SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

Contreras Toledo, Aremi Rebeca.

A partir de la domesticación de chile (Capsicum annuum L.) en México, se ha generado una gran diversidad dentro de esta especie en nuestro país, derivada de la selección de los agricultores para diferentes usos, siendo el chile Poblano uno de los más importantes y el más representativo del Estado de Puebla; sin embargo, el rendimiento de chile poblano en esta región ha presentado una reducción en los últimos años, debido, en parte, a la falta de semilla mejorada que debe ser seleccionada con base en las necesidades de los propios productores, existiendo la potencial pérdida de este germoplasma. Los objetivos de este estudio fueron estimar la diversidad genética y determinar sus posibles patrones de distribución, diferenciar grupos genéticos de variedades y...

Palavras-chave: Capsicum annuum; SSR; Polimorfismo; Diferenciación genética; Polymorphism; Genetic differentiation; Maestría; Genética.

Ano: 2011

URL: http://hdl.handle.net/10521/400

Marcadores moleculares de secuencias simples repetidas en la caracterización de Lolium perenne, Lolium multiflorum, Lolium hybridum, y Dactylis glomerata

Aguirre Robert, Cinthia Jimena.

En Valles Altos Centrales de México ha aumentado el cultivo de Lolium, Festuca, Dactylis y Vicia, géneros de especies forrajeras mejor adaptadas a la zona, pero su desventaja son recursos genéticos limitados para continuar la mejora genética de las especies. Por tanto, el objetivo del presente estudio fue realizar una evaluación agronómica y molecular de 8 accesiones de Lolium: Ansyl France (AF), New Zealand (NZ), Uruguay (U), Netherland Barenza (NB), USA Manhattan II (UMII), Canada Uri (4n) (CU4n), Australia Wimmera 62 (AW62) y France Itaque (FI); y tres de Dactylis: Canada Hércules (CH), USA Potomac (UP) y USA Napier (UN). La estructura poblacional y similitud genética entre accesiones se determinó con 13 loci-SSR, y se estimó la asociación...

Tipo: Tesis

Palavras-chave: Accesiones; Loci; Caracteres morfológicos; SSR accesions; Loci; Morphological traits; SSR.

Ano: 2009

URL: http://hdl.handle.net/10521/1100

Marcadores moleculares de secuencias simples repetidas en la caracterización de Lolium perenne, Lolium multiflorum, Lolium hybridum, y Dactylis glomerata

Aguirre Robert, Cinthia Jimena.

Tipo: Tesis

Palavras-chave: Accesiones; Loci; Caracteres morfológicos; SSR; Maestría; Ganadería; Accesions; Loci; Morphological traits.

Ano: 2009

URL: http://hdl.handle.net/10521/1448

Análisis de la diversidad genética de variedades nativas de chile "Poblano" por medio de microsatélites.

Contreras Toledo, Aremi Rebeca.

Palavras-chave: Capsicum annuum; SSR; Polimorfismo; Diferenciación genética; Polymorphism; Genetic differentiation; Maestría; Genética.

Ano: 2011

URL: http://hdl.handle.net/10521/400

Evaluation of cassava plants generated by somatic embryogenesis at different stages of development using molecular markers

Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers

Osorio,Mayra; Gámez,Elizabeth; Molina,Sandy; Infante,Diógenes.

Background: Cassava (Manihot esculenta Crantz) is a crop that is high in carbohydrates in the roots and in protein in the leaves, important for both human consumption and animal feed, and also has a significant industrial use for its starches. In this study we evaluated the genetic variability with molecular markers in different stages in micropropagated plants from somatic embryos of Venezuelan native clone 56. Results: Three markers were used: ISTR, AFLP and SSR, finding that ISTR showed the highest polymorphism among individuals tested. With AFLP a high similarity between the evaluated individuals was observed and with SSR total monomorphism was seen. Using cluster analysis it was found that individuals from an embryo labeled as fasciated at the...

Tipo: Journal article

Palavras-chave: AFLP; Genetic stability; ISTR; SSR; UPGMA.

Ano: 2012

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582012000400003

Ghneim Herrera,Thaura; Posso Duque,Duina; Pérez Almeida,Iris; Torrealba Núñez,Gelis; Pieters,Alejandro J; Martinez,César P; Tohme,Joe M.

