Artículo

Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

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.

Registro:

Documento: Artículo
Título:Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae
Autor:Barboza, K.; Beretta, V.; Kozub, P.C.; Salinas, C.; Morgenfeld, M.M.; Galmarini, C.R.; Cavagnaro, P.F.
Filiación:Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Nacional de Tecnología Agropecuaria (INTA)-E.E.A. La Consulta, Mendoza, Argentina
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
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
Facultad de Ciencias Agrarias, Instituto de Horticultura, Universidad Nacional de Cuyo, Mendoza, Argentina
Palabras clave:Allium; Cross-amplification; Garlic; Genetic diversity; Microsatellite markers; SSRs; transcriptome; trinucleotide; microsatellite DNA; transcriptome; allele; Allium tuberosum; Article; asparagus; breeding; chive; controlled study; cultivar; expressed sequence tag; flowering; garlic; genetic polymorphism; genetic variability; ginger; leek; microsatellite instability; microsatellite marker; monocot; nonhuman; onion; polymerase chain reaction; priority journal; rice; Saccharum officinarum; shallot; species; Welsh onion; Allium; classification; garlic; genetic marker; genetic polymorphism; genetic screening; genetics; plant breeding; plant genome; Allium; Expressed Sequence Tags; Garlic; Genetic Markers; Genetic Testing; Genome, Plant; Microsatellite Repeats; Plant Breeding; Polymorphism, Genetic; Transcriptome
Año:2018
Volumen:293
Número:5
Página de inicio:1091
Página de fin:1106
DOI: http://dx.doi.org/10.1007/s00438-018-1442-5
Título revista:Molecular Genetics and Genomics
Título revista abreviado:Mol. Genet. Genomics
ISSN:16174615
CODEN:MGGOA
CAS:Genetic Markers
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_16174615_v293_n5_p1091_Barboza

Referencias:

