Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae

Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and r...

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Autor principal: Barboza, K.
Otros Autores: Beretta, V., Kozub, P.C, Salinas, C., Morgenfeld, M.M, Galmarini, C.R, Cavagnaro, P.F
Formato: Capítulo de libro
Lenguaje:Inglés
Publicado: Springer Verlag 2018
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100 1 |a Barboza, K. 
245 1 0 |a Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae 
260 |b Springer Verlag  |c 2018 
270 1 0 |m Cavagnaro, P.F.; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La ConsultaArgentina; email: pablocavagnaro@hotmail.com 
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520 3 |a Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized—along with 112 previously developed SSRs—at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis. Among the Allium species analyzed, garlic ESTs had the highest overall SSR density, the lowest frequency of trinucleotides, and the highest of di- and tetranucleotides. When compared to more distantly related monocots, outside the Asparagales order, it was evident that ESTs of Allium species shared major commonalities with regards to SSR density, frequency distribution, sequence motifs, and GC content. A significant fraction of the SSR markers were successfully transferred across Allium species, including crops for which no SSR markers have been developed yet, such as leek, shallot, chives, and elephant garlic. Diversity analysis of garlic cultivars with selected SSRs revealed 36 alleles, with 2–5 alleles/locus, and PIC = 0.38. Cluster analysis grouped the accessions according to their flowering behavior, botanical variety, and ecophysiological characteristics. Results from this study contribute to the characterization of Allium transcriptomes. The new SSR markers developed, along with the data from the polymorphism and transferability analyses, will aid in assisting genetic research and breeding in garlic and other Allium. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.  |l eng 
536 |a Detalles de la financiación: National Council for Scientific Research 
536 |a Detalles de la financiación: Consejo Nacional de Investigaciones Científicas y Técnicas 
536 |a Detalles de la financiación: Consejo Nacional de Investigaciones Científicas y Técnicas, PICT-PRH-69 
536 |a Detalles de la financiación: Funding This work was supported by the Agencia Nacional de Pro-moción Científica y Técnica (ANPCyT) through the grant PICT-PRH-69. Karina Barboza, Vanesa Beretta, Perla C Kozub, and Cecilia Salinas have fellowships granted by the Argentine National Scientific and Technical Research Council (CONICET). 
593 |a Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina 
593 |a Facultad de Ciencias Agrarias (FCA), Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina 
593 |a Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina 
593 |a Facultad de Ciencias Agrarias, Instituto de Horticultura, Universidad Nacional de Cuyo, Mendoza, Argentina 
690 1 0 |a ALLIUM 
690 1 0 |a CROSS-AMPLIFICATION 
690 1 0 |a GARLIC 
690 1 0 |a GENETIC DIVERSITY 
690 1 0 |a MICROSATELLITE MARKERS 
690 1 0 |a TRANSCRIPTOME 
690 1 0 |a TRINUCLEOTIDE 
690 1 0 |a MICROSATELLITE DNA 
690 1 0 |a TRANSCRIPTOME 
690 1 0 |a ALLELE 
690 1 0 |a ALLIUM TUBEROSUM 
690 1 0 |a ARTICLE 
690 1 0 |a ASPARAGUS 
690 1 0 |a BREEDING 
690 1 0 |a CHIVE 
690 1 0 |a CONTROLLED STUDY 
690 1 0 |a CULTIVAR 
690 1 0 |a EXPRESSED SEQUENCE TAG 
690 1 0 |a FLOWERING 
690 1 0 |a GARLIC 
690 1 0 |a GENETIC POLYMORPHISM 
690 1 0 |a GENETIC VARIABILITY 
690 1 0 |a GINGER 
690 1 0 |a LEEK 
690 1 0 |a MICROSATELLITE INSTABILITY 
690 1 0 |a MICROSATELLITE MARKER 
690 1 0 |a MONOCOT 
690 1 0 |a NONHUMAN 
690 1 0 |a ONION 
690 1 0 |a POLYMERASE CHAIN REACTION 
690 1 0 |a PRIORITY JOURNAL 
690 1 0 |a RICE 
690 1 0 |a SACCHARUM OFFICINARUM 
690 1 0 |a SHALLOT 
690 1 0 |a SPECIES 
690 1 0 |a WELSH ONION 
690 1 0 |a ALLIUM 
690 1 0 |a CLASSIFICATION 
690 1 0 |a GARLIC 
690 1 0 |a GENETIC MARKER 
690 1 0 |a GENETIC POLYMORPHISM 
690 1 0 |a GENETIC SCREENING 
690 1 0 |a GENETICS 
690 1 0 |a PLANT BREEDING 
690 1 0 |a PLANT GENOME 
690 1 0 |a ALLIUM 
690 1 0 |a EXPRESSED SEQUENCE TAGS 
690 1 0 |a GARLIC 
690 1 0 |a GENETIC MARKERS 
690 1 0 |a GENETIC TESTING 
690 1 0 |a GENOME, PLANT 
690 1 0 |a MICROSATELLITE REPEATS 
690 1 0 |a PLANT BREEDING 
690 1 0 |a POLYMORPHISM, GENETIC 
690 1 0 |a TRANSCRIPTOME 
650 1 7 |2 spines  |a SSRS 
700 1 |a Beretta, V. 
700 1 |a Kozub, P.C. 
700 1 |a Salinas, C. 
700 1 |a Morgenfeld, M.M. 
700 1 |a Galmarini, C.R. 
700 1 |a Cavagnaro, P.F. 
773 0 |d Springer Verlag, 2018  |g v. 293  |h pp. 1091-1106  |k n. 5  |p Mol. Genet. Genomics  |x 16174615  |t Molecular Genetics and Genomics 
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