In Venezuela, pedigree analyses indicate that the rice varieties currently under cultivation are closely related. Effective breeding programs, based on knowledge of the genetic diversity of cultivars, are needed to broaden the genetic bases of rice germplasm in the country. In this study, we used a set of 48 simple-sequence-repeat (SSR) markers to assess the genetic diversity of 11 Venezuelan rice cultivars, released by the National Rice Breeding Program between 1978 and 2007. A total of 203 alleles were detected, the number of alleles (NA) per marker ranged from 2 to 9, with an average of 4.23. The average genic diversity (H) over all SSR loci for the 18 genotypes was 0.524, ranging from 0.105 to 0.815. Positive correlations were found between H at each...

Tipo: Journal article

Palavras-chave: DNA fingerprinting; Genetic diversity; Rice; SSR.

Ano: 2008

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582008000500003

Identification of groundnut (Arachis hypogaea) SSR markers suitable for multiple resistance traits QTL mapping in African germplasm

Genetic mapping of EST-SSR, SSR and InDel to improve saturation of genomic regions in a previously developed sunflower map

Ncube Kanyika,Busisiwe T; Lungu,Davies; Mweetwa,Alice M; Kaimoyo,Evans; Njung'e,Vincent M; Monyo,Emmanuel S; Siambi,Moses; He,Guohao; Prakash,Channapata S; Zhao,Yongli; de Villiers,Santie M.

Background This study aimed to identify and select informative Simple Sequence Repeat (SSR) markers that may be linked to resistance to important groundnut diseases such as Early Leaf Spot, Groundnut Rosette Disease, rust and aflatoxin contamination. To this end, 799 markers were screened across 16 farmer preferred and other cultivated African groundnut varieties that are routinely used in groundnut improvement, some with known resistance traits. Results The SSR markers amplified 817 loci and were graded on a scale of 1 to 4 according to successful amplification and ease of scoring of amplified alleles. Of these, 376 markers exhibited Polymorphic Information Content (PIC) values ranging from 0.06 to 0.86, with 1476 alleles detected at an average of 3.7...

Tipo: Journal article

Palavras-chave: Arachis; African varieties; Disease; SSR.

Ano: 2015

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000200001

Talia,Paola; Nishinakamasu,Verónica; Hopp,Horacio Esteban; Heinz,Ruth Amelia; Paniego,Norma.

In order to saturate a sunflower genetic map and facilitate marker-assisted selection (MAS) breeding for stress response, it is necessary to enhance map saturation with molecular markers localized in linkage groups associated to genomic regions involved in these traits. This work describes the identification and characterization of 1,134 simple sequence repeat (SSR) containing expressed sequence tags (EST) from unigenes available databases. Twelve of these functional markers as well as 41 public SSR markers were successfully localized in linkage groups, thus contributing to the saturation of specific regions on a reference genetic-linkage-map derived from recombinant inbred lines (RIL) mapping population from the cross between PAC2 x RHA266 lines. The...

Tipo: Journal article

Palavras-chave: EST-SSR; InDels; Linkage map; SSR; Sunflower.

Ano: 2010

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582010000600007

Development of cDNA-derived SSR markers and their efficiency in diversity assessment of Cymbidium accessions

Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

Moe,Kyaw Thu; Hong,Woo-Ju; Kwon,Soon-Wook; Park,Yong-Jin.

Cymbidium spp. are popular ﬂowering plants. Assessment of the genetic diversity in cultivated Cymbidium facilitates conservation of germplasm and subsequent cultivar improvement. Thus, it is important to develop more efficient polymorphic DNA markers. Although more motifs (403) were identified and more primers (206) were designed in the genomic library compared to the cDNA library, a larger number of successful primers were obtained from the cDNA library (59.9%) than from genomic DNA library (51.1%). However, higher PIC and gene diversity were identified in genomic SSRs. The average allele number per locus was also higher in genomic SSRs (7.3) than EST-SSRs (5.2), among the 24 evaluated Cymbidium accessions. AT/TA was comparatively high in...

Tipo: Journal article

Palavras-chave: CDNA library; Cymbidium; Enriched library; Molecular diversity; SSR.

Ano: 2012

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582012000200004

Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis

Li,Ai Qin; Zhao,Chuan Zhi; Wang,Xing Jun; Liu,Zhan Ji; Zhang,Li Feng; Song,Guo Qi; Yin,Juan; Li,Chang Sheng; Xia,Han; Bi,Yu Ping.

Microsatellites, or simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated by 454 sequencing and representing 70,654 contigs and 52,082 singletons) from soybean globular stage embryos. Among 122,736 unique ESTs, 3,729 contained one or more SSRs. In total, 3,989 SSRs were identified including 304 mono, 1,374 di, 2,208 tri, 70 tetra, 13 penta and 20 hexanucleotide SSRs. Thirty three EST-SSRs were selected for primer design and polymorphism analysis using twenty soybean cultivars and one wild-type soybean. Successful amplification was obtained using 21 of these primer pairs, 11 of which detected polymorphisms in these soybean cultivars. These...