  • Arnold, C., Rossetto, M., McNally, J., Henry, R.J., The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae (2002) Am J Bot, 89, pp. 22-28. , PID: 21669708
  • Arumuganathan, K., Earle, E.D., Nuclear DNA content of some important plant species (1991) Plant Mol Biol Report, 9, pp. 208-218
  • Baldwin, S., Pither-Joyce, M., Wright, K., Chen, L., McCallum, J., Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations (2012) Mol Breed, 30, pp. 1401-1411
  • Block, E., (2010) Garlic and other Alliums: the lore and the science, , Royal Society of Chemistry, Cambridge
  • Bodénès, C., Chancerel, E., Gailing, O., Vendramin, G.G., Bagnoli, F., Durand, J., Goicoechea, P.G., Plomion, C., Comparative mapping in the Fagaceae and beyond using EST-SSRs (2012) BMC Plant Biol, 12, p. 153. , PID: 22931513
  • Bradley, K.F., Rieger, M.A., Collins, G.G., Classification of Australian garlic cultivars by DNA fingerprinting (1996) Aust J Exp Agric, 36, pp. 613-618
  • Burba, J.L., Panorama mundial y nacional de poblaciones y cultivares de ajo, posibilidades de adaptación (1997) 50 Temas Sobre La producción De Ajo, INTA EEA La Consulta, Mendoza-Argentina, 2, pp. 11-31. , Burba JL
  • Cavagnaro, P.F., Camargo, A., Piccolo, R.J., García-Lampasona, S., Burba, J.L., Masuelli, R.W., Resistance to Penicillium hirsutum Dierckx in garlic accessions (2005) Eur J Plant Pathol, 112, pp. 195-199
  • Cavagnaro, P.F., Chung, S.M., Manin, S., Yildiz, M., Ali, A., Alessandro, M.S., Iorizzo, M., Simon, P.W., Microsatellite isolation and marker development in carrot-genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae (2011) BMC Genomics, 12, p. 1
  • Cavagnaro, P.F., Iorizzo, M., Yildiz, M., Senalik, D., Parsons, J., Ellison, S., Simon, P.W., A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation (2014) BMC Genomics, 15, p. 1118. , PID: 25514876
  • Chand, S.K., Nanda, S., Rout, E., Joshi, R.K., Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L (2015) Bioinformation, 11, p. 145. , PID: 25987765
  • Chen, S., Chen, W., Shen, X., Yang, Y., Qi, F., Liu, Y., Meng, H., Analysis of the genetic diversity of garlic (Allium sativum L.) by simple sequence repeat and inter simple sequence repeat analysis and agro-morphological traits (2014) Biochem Syst Ecol, 55, pp. 260-267
  • Cunha, C.P., Hoogerheide, E.S., Zucchi, M.I., Monteiro, M., Pinheiro, J.B., New microsatellite markers for garlic, Allium sativum (Alliaceae) (2012) Am J Bot, 9
  • Fischer, D., Bachmann, K., Onion microsatellites for germplasm analysis and their use in assessing intra-and interspecific relatedness within the subgenus Rhizirideum (2000) Theor Appl Genet, 101, pp. 153-164
  • Friesen, N., Fritsch, R.M., Blattner, F.R., Phylogeny and new intrageneric classification of Allium (Alliaceae) based on nuclear ribosomal DNA ITS sequences (2006) Aliso, 22, pp. 372-395
  • García-Lampasona, S., Martínez, L., Burba, J., Genetic analysis of a garlic (Allium sativum L.) germplasm collection from Argentina (2003) Euphytica, 132, p. 115
  • García-Lampasona, S., Asprelli, P., Burba, J.L., Genetic analysis of a garlic (Allium sativum L.) germplasm collection from Argentina (2012) Sci Hortic, 138, pp. 183-189
  • González, R.E., Soto, V.C., Sance, M.M., Camargo, A.B., Galmarini, C.R., Variability of solids, organosulfur compounds, pungency and health-enhancing traits in garlic (Allium sativum L.) cultivars belonging to different ecophysiological groups (2009) J Agric Food Chem, 57, pp. 10282-10288. , PID: 19827749
  • Huang, X., Madan, A., CAP3: a DNA sequence assembly program (1999) Genome Res, 9, pp. 868-877. , PID: 10508846
  • Huang, D., Zhang, Y., Jin, M., Li, H., Song, Z., Wang, Y., Chen, J., Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae) (2014) Mol Ecol Resour, 14, pp. 569-577. , PID: 24286608
  • Ipek, M., Ipek, A., Simon, P.W., Comparison of AFLPs, RAPD markers and isozymes for diversity assessment of garlic and detection of putative duplicates in germplasm collections (2003) J Am Soc Hortic Sci, 128, pp. 246-252
  • Ipek, M., Sahin, N., Ipek, A., Cansev, A., Simon, P.W., Development and validation of new SSR markers from expressed regions in the garlic genome (2015) Sci Agric, 72, pp. 41-46
  • Jones, R., Rees, H., Nuclear DNA variation in Allium (1968) Heredity, 23, pp. 591-605
  • Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., Dhawan, A.K., Microsatellite markers: an overview of the recent progress in plants (2011) Euphytica, 177, pp. 309-334
  • Kalinowski, S.T., Taper, M.L., Marshall, T.C., Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment (2007) Mol Ecol, 16, pp. 1099-1106. , PID: 17305863
  • Kamenetsky, R., Faigenboim, A., Mayer, E., Michael, T., Gershberg, C., Kimhi, S., Esquira, I., Sherman, A., Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.) (2015) BMC Genom, 16, p. 12
  • King, J.J., Bradeen, J.M., Bark, O., McCallum, J.A., Havey, M.J., A low-density genetic map of onion reveals a role for tandem duplication in the evolution of an extremely large diploid genome (1998) Theor Appl Genet, 96, pp. 52-62
  • Kirk, J.T., Rees, H., Evans, G., Base composition of nuclear DNA within the genus Allium (1970) Heredity, 25, pp. 507-512
  • Kuhl, J.C., Cheung, F., Yuan, Q., Martin, W., Zewdie, Y., McCallum, J., Catanach, A., Havey, M.J., A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales (2004) Plant Cell, 16, pp. 114-125. , PID: 14671025
