EST-SSR analysis of genetic diversity of Psammosilene tunicoides in Yunnan- Guizhou provincial region / 中草药

Objective To analyze the genetic diversity and variation of Psammosilene tunicoides in Yunnan-Guizhou provincial region. Methods The genetic diversity of different populations of P. tunicoides with high polymorphism was analyzed by using EST-SSR primers developed from transcriptomic sequencing technique. Results A total of 17 530 SSR-containing EST sequences were obtained by transcriptomic sequencing, 14 pairs of polymorphism EST-SSR primers were used to analyze the genetic diversity of 17 populations of P. tunicoides in Yunnan-Guizhou region, the results showed that the P. tunicoides in different populations had a high level of genetic diversity with the polymorphic information content (PIC) in the range from 0.350 0 to 0.795 0 in locus level; and had a lower value in group level with percentage of polymorphic bands (PPB) of 64.29%-100%. And the range of Nei’s genetic similarity coefficient was from 0.188 2 to 0.477 7 with mean value of 0.323 2. The gene flow in P. tunicoides in Yunnan-Guizhou region was small with Nm mean value of 0.302 0, and there is a large genetic differentiation between groups with Fst mean value of 0.452 9. Conclusion Transcriptomic sequencing enriched P. tunicoides EST database. The genetic diversity of P. tunicoides might be related to the long evolutionary history of reproductive pattern and distribution area. And there was a highly genetic diversity among the populations of P. tunicoides in Yunnan-Guizhou region, it might be that the geographic barrier cut off the genes exchange among different populations.

Development, characterization and use of genomic SSR markers for assessment of genetic diversity in some Saudi date palm (Phoenix dactylifera L. ) cultivars

Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm (Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia. Results: Ninety-three novel simple sequence repeat markers were developed and screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs were dinucleotide, 25% tri, 3% tetra and 1% penta nucleotide motives. Twenty-two primers generated a total of 91 alleles with a mean of 4.14 alleles per locus and 100% polymorphism percentage. A 0.595 average polymorphic information content and 0.662 primer discrimination power values were recorded. The expected and observed heterozygosities were 0.676 and 0.763 respectively. Pair-wise similarity values ranged from 0.06 to 0.89 and the overall cultivars averaged 0.41. The UPGMA cluster analysis recovered by principal coordinate analysis illustrated that cultivars tend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) revealed that genetic variation among and within cultivars were 27% and 73%, respectively according to geographical distribution of cultivars. Conclusions: The developed microsatellite markers are additional values to date palm characterization tools that can be used by researchers in population genetics, cultivar identification as well as genetic resource exploration and management. The tested cultivars exhibited a significant amount of genetic diversity and could be suitable for successful breeding program. Genomic sequences generated from this study are available at the National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).

Comparison of PCR based marker systems for genetic analysis in different cultivars of mango.

Native diversity is well represented in northern and eastern parts of India for mango. We evaluated three important polymerase chain reaction (PCR) based marker techniques viz., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplified mini satellite DNA (DAMD) and examined their suitability for depicting genetic relationships and discrimination among closely related group of 46 mango varieties grown in the different agro-ecological zones in Uttar Pradesh, Bihar and West Bengal. Nine RAPD, eleven ISSR and four DAMD primers generated 110, 160 and 43 discrete fragments, respectively, accounting for polymorphism of 87.3, 79.83 and 83.72%, respectively. Cumulative analysis of these markers resulted in comprehensive UPGMA based dendrogram where in native mangoes representing important breeding lines and varieties from Uttar Pradesh fall more or less in separate cluster, while Bihar and West Bengal cultivars represent genetically different lineage forming distinct separate cluster. The prime focus on the study was towards identification of genetic variability that warrants establishing origin and molecular evolution of mango cultivars of eastern and northern India because they are the rich gene pool for conservation. Highest diversity index (DI) and polymorphic information content (PIC) values were found in DAMD indicating it to be more informative than others. Similarly, high effective multiplex ratio (EMR) and marker index (MI) were recorded by ISSR reflecting ability to simultaneously detect a large number of bands. The study accomplished establishing genetic relationship and also DNA fingerprint development. The data is also useful for mapping studies for gene identification.