KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping

Comparing genetic differentiation and variation using ISSR and SCoT among Juniper plant markers in Saudi Arabia

Juniperus, a genus of fragrant evergreen trees in the Cupressaceae family, encompasses up to 67 distinct species distributed globally. Among these, Juniperus procera, also known as the East African pencil cedar or African Juniper, stands out for its notable medicinal properties. Due to the well-recognized therapeutic benefits of Juniper species, assessing genetic diversity is essential for various breeding initiatives. Thus, in this work, six ISSR and six SCoT primers were utilized to evaluate the genetic diversity between 23 Juniper genotypes collected from different locations in Saudi Arabia. 29 out of 103 and 26 out of 105 amplified bands, respectively, were found to be polymorphic markers using the ISSR and SCoT studies. With the help of 120 genotype-specific markers, including 60 for ISSR and 60 for SCoT, several varieties of Juniper were discovered. In addition, the polymorphism information content (PIC) was computed to assess the effectiveness of the markers. The findings of this study highlight the importance of conserving the genetic diversity of Juniperus procera, as it holds immense potential for developing new medicinal products. Additionally, the results provide valuable insights into the genetic structure of Juniper populations in western Saudi Arabia, which can inform future conservation and management efforts. However, all of the techniques utilized to profile the genotypes of Juniper can be regarded as useful techniques for long-term fingerprinting and diagnostic markers.

Designing Allele-Specific Competitive-Extension PCR-Based Assays for High-Throughput Genotyping and Gene Characterization

Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation in basic research applications, agriculture, and medicine. Variants of PCR, collectively known as allele-specific PCR (AS-PCR), use a competitive reaction in the presence of allele-specific primers to preferentially amplify only certain alleles. This method, originally named by its developers as Kompetitive Allele Specific PCR (KASP), is an AS-PCR variant adapted for fluorescence-based detection of amplification results. We developed a bioinformatic tool for designing probe sequences for PCR-based genotyping assays. Probe sequences are designed in both directions, and both single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) may be targeted. In addition, the tool allows discrimination of up to four-allelic variants at a single SNP site. To increase both the reaction specificity and the discriminative power of SNP genotyping, each allele-specific primer is designed such that the penultimate base before the primer's 3' end base is positioned at the SNP site. The tool allows design of custom FRET cassette reporter systems for fluorescence-based assays. FastPCR is a user-friendly and powerful Java-based software that is freely available (http://primerdigital.com/tools/). Using the FastPCR environment and the tool for designing AS-PCR provides unparalleled flexibility for developing genotyping assays and specific and sensitive diagnostic PCR-based tests, which translates into a greater likelihood of research success.

Genome-wide microsatellites in amaranth: development, characterization, and cross-species transferability

Amaranth (Amaranthus spp.) belonging to Amaranthaceae, is known as "the crop of the future" because of its incredible nutritional quality. Amaranthus spp. (> 70) have a huge diversity in terms of their plant morphology, production and nutritional quality; however, these species are not well characterized at molecular level due to unavailability of robust and reproducible molecular markers, which is essential for crop improvement programs. In the present study, 13,051 genome-wide microsatellite motifs were identified and subsequently utilized for marker development using A. hypochondriacus (L.) genome (JPXE01.1). Out of those, 1538 motifs were found with flanking sequences suitable for primer designing. Among designed primers, 225 were utilized for validation of which 119 (52.89%) primers were amplified. Cross-species transferability and evolutionary relatedness among ten species of Amaranthus (A. hypochondriacus, A. caudatus, A. retroflexus, A. cruentus, A. tricolor, A. lividus, A. hybridus, A. viridis, A. edulis, and A. dubius) were also studied using 45 microsatellite motifs. The maximum (86.67%) and minimum (28.89%) cross-species transferability were observed in A. caudatus and A. dubius, respectively, that indicated high variability present across the Amaranthus spp. Total 97 alleles were detected among 10 species of Amaranthus. The averages of major allele frequency, gene diversity, heterozygosity and PIC were 0.733, 0.347, 0.06, and 0.291, respectively. Nei's genetic dissimilarity coefficients ranged from 0.0625 (between A. tricolor and A. hybridus) to 0.7918 (between A. viridis and A. lividus). The phylogenetic tree grouped ten species into three major clusters. Genome-wide development of microsatellite markers and their transferability revealed relationships among amaranth species which ultimately can be useful for species identification, DNA fingerprinting, and QTLs/gene(s) identification.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02930-5.

