Dataset Information

Development of SSR markers by 454 sequencing in the endemic species Gentianella praecox subsp. bohemica (Gentianaceae).

ABSTRACT: PREMISE OF THE STUDY:Polymorphic microsatellite loci were developed and used to genotype individuals of Gentianella praecox subsp. bohemica (Gentianaceae), a highly protected taxon in Europe, to study the genetic structure of the remaining populations. METHODS AND RESULTS:Thirty-eight primer pairs were successfully amplified; of these, 12 polymorphic microsatellite loci were developed using a 454 sequencing approach and used to genotype 180 individuals of G. praecox subsp. bohemica from six populations. Allelic richness ranged between one and nine alleles per locus. We detected a high frequency of polyploid individuals (77.8%). The highest average percentage of heterozygous genotypes was identified for samples from the Hroby population (75.5%). All loci can also be amplified in the congeneric species G. praecox subsp. praecox, G. amarella subsp. amarella, and G. obtusifolia subsp. sturmiana. CONCLUSIONS:These markers will provide knowledge on patterns of gene flow and population genetic structure, which is necessary for current protection actions and for effective conservation of this species in the future.

SUBMITTER: Surinova M

PROVIDER: S-EPMC5231916 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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Development of SSR markers by 454 sequencing in the endemic species <i>Gentianella praecox</i> subsp. <i>bohemica</i> (Gentianaceae).

Šurinová Mária M Brabec Jiří J Münzbergová Zuzana Z

Applications in plant sciences 20170105 1

<h4>Premise of the study</h4>Polymorphic microsatellite loci were developed and used to genotype individuals of <i>Gentianella praecox</i> subsp. <i>bohemica</i> (Gentianaceae), a highly protected taxon in Europe, to study the genetic structure of the remaining populations.<h4>Methods and results</h4>Thirty-eight primer pairs were successfully amplified; of these, 12 polymorphic microsatellite loci were developed using a 454 sequencing approach and used to genotype 180 individuals of <i>G. praec ...[more]

PMID: 28090411

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Project description:Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.

Dataset Information

Development of SSR markers by 454 sequencing in the endemic species Gentianella praecox subsp. bohemica (Gentianaceae).

Publications

Development of SSR markers by 454 sequencing in the endemic species <i>Gentianella praecox</i> subsp. <i>bohemica</i> (Gentianaceae).

Similar Datasets

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