SSR and ISSR markers in assessing genetic diversity in Gallus gallus domesticus: a quantitative analysis of scientific production / Marcadores SSR e ISSR na avaliação da diversidade genética em Gallus gallus domesticus: uma análise quantitativa da produção científica

Poultry meat is a major source of animal protein in the world. Research indicates a high inbreeding rate derived from a relative absence of heterozygous subpopulations of chicken from different suppliers. Molecular markers can provide information for the genetic basis of chicken consumed in rural areas and help establishing a chicken database for product quality and warranty. The bibliometric research, comprises between 1994 and 2018, from five previously selected databases: Google Scholar, PubMed, ScienceDirect, Scopus and Web of Science, using the following descriptors: microsatellites, SSR, ISSR, genetic variability and genetic diversity, all of them coupled to chicken and/or birds results in 66 scientific publications. The publications were then categorized according to their titles to the use of ISSR or SSR markers. They were also addressed by countries according first author cited. The publications data appointed that countries with the height production of poultry meat and hens are the most interested in the genetic diversity study of these species. The SSR markers, due to its more specific characteristic, are more frequently applied to genetic diversity assignment, compared to ISSR.(AU)

A carne de frango é uma das principais fontes de proteína animal do mundo. Pesquisas indicam uma alta taxa de endogamia derivada de uma relativa ausência de subpopulações heterozigotas de frango de diferentes fornecedores. Marcadores moleculares podem fornecer informações para a base genética de frango consumido em áreas rurais, e ajudar a estabelecer um banco de dados de frango para qualidade e garantia do produto. A pesquisa bibliométrica compreende entre 1994 e 2018, a partir de cinco bancos de dados selecionados anteriormente: Google Scholar, PubMed, ScienceDirect, Scopus e Web of Science, usando os seguintes descritores: microssatélites, SSR, ISSR, variabilidade genética e diversidade genética, todos eles associados a resultados de galinha e / ou aves o que resultou em 66 publicações científicas. As publicações foram então categorizadas de acordo com seus títulos para o uso de marcadores ISSR ou SSR. Eles também foram abordados pelos países, segundo o primeiro autor citado. Os dados das publicações obtidas apontam que os países com grande produção de carnes de frangos são os mais interessados no estudo da diversidade genética dessas espécies. Os marcadores SSR, devido à sua característica mais específica, são frequentemente aplicados à atribuição de diversidade genética, em comparação com o ISSR.(AU)

Development and characterization of microsatellite loci for Campomanesia xanthocarpa (Myrtaceae) and cross amplification in related species

Campomanesia xanthocarpa is a native tree, of common occurrence in almost all Brazilian Forest formations, which has its fruits and timber with high commercial value. Using an enriched genomic library we isolated and characterized microsatellite loci for C. xanthocarpa (Myrtaceae), in order to estimate genetic diversity parameters for this and related species. Twenty-eight microsatellite loci were identified and ten of them successfully amplified and showed polymorphism in a sample of 96 individuals, from four natural populations. The number of alleles per locus ranged from two to eight, and the observed and expected heterozygosities varied from 0.042 to 1.000 and from 0.294 to 0.855, respectively. These markers were tested and validated in two related species (C. eugenioides and C. guazumifolia). The microsatellite markers will be used in further studies of population genetics of C. xanthocarpa, in order to understand the genetic variability and to define the strategies needed for the conservation of the species.

Development and characterization of microsatellite loci for Campomanesia xanthocarpa (Myrtaceae) and cross amplification in related species

Campomanesia xanthocarpa is a native tree, of common occurrence in almost all Brazilian Forest formations, which has its fruits and timber with high commercial value. Using an enriched genomic library we isolated and characterized microsatellite loci for C. xanthocarpa (Myrtaceae), in order to estimate genetic diversity parameters for this and related species. Twenty-eight microsatellite loci were identified and ten of them successfully amplified and showed polymorphism in a sample of 96 individuals, from four natural populations. The number of alleles per locus ranged from two to eight, and the observed and expected heterozygosities varied from 0.042 to 1.000 and from 0.294 to 0.855, respectively. These markers were tested and validated in two related species (C. eugenioides and C. guazumifolia). The microsatellite markers will be used in further studies of population genetics of C. xanthocarpa, in order to understand the genetic variability and to define the strategies needed for the conservation of the species.(AU)

