Assessment of genetic diversity in different geographically isolated Alhagi graecorum Boiss. populations using SCoT marker

The genetic diversity of 39 Iranian black cumin (Nigella sativa L.) landraces was analysed using 14 polymorphic Start Codon Targeted (SCoT) markers. A total of 106 bands ranging from 3 (for SCoT70) to 13 (for SCoT23) were observed. Of them, 33 (31%) bands were polymorphic with a mean of 1.65 bands per primer. Polymorphism information content (PIC) per primer ranged from 0.035 (for SCoT12) to 0.133 (for SCoT70), with an average of 0.078. Besides PIC, Simpson's diversity (D) index was also calculated for each SCoT marker as an indication of discrimination power across population. The D index was used to adjust the PIC of the SCoT markers. As the adjusted PIC (PICD= PIC × D) was calculated based on both the PIC and the rate of band dispersion, this reflected the informativeness of a dominant marker more precisely than PIC. Genetic relationships were estimated using Jaccard's similarity coefficient-generated values between different pairs of genotypes that varied from 80 to 97% with an average of 88%. These coefficients were applied to construct a dendrogram using the UPGMA algorithm. A high genetic similarity was observed that might be due to the fact that N. sativa is a self-pollinated plant not originated from Iran and might have been imported from the Mediterranean regions.

Download Full-text

Gene-Targeted markers to assess genetic diversity and population structure within Tunisian Phoenix dactylifera L. cultivars

Silvae Genetica ◽

10.2478/sg-2020-0005 ◽

2020 ◽

Vol 69 (1) ◽

pp. 29-35

Author(s):

Rhouma-Chatti Soumaya ◽

Choulak Sarra ◽

Moussa Maha ◽

Chatti Khaled ◽

Chatti Noureddine

Keyword(s):

Genetic Diversity ◽

Date Palm ◽

Gene Diversity ◽

Phoenix Dactylifera ◽

Start Codon ◽

Marker System ◽

Average Value ◽

Information Index ◽

Scot Marker ◽

Phoenix Dactylifera L

AbstractGenetic variability in date palm genotypes collected from different regions of southern Tunisia was analyzed using a Start Codon Targeted (SCoT) marker system. Thirty-one accessions collected from three locations were investigated. One hundred and nine amplicons were produced among which 84 % were polymorphic. The PIC value and the Rp values testified of the efficiency of used primers. The percentage of polymorphic loci (Pp) varied from 44.57 to 83.70 %, Nei‘s gene diversity (H) from 0.175 to 0.273 with a mean of 0.228, and Shannon‘s information index (I) values ranging from 0.257 to 0.409 with an average value of 0.338 were illustrated. The Tunisian date palm populations exhibited high genetic differentiation (GST = 0.319) and gene flow (Nm = 1.063). The AMOVA analysis presented 70 % of the variation within the population and 30 % of the variation between them. Phylogenetic analysis and the Bayesian clustering approach also revealed high genetic variation among genetic variants with a net divergence of the wild insular population of Kerkennah from other cultivars. The present investigation suggests the effectiveness of the SCoT marker system to estimate the genetic diversity of Phoenix dactylifera genotypes.

Download Full-text

Start codon targeted (SCoT) polymorphism reveals genetic diversity of Manilkara in Thailand

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210232 ◽

2020 ◽

Vol 21 (2) ◽

Author(s):

Ongkarn Vanijajiva

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Genetic Improvement ◽

Morphological Characters ◽

Start Codon ◽

Similarity Coefficients ◽

Scot Marker ◽

Marker Analysis ◽

Dna Profiles ◽

Relationship Of

Abstract. Vanijajiva O. 2020. Start codon targeted (SCoT) polymorphism reveals genetic diversity of Manilkara in Thailand. Biodiversitas 21: 666-673. Manilkara consists of four species, namely, Manilkara hexandra, M. kauki, M. littoralis, and M. zapota in Thailand. Particularly, M. zapota (sapodilla), commonly known as Lamut in Thailand, is one of commercially notable edible fruits continues to be a highly valued tree and the fruits are a source of food and income. The objective of this research was to determine the diversity and relationship of Manilkara accessions derived from districts in Thailand based on DNA profiles. Genetic diversity and relationship of all accessions were investigated using Start Codon Targeted (SCoT) marker analysis. Of 30 SCoT primers screened, 27 SCoT primers were identified to be polymorphism. A total of 176 DNA bands with size varied from 120 bp to 1200 bp were amplified, and 101 (57.38%) of them were polymorphic. Based on similarity coefficients, total of 36 accessions were clustered into two groups. The cluster of polymorphism generated by SCoT was associated with their locality and morphological characters. Therefore, the present data provide high-valued information for the management of germplasm, genetic improvement, and conservation of the genetic resources of Manilkara accessions.

Download Full-text