  • Lee, G.A., Kwon, S.J., Park, Y.J., Lee, M.C., Kim, H.H., Lee, J.S., Lee, S.Y., Ma, K.H., Cross-amplification of SSR markers developed from Allium sativum to other Allium species (2011) Sci Hortic, 128, pp. 401-407
  • Liu, T., Zeng, L., Zhu, S., Chen, X., Tang, Q., Mei, S., Tang, S., Large-scale development of expressed sequence tag-derived simple sequence repeat markers by deep transcriptome sequencing in garlic (Allium sativum L.) (2015) Mol Breed, 35, p. 204
  • Ma, K.H., Kwag, J.G., Zhao, W., Dixit, A., Lee, G.A., Kim, H.H., Chung, I.M., Park, Y.J., Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.) (2009) Sci Hortic, 122, pp. 355-361
  • Mallor, C., Arnedo-Andrés, M.S., Garcés-Claver, A., Assessing the genetic diversity of Spanish Allium cepa landraces for onion breeding using microsatellite markers (2014) Sci Hortic, 170, pp. 24-31
  • Martin, W.J., McCallum, J., Shigyo, M., Jakse, J., Kuhl, J.C., Yamane, N., Pither-Joyce, M., Havey, M.J., Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity (2005) Mol Genet Genomics, 274, p. 197. , PID: 16025250
  • Morales, R.G., Resende, J.T., Resende, F.V., Delatorre, C.A., Figueiredo, A.S., Da-Silva, P.R., Genetic divergence among Brazilian garlic cultivars based on morphological characters and AFLP markers (2013) Genet Mol Res, 12, pp. 270-281. , PID: 23408414
  • Murray, M.G., Thompson, W.F., Rapid isolation of high molecular weight plant DNA (1980) Nucleic Acids Res, 8, pp. 4321-4326. , PID: 7433111
  • Ovesná, J., Mitrová, K., Kučera, L., Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content (2015) BMC Genet, pp. 16-53
  • Panthee, D.R., Kc, R.B., Regmi, H.N., Subedi, P.P., Bhattarai, S., Dhakal, J., Diversity analysis of garlic (Allium sativum L.) germplasms available in Nepal based on morphological characters (2006) Genet Resour Crop Evol, 53, pp. 205-212
  • Paredes, M., Becerra, V., Gonzalez, M.I., Low genetic diversity among garlic (Allium sativum L.) accessions detected using random amplified polymorphic DNA (RAPD) (2008) Chilean J Agric Res, 68, pp. 3-12
  • Pearce, S.R., Pich, U., Harrison, G., Flavell, A.J., Heslop-Harrison, J.S., Schubert, I., Kumar, A., The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin (1996) Chromosome Res, 4, pp. 357-364. , PID: 8871824
  • Ranjekar, P.K., Pallotta, D., Lafontaine, J.G., Analysis of plant genomes V Comparative study of molecular properties of DNAs of seven Allium species (1978) Biochem Genet, 16, pp. 957-970. , PID: 743197
  • Rossetto, M.F., Harriss, C.L., Mclauchlan, A., Henry, R.J., Baverstock, P.R., Lee, L.S., Interspecific amplification of tea tree (Melaleuca alternifolia-Myrtaceae) microsatellite loci: potential implications for conservation studies (2000) Aust J Bot, 48, pp. 367-373
  • Sokal, R.R., Rohlf, F.J., The comparison of dendrograms by objective methods (1962) Taxon, 11, pp. 33-40
  • Stack, S.M., Comings, D.E., The chromosomes and DNA of Allium cepa (1979) Chromosoma, 70, p. 161
  • Sun, X., Zhou, S., Meng, F., Liu, S., De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing (2012) Plant Cell Rep, 31, pp. 1823-1828. , PID: 22684307
  • Tang, Q., Yi, L., Yuan, X., Li, F., Large-scale development, characterization, and cross-amplification of EST-SSR markers in Chinese chive (2017) Genet Mol Res, 17
  • Thiel, T., Michalek, W., Varshney, R., Graner, A., Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) (2003) Theor Appl Genet, 106, pp. 411-422. , PID: 12589540
  • Tsukazaki, H., Yamashita, K.I., Yaguchi, S., Masuzaki, S., Fukuoka, H., Yonemaru, J., Kanamori, H., Wako, T., Construction of SSR-based chromosome map in bunching onion (Allium fistulosum) (2008) Theor Appl Genet, 117, pp. 1213-1223. , PID: 18818898
  • Tsukazaki, H., Yaguchi, S., Sato, S., Hirakawa, H., Katayose, Y., Kanamori, H., Kurita, K., Hamada, M., Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum) (2015) Mol Breed, 35, p. 55
  • Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B.C., Remm, M., Rozen, S.G., Primer3-new capabilities and interfaces (2012) Nucleic Acids Res, 40. , PID: 22730293
  • Varshney, R.K., Graner, A., Sorrells, M.E., Genic microsatellite markers in plants: features and applications (2005) Trends Biotechnol, 23, pp. 48-55. , PID: 15629858
  • Volk, G.M., Henk, A.D., Richards, C.M., Genetic diversity among U.S. garlic clones as detected using AFLP methods (2004) J Amer Soc Hort Sci, 129, pp. 559-569
  • Weber, J.L., Informativeness of human (dC–dA)n·(dG–dT)n polymorphisms (1990) Genomics, 7, pp. 524-530. , PID: 1974878
  • Wierdl, M., Dominska, M., Petes, T.D., Microsatellite instability in yeast: dependence on the length of the microsatellite (1997) Genetics, 146, pp. 769-779. , PID: 9215886
  • (2016) Data analysis and Statistical Solution for Microsoft Excel, , Addinsoft, Paris
  • Xu, Y., Ma, R.C., Xie, H., Liu, J.T., Cao, M.Q., Development of SSR markers for the phylogenetic analysis of almond trees from China and the Mediterranean region (2004) Genome, 47, pp. 1091-1104. , PID: 15644967
  • Yang, L., Wen, C., Zhao, H., Liu, Q., Yang, J., Liu, L., Wang, Y., Development of polymorphic genic SSR markers by transcriptome sequencing in the welsh onion (Allium fistulosum L.) (2015) Appl Sci, 5, pp. 1050-1063
  • Zhao, W.G., Chung, J.W., Lee, G.A., Ma, K.H., Kim, H.H., Kim, K.T., Chung, I.M., Park, Y.J., Molecular genetic diversity and population structure of a selected core set in garlic and its relatives using novel SSR markers (2011) Plant Breed, 130, pp. 46-54