The genetic diversity among strawberry breeding resources based on SSRs

Cultivated strawberry (Fragaria × ananassa Duch.) is a high value horticultural crop. In this study, the genetic diversity of 160 strawberry accessions was determined using five highly polymorphic simple sequence repeat (SSR) markers. Sixty different alleles were identified, with allele frequencies in the range of 0.006 to1. Similarity scores were in the range of 0.034 to 0.963 (average: 0.507). The accessions were categorized into five groups. Group 1 contained two diploid Fragaria vesca species and one unknown accession. Group 2 contained one accession (F x ananassa). Group 3 contained 20 F × ananassa accessions and six unknown accessions. Group 4 contained 48 F. × ananassa accessions, one octaploid Fragaria chiloensis species, and six unknown accessions while Group 5 contained 69 F. × ananassa accessions and six unknown accessions. Accessions within a pedigree were frequently grouped together. A total of 30 novel accessions were categorized alongside existing accessions. These results will allow breeders to develop strategies which incorporate more genetic diversity into new cultivars.

The genetic diversity among strawberry breeding resources based on SSRs

Cultivated strawberry (Fragaria × ananassa Duch.) is a high value horticultural crop. In this study, the genetic diversity of 160 strawberry accessions was determined using five highly polymorphic simple sequence repeat (SSR) markers. Sixty different alleles were identified, with allele frequencies in the range of 0.006 to1. Similarity scores were in the range of 0.034 to 0.963 (average: 0.507). The accessions were categorized into five groups. Group 1 contained two diploid Fragaria vesca species and one unknown accession. Group 2 contained one accession (F x ananassa). Group 3 contained 20 F × ananassa accessions and six unknown accessions. Group 4 contained 48 F. × ananassa accessions, one octaploid Fragaria chiloensis species, and six unknown accessions while Group 5 contained 69 F. × ananassa accessions and six unknown accessions. Accessions within a pedigree were frequently grouped together. A total of 30 novel accessions were categorized alongside existing accessions. These results will allow breeders to develop strategies which incorporate more genetic diversity into new cultivars.(AU)

Development and characterization of microsatellite markers for Tibouchina hatschbachii (Melastomataceae), an endemic and habitatrestricted shrub from Brazil / Desenvolvimento e caracterização de marcadores microssatélites para Tibouchina hatschbachii (Melastomataceae), um arbusto endêmico e com restrição de habitat da região subtropical do Brasil

Tibouchina hatschbachii Wurdack (Melastomataceae) is an autogamous shrub restricted to granite (GO) and sandstone (SO) rock outcrops from subtropical Brazil. We designed primers for the amplification of microsatellite regions for T. hatschbachii, and characterized these primers to estimate genetic diversity parameters and contemporary genetic structure patterns. Eight loci were successfully amplified and were characterized using 70 individuals from three natural populations. Polymorphic information content ranged from 0.200 to 0.772 per locus. All loci were polymorphic, with allele numbers ranging from two to eight. The low degree of polymorphism may be explained by the fact that T. hatschbachii has disjunct populations and a recent genetic bottleneck, and also that it is self-pollinated. The observed and expected heterozygosities ranged from 0.115 to 1.000 and from 0.112 to 0.800, respectively. We observed private alleles in all loci. These are important features that enable us to identify population differentiation and help to us understand gene flow patterns for T. hatschbachii in subtropical Brazil. Eight microsatellite loci from other species of Tibouchina amplified positively in T. hatschbachii.

Tibouchina hatschbachii Wurdack (Melastomataceae) é um arbusto autógamo, com ocorrência restrita em afloramentos rochosos graníticos (GO) e areníticos (SO) na região subtropical do Brasil. Neste trabalho, foram desenvolvidos marcadores para a amplificação de regiões microssatélites para T. hatschbachii e caracterizados esses primers para estimar parâmetros de diversidade genética. Oito loci foram amplificados com sucesso e caracterizados, utilizando 70 indivíduos de três populações naturais. O conteúdo de informação polimórfica variou de 0,200 a 0,772 por locus. Todos os loci foram polimórficos, com números de alelos que variam de dois a oito. O baixo grau de polimorfismo pode ser explicado pelo fato de que T. hatschbachii possui populações disjuntas e uma história recente de gargalo genético populacional, e também pelo fato de apresentar um sistema reprodutivo de autopolinização, tendendo a favorecer a baixa variação. As heterozigosidades observadas e esperadas variaram entre 0,115-1,000 e 0,112-0,800, respectivamente. Também foi observada a presença de alelos privados em todos os loci. Estas são características importantes que nos permitirão identificar a diferenciação entre populações e poderão ajudar na compreensão dos padrões de fluxo gênico atual de T. hatschbachii na região subtropical do Brasil. Oito loci microssatélites de outras espécies de Tibouchina amplificaram