Tipo: Journal article

Palavras-chave: 454 sequencing; EST; Glycine max; Polymorphism; SSR.

Ano: 2010

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582010000500006

Arias,Renée S; Stetina,Salliana R; Scheffler,Brian E.

Currently, a large number of microsatellites are available for Rotylenchulus reniformis (reniform nematode); however, two barriers exist for genotyping samples from different geographical areas. The limited amount of nucleic acids obtained from single nematodes which would require their multiplication to obtain enough DNA for testing; and the strictly regulated transport of live samples and multiplication in greenhouse for being a plant pathogen. Whole-genome amplification (WGA) of samples consisting of one and five dead gravid females with their associated egg masses was successfully performed on disrupted tissue using three commercial kits. DNA yield after WGA ranged from 0.5 to 8 Âµg and was used to test 96 microsatellite markers we previously developed...

Tipo: Journal article

Palavras-chave: Genotyping; Reniform nematode; SSR; STR; WGA.

Ano: 2011

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582011000300014

Microsatellite markers in candidate genes for wood properties and its application in functional diversity assessment in Eucalyptus globulus

Acuña,Cintia V; Villalba,Pamela V; García,Martín; Pathauer,Pablo; Hopp,H. Esteban; Marcucci Poltri,Susana N.

Background: Functional genetic markers have important implications for genetic analysis by providing direct estimation of functional diversity. Although high throughput sequencing techniques for functional diversity analysis are being developed nowadays, the use of already well established variable markers present in candidate genes is still an interesting alternative for mapping purposes and functional diversity studies. SSR markers are routinely used in most plant and animal breeding programs for many species including Eucalyptus. SSR markers derived from candidate genes (SSR-CG) can be used effectively in co-segregation studies and marker-assisted diversity management. Results: In the present study, eight new non reported SSRs were identified in seven...

Tipo: Journal article

Palavras-chave: Functional markers; Genetic diversity; Lignin pathway; SSR; Wood density.

Ano: 2012

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582012000200002

Genetic diversity in two Italian almond collections

Agronomic and molecular analyses for the characterisation of accessions in Tunisian olive germplasm collections

Rigoldi,Maria Pia; Rapposelli,Emma; De Giorgio,Donato; Resta,Paolo; Porceddu,Andrea.

Background Sweet-seeded domesticated almonds were brought to the Mediterranean Basin from central Asia about 4000 years ago. In Italy, most of the almonds produced are cultivated in the southern part of the country. Local populations of the tree in Sardinia are largely seed-derived and mostly self-incompatible, so have developed extensive genetic diversity. The need to protect biodiversity has prompted a revived interest in local genetic materials in almond. Two Italian collections have been established, one in Sardinia and the other in Apulia. These collections were the focus of the present evaluation of genetic diversity. Results Eleven SSRs (microsatellites) were used for fingerprinting. The Sardinian germplasm was highly polymorphic, revealing a mean...

Tipo: Journal article

Palavras-chave: Biodiversity; Genetic structure; Prunus amygdalus; SSR.

Ano: 2015

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000100008

Identification of a minimal microsatellite marker panel for the fingerprinting of peach and nectarine cultivars

Taamalli,Wael; Geuna,Filippo; Banfi,Riccardo; Bassi,Daniele; Daoud,Douja; Zarrouk,Mokhtar.

In this study, a total of 14 agronomic traits, five AFLP primer combinations and ten SSR loci were used to describe and to classify a group of Tunisian olive genotypes into groups based on molecular profiles and agronomic traits. The analysis of variance of the agronomical data revealed significant differences among accessions for all measured traits. The mean phenotypic dissimilarity (0.34 with a range of 0.08-0.6) was low in comparison to dissimilarity calculated using AFLP (0.50 with a range of 0.16-0.70) and SSR markers (0.76 with a range 0.35-0.94). The correlation between the agronomical dissimilarity matrix and the matrices of genetic dissimilarity based on SSR and AFLP markers was very weak: 0.156 (p = 0.05) and 0.185 (p = 0.05), respectively. The...

Tipo: Journal article

Palavras-chave: Agronomic traits; AFLP; Olea europaea; SSR.

Ano: 2006

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582006000500002

Quantitative trait loci mapping of pubescence density and flowering time of insect-resistant soybean (Glycine max L. Merr.)

Rojas,Gabriela; Méndez,Marco A; Muñoz,Carlos; Lemus,Gamalier; Hinrichsen,Patricio.

