SCoT molecular markers and genetic fingerprinting of date palm (Phoenix dactylifera L.) cultivars

Saboori, Somayeh; Noormohammadi, Zahra; Sheidai, Masoud; Marashi, S H

doi:10.1007/s10722-019-00854-x

Cited by 39 publications

(24 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Private alleles present in populations are useful for conservation and utilization of plant germplasm resources (Kalinowski 2004 ; Lee et al 2020 ). In our study, the highest number of private alleles was observed in LVC population (private bands = 11), followed by JP population (private bands = 6), more number of private bands indicates the presence of specific genes or sequences in both populations (Saboori et al 2020 ). The JP and LVC populations showed much higher diversity parameters, and those two populations are located at the southeast of the Yunnan Province—a traditional A. tsao-ko growing region.…”

Section: Discussionmentioning

confidence: 54%

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Wang

2021

Genet Resour Crop Evol

View full text Add to dashboard Cite

Amomum tsao-ko Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of A. tsao-ko grown in Southwest China were examined using sequencerelated amplified polymorphism (SRAP) and intersimple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of A. tsao-ko mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for A. tsao-ko germplasm characterization, conservation, and utilization.

show abstract

Section: Discussionmentioning

confidence: 54%

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Wang

2021

Genet Resour Crop Evol

View full text Add to dashboard Cite

show abstract

“…A combination of stable morphological characters and molecular markers may be used in date palm genetic diversity studies and discrimination among closely related date palm cultivars and clones (Johnson et al 2015). Different molecular markers (neutral, multilocus and DNA-sequence based markers) have been utilized in date palm genetic diversity investigations as well as cultivar phylogeny analyses (see for example, Sharifi et al 2018, Saboori et al 2019, Saboori et al 2020). Among these molecular markers, the nuclear microsatellite markers (simple sequence repeat, SSRs) are known to be precise and accurate in genetic finger printing of date palm cultivars (Ahmed et al, 2013, Johnson et al 2015, Zehdi-Azouzi.…”

Section: Introductionmentioning

confidence: 99%

Genetic (SSRs) versus morphological differentiation of date palm cultivars: Fst versus Pst estimates

et al. 2021

Self Cite

View full text Add to dashboard Cite

Date Palm (Phoenix dactylifera L.) is one of the oldest domesticated fruit trees. For future breeding program, knowledge on genetic structure of cultivars is necessary. Therefore, the present study was performed with the following aims: 1- To provide data on genetic diversity and genetic structure of 36 date palm cultivars, 2- To provide data on the association between fruit characteristics and the genetic features of the cultivars. We used nine SSRs and EST-SSR loci for our genetic investigation. The most of SSR loci obtained have a high Gst value (0.70), and therefore have a good discrimination power for date palm cultivar differentiation task. K-Means clustering grouped date palm cultivars either in two broad clusters, or in 16 smaller genetic groups. This was supported by delta K = 2 of the STRUCTURE analysis. AMOVA produced significant genetic difference among date palm cultivars (PhiPT = 0.70, P = 0.001). New genetic differentiation parameters estimated also produced significant difference among date palm cultivars (G’st(Nei) = 0.673, P =0.001; G’st(Hed) = 0.738, P = 0.001). Test of assignment revealed that some of the cultivars have 33-66% misassignment, probably due to genetic admixture. Heatmaps of genetic versus morphological/or agronomical characters in date palm cultivars differed from each other showing the cultivars morphological changes is not merely related to their genetic content. It points toward the potential role played either by environmental conditions or local selection practice. The new findings can be utilized in future conservation and breeding of date palms in the country.

show abstract

“…Compared with random ampli ed polymorphic DNA (RAPD), ampli ed fragment length polymorphism (AFLP), SSR, and ISSR markers, SCoT markers have been e ciently produced and linked to traits, making them convenient for use in molecular markerassisted breeding. SCoT markers have been used in various plant species, such as Phoenix dactyifera (Somayeh Saboori et al 2020), Mangifera indica (Li Zhou et al 2020) and Diospyros spp. (Changfei Guana et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Analysis of Genetic Diversity in Prunus Sibirica L. in Inner Mongolia Using SCoT Molecular Markers

Habuer

Sarula

Yuan

et al. 2021

Preprint

View full text Add to dashboard Cite

Population genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 97.94% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT3 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of Prunus sibirica in Inner Mongolia. The analysis of molecular variance (AMOVA) showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic (UPGMA) cluster analysis, principal coordinate analysis (PCoA) and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of Prunus sibirica in Inner Mongolia can provide a reference for Prunus sibirica variety breeding and resource development.

show abstract

SCoT molecular markers and genetic fingerprinting of date palm (Phoenix dactylifera L.) cultivars

Cited by 39 publications

References 16 publications

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers

Genetic (SSRs) versus morphological differentiation of date palm cultivars: Fst versus Pst estimates

Analysis of Genetic Diversity in Prunus Sibirica L. in Inner Mongolia Using SCoT Molecular Markers

Contact Info

Product

Resources

About