Development and characterization of microsatellite markers for Tibouchina hatschbachii (Melastomataceae), an endemic and habitatrestricted shrub from Brazil / Desenvolvimento e caracterização de marcadores microssatélites para Tibouchina hatschbachii (Melastomataceae), um arbusto endêmico e com restrição de habitat da região subtropical do Brasil

Tibouchina hatschbachii Wurdack (Melastomataceae) is an autogamous shrub restricted to granite (GO) and sandstone (SO) rock outcrops from subtropical Brazil. We designed primers for the amplification of microsatellite regions for T. hatschbachii, and characterized these primers to estimate genetic diversity parameters and contemporary genetic structure patterns. Eight loci were successfully amplified and were characterized using 70 individuals from three natural populations. Polymorphic information content ranged from 0.200 to 0.772 per locus. All loci were polymorphic, with allele numbers ranging from two to eight. The low degree of polymorphism may be explained by the fact that T. hatschbachii has disjunct populations and a recent genetic bottleneck, and also that it is self-pollinated. The observed and expected heterozygosities ranged from 0.115 to 1.000 and from 0.112 to 0.800, respectively. We observed private alleles in all loci. These are important features that enable us to identify population differentiation and help to us understand gene flow patterns for T. hatschbachii in subtropical Brazil. Eight microsatellite loci from other species of Tibouchina amplified positively in T. hatschbachii.(AU)

Tibouchina hatschbachii Wurdack (Melastomataceae) é um arbusto autógamo, com ocorrência restrita em afloramentos rochosos graníticos (GO) e areníticos (SO) na região subtropical do Brasil. Neste trabalho, foram desenvolvidos marcadores para a amplificação de regiões microssatélites para T. hatschbachii e caracterizados esses primers para estimar parâmetros de diversidade genética. Oito loci foram amplificados com sucesso e caracterizados, utilizando 70 indivíduos de três populações naturais. O conteúdo de informação polimórfica variou de 0,200 a 0,772 por locus. Todos os loci foram polimórficos, com números de alelos que variam de dois a oito. O baixo grau de polimorfismo pode ser explicado pelo fato de que T. hatschbachii possui populações disjuntas e uma história recente de gargalo genético populacional, e também pelo fato de apresentar um sistema reprodutivo de autopolinização, tendendo a favorecer a baixa variação. As heterozigosidades observadas e esperadas variaram entre 0,115-1,000 e 0,112-0,800, respectivamente. Também foi observada a presença de alelos privados em todos os loci. Estas são características importantes que nos permitirão identificar a diferenciação entre populações e poderão ajudar na compreensão dos padrões de fluxo gênico atual de T. hatschbachii na região subtropical do Brasil. Oito loci microssatélites de outras espécies de Tibouchina amplificaram(AU)

Development and validation of new SSR markers from expressed regions in the garlic genome

Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC) of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.

Development and validation of new SSR markers from expressed regions in the garlic genome

Only a limited number of simple sequence repeat (SSR) markers is available for the genome of garlic (Allium sativum L.) despite the fact that SSR markers have become one of the most preferred DNA marker systems. To develop new SSR markers for the garlic genome, garlic expressed sequence tags (ESTs) at the publicly available GarlicEST database were screened for SSR motifs and a total of 132 SSR motifs were identified. Primer pairs were designed for 50 SSR motifs and 24 of these primer pairs were selected as SSR markers based on their consistent amplification patterns and polymorphisms. In addition, two SSR markers were developed from the sequences of garlic cDNA-AFLP fragments. The use of 26 EST-SSR markers for the assessment of genetic relationship was tested using 31 garlic genotypes. Twenty six EST-SSR markers amplified 130 polymorphic DNA fragments and the number of polymorphic alleles per SSR marker ranged from 2 to 13 with an average of 5 alleles. Observed heterozygosity and polymorphism information content (PIC) of the SSR markers were between 0.23 and 0.88, and 0.20 and 0.87, respectively. Twenty one out of the 31 garlic genotypes were analyzed in a previous study using AFLP markers and the garlic genotypes clustered together with AFLP markers were also grouped together with EST-SSR markers demonstrating high concordance between AFLP and EST-SSR marker systems and possible immediate application of EST-SSR markers for fingerprinting of garlic clones. EST-SSR markers could be used in genetic studies such as genetic mapping, association mapping, genetic diversity and comparison of the genomes of Allium species.(AU)