Molecular Assessment of Genetic Stability Using CDDP and DNA-barcoding Assays in Long-term Micropropagated Rose Plant

BACKGROUND AND OBJECTIVE

Roses are the world's best-known garden plants, established as ornamental plants cultivated for their blooms. Taif rose (Rosa damascena trigintipetala) refers to the Damascus Rose species and is regarded one of Taif Governorate's most significant financial goods, which produces an extremely fragrant commercially precious essential oil. The objective of current study was to assess the genetic stability of micropropagated Taif rose and to assess the usefulness of Conserved DNA Derived Polymorphism (CDDP) and DNA-barcoding genes such as; rpoC1 (chloroplast gene RNA polymerase1) in the detection of somaclonal variation.

MATERIALS AND METHODS

Ten combinations of CDDP PCR primers were employed and the rpoC1 gene region was sequenced for mother plant (control) and micropropagated plantlets of Taif rose plant.

RESULTS

Based on CDDP data, phylogenetic divergence indicated that the distinct specimens of Taif rose micro-propagated plantlets and control were genetically differentiated by a difference of 1% of genetic dissimilarity. Phylogenetic tree which developed using rpoC1 DNA showed that rpoC1 DNA sequencing discovered a genetic difference between the control and micro-propagated plantlets of Taif rose.

CONCLUSION

Furthermore, CDDP and DNA barcoding using rpoC1 gene have demonstrated their usefulness in investigating the genetic history of Rosa species and their ability to explore genetic mutation.

DNA Fingerprinting of <i>in vitro</i> Micropropagated Pomegranate Genotypes

BACKGROUND AND OBJECTIVE

Pomegranate is grown for its rich flavour in numerous tropical and subtropical areas, like Egypt and the Kingdom of Saudi Arabia (KSA). Assessing the genetic background of the pomegranate is the key to its expansion through the Middle East, where tissue culture reproduction strategies could be used to solve environmental and economic problems. This study aimed at studying the genetic stability of 2 pomegranate genotypes in vitro micro-propagated in the Kingdom of Saudi Arabia by using the random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) and inter simple sequence repeats (ISSR) tools.

MATERIALS AND METHODS

The two above mentioned molecular tools were used to evaluate the DNA fingerprints of Taify and Yemeni pomegranate genotypes 12 weeks post in vitro propagation in Taif, Kingdom of Saudi Arabia compared to the mother plant. Shoot tip explants of 4-5 cm long were grown on Murashige and Skoog (MS) medium supplemented by 1.0 mg L-1 NAA, 2.00 mg L-1 IBA and 2 g L-1 activated carbon for 4 weeks for rooting. On 12 weeks DNA extracts were prepared from the acquired plantlets obtained and used as templates for each of RAPD-PCR and ISSR tools.

RESULTS

The RAPD-PCR and ISSR assays generated a total of 79-94 and 57-72 DNA fragments, respectively. In case of RAPD-PCR 80 and 90% of the primers used and developed monomorphic fragments of the Yemeni and Taify genotypes, respectively, particularly OPG08 primer for Taify genotype and OPA04 and OPD07 primers for the Yemeni genotype. Regarding ISSR, no DNA polymorphic for the micropropagated clones were recorded compared to the mother plant.

CONCLUSION

The ISSR assay's findings indicated the genetic homogeneity between the in vitro micropropagated clones of both pomegranate genotypes and the mother plants.

Suadian Acacia Gerrardii: Antidiabetic Effect in Rats Suffering from Diabetic Nephropathy and DNA Fingerprinting Using ISSR

BACKGROUND AND OBJECTIVE

There is a widespread use of medicinal herbs with beneficial uses against different diseased conditions. This study was carried out to identify and study the biological effect of Acacia gerrardii leaf extract on lowering blood sugar in rats suffering from diabetic nephropathy.

MATERIALS AND METHODS

It studied the effects of leaf extract at concentrations ranging from 100-500 mg kg-1 b.wt. per day for 4 weeks. Serum glucose levels, total lipids profile and kidney functions were estimated. Plasma levels of sodium and potassium as well as total bilirubin levels were assessed and kidneys from different groups were histopathologically examined.

RESULTS

The results showed that leaves were rich in the major compounds of phenolic acids, including salicylic acid and flavonoids with reduction of total lipids, triglycerides and total cholesterol in diabetic rats with renal failure together with reduction in uric acid, creatinine and urea with reduced vacuolar degeneration of tubules and basement membrane thickening. Additionally, the phylogenetic analysis using ISSR primers detected a genetic divergence among different samples. The results showed that the rich antioxidant content of Acacia gerrardii improved lipid, serum antioxidant and kidney function profiles in diabetic rats.

CONCLUSION

Acacia gerrardii could be used as a safe source of antioxidants. Moreover, the ISSR assay proved its usefulness in detecting genetic variations among different Acacia gerrardii samples.