The genetic characterization of 117 peach and nectarine cultivars (Prunus persica (L.) Batsch) using microsatellite (SSR) markers is presented. Analyzed genotypes include the complete list of cultivars under intellectual property (IP) protection in Chile. One hundred and two out of the 117 cultivars under study could be identified using only 7 SSRs. Other 5 cultivars were differentiated using 3 additional markers, but 5 pairs of genotypes were not differentiable. The average expected heterozygosity for the set of markers was 0.55, ranging from 0.28 in BPPCT-008 to 0.81 in CPPCT-022, with an F value of 0.37. A Neighbor-Joining dendrogram showed that, with few exceptions, peaches and nectarines clustered separately. These results are the basis for the...

Tipo: Journal article

Palavras-chave: Cultivar identification; Fingerprinting; Prunus persica; Simple sequence repeats; SSR.

Ano: 2008

URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582008000500004

Komatsu,Kunihiko; Okuda,Shiori; Takahashi,Masakazu; Matsunaga,Ryoichi; Nakazawa,Yoshinori.

Analysis of antibiosis resistance to common cutworm (Spodoptera litura Fabricius) in soybean (Glycine max (L.) Merr.) has progressed significantly, but the immediate cause remains unknown. We performed quantitative trait loci (QTL) analysis of pubescence density and plant development stage because these factors are assumed to be the immediate cause of resistance to cutworm. The QTLs for pubescence appeared to be identical to the previously detected the Pd1 and Ps loci controlling pubescence density. We found no candidate loci for flowering time QTLs, although one could be identical to the gene governing the long-juvenile trait or to the E6 loci controlling maturity. None of the QTLs overlapped with the QTLs for antibiosis resistance.

Tipo: Info:eu-repo/semantics/other

Palavras-chave: Glycine max; Hair; Maturity; Pest resistance; QTL; SSR.

Ano: 2007

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000400022

Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers

Veasey,Elizabeth Ann; Borges,Aline; Rosa,Mariana Silva; Queiroz-Silva,Jurema R.; Bressan,Eduardo de Andrade; Peroni,Nivaldo.

We used simple sequence repeat (SSR) markers to investigate the genetic diversity of 78 sweet potato (Ipomoea batatas) accessions (58 landraces and 20 putative clones) from traditional agricultural households from 19 local communities in the Vale do Ribeira, São Paulo, Brazil. Eight SSR loci were assessed using 6% (w/v) polyacrylamide gels stained with silver nitrate and the accessions genotyped considering the presence or absence of bands. The results were subjected to analysis of molecular variance (AMOVA), and cluster and principal coordinate analyses. Spatial structure was assessed using Mantel's test to compare genetic and geographic distances. Each primer pair generated between three and ten clearly scorable polymorphic fragments. Cluster analyses...

Tandem repeat distribution of gene transcripts in three plant families

Palavras-chave: Genetic variability; Landraces; SSR; Traditional agriculture; Vale do Ribeira.

Ano: 2008

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000400020

Maia,Luciano Carlos da; Souza,Velci Queiróz de; Kopp,Mauricio Marini; Carvalho,Fernando Irajá Félix de; Oliveira,Antonio Costa de.

Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size...

In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

Palavras-chave: SSR; EST; Comparative genomics; Molecular markers.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000400025

Freitas,Patrícia Domingues de; Pinheiro,Allysson Pontes; Silva,Thiago Buosi; Galetti Junior,Pedro Manoel.

We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta- and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most...

SSR and AFLP based genetic diversity of soybean germplasm differing in photoperiod sensitivity

Palavras-chave: Crustacea; Microsatellite structure; Penaeidae; SSR.

Ano: 2007

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000600027

Singh,Ram K.; Bhatia,Virendra S.; Bhat,K.V.; Mohapatra,Trilochan; Singh,Nagendra K.; Bansal,Kailash C.; Koundal,K.R..

Forty-four soybean genotypes with different photoperiod response were selected after screening of 1000 soybean accessions under artificial condition and were profiled using 40 SSR and 5 AFLP primer pairs. The average polymorphism information content (PIC) for SSR and AFLP marker systems was 0.507 and 0.120, respectively. Clustering of genotypes was done using UPGMA method for SSR and AFLP and correlation was 0.337 and 0.504, respectively. Mantel's correlation coefficients between Jaccard's similarity coefficient and the cophenetic values were fairly high in both the marker systems (SSR = 0.924; AFLP = 0.958) indicating very good fit for the clustering pattern. UPGMA based cluster analysis classified soybean genotypes into four major groups with fairly...