Cross genera transferability of microsatellite markers from other members of family Bignoniaceae to Tecomella undulata (Sm.) Seem

Kalia, Rajwant K.; Chhajer, Sidhika; Pathak, Rakesh

doi:10.1007/s11738-020-03138-5

Cited by 2 publications

(2 citation statements)

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“…In the present study, the transferability observed (9.05%) was similar to the average of approximately 10% reported in cross-genera transferability studies of eudicots between 1997 and mid-2006 ( Barbará et al, 2007 ). However, the percentage transferability determined here was lower than the cross-genera amplification percentage observed in some families, such as Bignoniaceae (40.58%) ( Kalia et al, 2020 ) and Cactaceae (35.16%) ( Bombonato et al, 2019 ), and much lower than that between species within the same genus ( Miranda et al, 2020 ; Pern et al, 2020 ; Li et al, 2021 ). The transferability of SSR markers between species or genera is determined by the conservation of DNA sequences and the stability of primer binding sites in flanking regions of SSRs during evolution ( Ellegren, 2000 ; Saeed et al, 2016 ).…”

Section: Discussioncontrasting

confidence: 76%

“…One reason might be that the selection of frameshift mutations limits the fixation of microsatellites whose motif lengths are not divisible by three (e.g., di-/tetra-/pentanucleotide repeats), whereas fixation of mutant microsatellite whose motif lengths are divisible by three (tri-/hexanucleotide repeats) is not affected by differential selection pressures in coding and non-coding regions ( Metzgar et al, 2000 ; Dutta et al, 2011 ; Shivakumar et al, 2017 ). Moreover, microsatellites based on a complex nucleotide sequence show a lower mutation rate and higher transferability than simple repeats ( Jin et al, 1996 ; Kalia et al, 2020 ). Given that more than 63% of the SSR markers used in the present study were di-nucleotide motif repeats, this may be an additional reason for the low transferability.…”

Section: Discussionmentioning

confidence: 99%

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Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

et al. 2022

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Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (NA), expected heterozygosity (HE), and Shannon’s information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (Nm = 1.252) and high genetic differentiation (Fst = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.

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Section: Discussioncontrasting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

et al. 2022

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Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

Gutiérrez

Filippi

Aguirre

et al. 2021

An. Acad. Bras. Ciênc.

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The Cactaceae family is native to the American continent with several centers of diversity. In South America, one of these centers is the Central Andes and many species are considered to be threatened or vulnerable according to the International Union for Conservation of Nature (IUCN). Stetsonia coryne is an emblematic giant columnar cacti of the Chaco phytogeographic province. It has an extensive geographical distribution in many countries of the continent. However, to date there are no specifi c molecular markers for this species, neither reports of population genetic variability studies, such as for many cactus species. The lack of information is fundamentally due to the lack of molecular markers that allow these studies. In this work, by applying a Genotyping by Sequencing (GBS) technique, we developed polymorphic SSR markers for the Stetsonia coryne and evaluated their transferability to phylogenetically close species, in order to account for a robust panel of molecular markers for multispecies-studies within Cactaceae.

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Cross genera transferability of microsatellite markers from other members of family Bignoniaceae to Tecomella undulata (Sm.) Seem

Cited by 2 publications

References 35 publications

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers

Development of novel SSR molecular markers using a Next-Generation Sequencing approach (ddRADseq) in Stetsonia coryne (Cactaceae)

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