Citas:

---------- APA ----------
Barboza, K., Beretta, V., Kozub, P.C., Salinas, C., Morgenfeld, M.M., Galmarini, C.R. & Cavagnaro, P.F. (2018) . Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae. Molecular Genetics and Genomics, 293(5), 1091-1106.
http://dx.doi.org/10.1007/s00438-018-1442-5
---------- CHICAGO ----------
Barboza, K., Beretta, V., Kozub, P.C., Salinas, C., Morgenfeld, M.M., Galmarini, C.R., et al. "Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae" . Molecular Genetics and Genomics 293, no. 5 (2018) : 1091-1106.
http://dx.doi.org/10.1007/s00438-018-1442-5
---------- MLA ----------
Barboza, K., Beretta, V., Kozub, P.C., Salinas, C., Morgenfeld, M.M., Galmarini, C.R., et al. "Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae" . Molecular Genetics and Genomics, vol. 293, no. 5, 2018, pp. 1091-1106.
http://dx.doi.org/10.1007/s00438-018-1442-5
---------- VANCOUVER ----------
Barboza, K., Beretta, V., Kozub, P.C., Salinas, C., Morgenfeld, M.M., Galmarini, C.R., et al. Microsatellite analysis and marker development in garlic: distribution in EST sequence, genetic diversity analysis, and marker transferability across Alliaceae. Mol. Genet. Genomics. 2018;293(5):1091-1106.
http://dx.doi.org/10.1007/s00438-018-1442-5