplasm, assess population structure.ResultsIn this study, a total of 414 alleles were obtained using 38 pairs of SCoT primers, with an average of 10.89 alleles per primer. The percentage of polymorphic bands (PPB), polymorphism information content (PIC), resolving power (Rp), effective multiplex ratio (EMR), average band informativeness (Ibav), and marker index (MI) were 96.14%, 0.79, 6.71, 10.47, 0.58, and 6.07 respectively. 338 alleles were amplified via 40 pairs of SRAP (8.45 per primer), with PPB, PIC, Rp, EMR, Ibav, and MI values of 89.35%, 0.77, 5.11, 7.55, 0.61, and 4.61, respectively. Furthermore, 320 alleles have been detected using 40 EST-SSR primers (8.00 per primer), with PPB, PIC, Rp, EMR, Ibav, and MI values of 94.06%, 0.85, 4.48, 7.53, 0.56, and 4.22 respectively. These results indicated that SCoT markers had higher efficiency.Mantel test was used to analyze the genetic distance matrix generated by EST-SSRs, SRAPs and SCoTs. The results showed that the correlation between the genetic distance matrix based on EST-SSR and that based on SRAP was very small (r = 0.01), followed by SCoT and SRAP (r = 0.17), then by SCoT and EST-SSR (r = 0.19).The 50 tea samples were divided into two sub-populations using STRUCTURE, Neighbor-joining (NJ) method and principal component analyses (PCA). The results produced by STRUCTURE were completely consistent with the PCA analysis. Furthermore, there is no obvious relationship between the results produced using sub-populational and geographical data.ConclusionAmong the three types of markers, SCoT markers has many advantages in terms of NPB, PPB, Rp, EMR, and MI. Nevertheless, the values of PIC showed different trends, with the highest values generated with EST-SSR, followed by SCoT and SRAP. The average band informativeness showed similar trends. Correlation between genetic distances produced by three different molecular markers were very small, thus it is not recommended to use a single marker to evaluate genetic diversity and population structure. It is hence suggested that combining of different types of molecular markers should be used to evaluate the genetic diversity and population structure. It also seems crucial to screen out, for each type of molecular markers, core markers of Camellia sinensis. This study revealed that genes of exotic plant varieties have been constantly integrated into the gene pool of Qinba area tea. A low level of genetic diversity was observed; this is shown by an average coefficient of genetic similarity of 0.74.
Highlights
Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown
38 Start codon targeted polymorphism (SCoT), 40 Sequence-related amplified polymorphism (SRAP) and 40 Expressed sequence tags-Simple sequence repeats (EST-SSR) primers were selected for further studies according to the percentage of polymorphic bands (PPB), polymorphism information content (PIC) and the degree of clear band selected markers using six selected genotypes (Table 1)
Different molecular markers and different primers of the same marker all yielded distinct amplification products, which reflected the polymorphism of the genomic regions; utilization of different marker designing strategies will produce different results
Summary
Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. 118 markers, including 40 EST-SSR, 40 SRAP and 38 SCoT markers were used to evaluate the genetic diversity of 50 tea plant (Camellia sinensis.) samples collected from Qinb. SCoT (Start codon targeted polymorphism) marker was designed according to the Kozak sequence pattern and was developed after the discovery of the conservativeness of the initiation codon ATG (+ 1, + 2, + 3) flanking sequences, in which the positions + 4, + 7, + 8, and + 9 are occupied by nucleotides G, A, C, and C, respectively. Tea plant is an allogamous species; theoretically, after prolonged spontaneous hybridization, the genetic background of tea plant should be increasingly complex
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
