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A lima bean core collection based on molecular markers Scientia Agricola
Gomes,Regina Lucia Ferreira; Costa,Marcones Ferreira; Alves-Pereira,Alessandro; Bajay,Miklos Maximiliano; Viana,João Paulo Gomes; Valente,Sérgio Emílio dos Santos; Lopes,Ângela Celis de Almeida; Zucchi,Maria Imaculada; Pinheiro,José Baldin.
ABSTRACT Some germplasm collections have a high number of accessions, which makes it difficult to explore the genetic variability present in the germplasm bank due to the redundancy and the difficulty of detailed analysis of all conserved accessions. Therefore, our study aimed to analyze the genetic diversity of 153 lima bean (Phaseolus lunatus) accessions for the purpose of constructing a core collection. Eleven SSRs were used for this purpose. The 153 lima bean accessions can be represented by low redundancy using a minimum of 34 accessions, thus representing 22 % of the size of the entire germplasm bank. The core collection had a higher Shannon diversity index and expected heterozygosity (1.906 and 0.811, respectively) than those presented by the entire...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Germplasm; Genetic diversity; Genetic structure; Microsatellite markers.
Ano: 2020 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162020000201100
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A note on the distribution of genetic diversity of Anglo-Nubian goats in central-northern farms of Piauí, Brazil R. Bras. Zootec.
Silvestre,Ellida de Aguiar; Costa,Márcio da Silva; Silva,Pollyana Oliveira da; Bajay,Miklos Maximiliano; Pinheiro,José Baldin; Zucchi,Maria Imaculada; Campelo,José Elivalto Guimarães; Britto,Fábio Barros.
The objective of this study was to characterize the genetic variability of Anglo-Nubian goats using microsatellite markers. The study was conducted using herds from four municipalities of Central-Northern Piauí (Teresina, José de Freitas, Campo Maior, and Angical), where technical information is scarce. Seven markers suggested by FAO were used (ILSTS11, McM527, INRA23, ETH10, OarfCB304, OarfCB48, and MAF209). The samples were genotyped using a 7% polyacrylamide gel. The average number of alleles per locus was 4.0, with observed and expected heterozygosity of 0.38 and 0.55, respectively. Few deviations from the Hardy-Weinberg equilibrium were observed for each population. Only two loci deviated significantly in two localities. The coefficient of gene...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Endogamy; Genetic structure; Microsatellite; Molecular markers.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982015000400155
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Allozymic variation in the clam genus Eurhomalea (Bivalvia: Veneriidae) along southern South American coast RChHN
GALLARDO,M.H; GONZÁLEZ,C; MENA,C; LOMOVASKY,B; MORRICONI,E; CLASING,E.
The correspondence between allozymic variation and specific differentiation was studied in four populations corresponding to the three nominal, allopatric species of clam genus Eurhomalea (E. rufa, E. lenticularis, E. exalbida) described for southern South America. Allozyme variation scored in 12 loci was high as indicated by heterozygosity levels (15.8-20.7 %) and by the presence of only three monomorphic loci (Hk-2, Icd-2, and Xdh-1). These high estimates of allelic variability were influenced by the low levels of interspecific genetic similarity (I = 0.64) and for the high conspecific values of genetic identity observed. The high estimates of substructuring found at the species level (F ST = 0.39) contrasted with the low differentiation (F ST = 0.027)...
Tipo: Journal article Palavras-chave: Allozymic variation; Genetic structure; Taxonomic status.
Ano: 2003 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-078X2003000300013
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Analysis by RAPD of the genetic structure of Astyanax altiparanae (Pisces, Characiformes) in reservoirs on the Paranapanema River, Brazil Genet. Mol. Biol.
Leuzzi,Maria Sueli Papa; Almeida,Fernanda Simões de; Orsi,Mário Luís; Sodré,Leda Maria Koelblinger.
In this study, the RAPD technique was used to analyze the genetic structure of populations of the fish Astyanax altiparanae (Characidae, Tetragonopterinae) living in the lower, middle and upper Paranapanema River, Brazil. The aim was to assess this structure regarding fish handling and conservation programs. The genetic variability (P) was found to be 42.64%, 75% and 75% in the low, middle and upper reaches, respectively. The dendrogram of genetic similarity, obtained by comparative analysis of the sets of samples from the three sites, showed the formation of three clusters. All of the genetic parameters used indicate that the population in the lower Paranapanema is genetically different from those in the middle and upper sections. The theta P test shows...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Astyanax altiparanae; RAPD; Genetic structure; Genetic conservation; Fish.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000300009
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Apport des informations moléculaires et cellulaires pour la caractérisation de la résistance de l'huître plate européenne vis-à-vis de la bonamiose, et pour la détection de signatures de la sélection naturelle ArchiMer
Harrang, Estelle.
The European flat oyster, an endemic species from European coasts, has been classified in the category of "endangered and/or declining species" since 2003. Indeed, the natural beds of this oyster, consumed since ancient times, have gradually been decimated by over-exploitation and by successive emergence of parasitic diseases. The parasite that causes the disease called bonamiosis has contributed to drastically reduce the French and European aquacultural production of flat oyster. Marine bivalve molluscs display two specificities that restrict possibilities to fight against diseases: they are grown in an open environment, and possess an innate immune system lacking in adaptive response. In this context, the selection of animaIs naturally resistant to...
Tipo: Text Palavras-chave: Huître plate Européenne; Ostre edulis; Bonamiose; Bonamia ostreae; Marqueurs SNP; Expression génique; Activité hémocytaire; Cartographie de liaison; QTL; EQTL; Populations naturelles; Diversité génétique; Sélection naturelle; European flat oyster; Ostrea edulis; Bonamiosis; Bonamia ostreae; SNP markers; Gene expression; Haemocytic activity; Linkage map; QTL; EQTL; Natural populations; Genetic diversity; Genetic structure; Natural selection.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00127/23785/21702.pdf
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Association mapping for yield and grain quality traits in rice (Oryza sativa L.). Repositório Alice
BORBA, T. C. de O.; BRONDANI, R. P. V.; BRESEGHELLO, F.; COELHO, A. S. G.; MENDONÇA, J. A.; RANGEL, P. H. N.; BRONDANI, C..
Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits,...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Association analysis; Core collection; Genetic structure; Arroz; Oryza sativa; Recurso genético; Germoplasma; Rice; Germplasm conservation.
Ano: 2010 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/862017
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Association mapping for yield and grain quality traits in rice (Oryza sativa L.) Genet. Mol. Biol.
Borba,Tereza Cristina de Oliveira; Brondani,Rosana Pereira Vianello; Breseghello,Flávio; Coelho,Alexandre Siqueira Guedes; Mendonça,João Antônio; Rangel,Paulo Hideo Nakano; Brondani,Claudio.
Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Association analysis; Core collection; Genetic structure.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000300023
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Characterization of 13 microsatellite loci developed from Meconopsis horridula Genet. Mol. Biol.
Zhao,Yu; Zhang,Shi-Bao; Yang,Jing; Zhang,Lu.
Meconopsis horridula is one of the eight most famous flowers in Chinese province of Yunnan. In this study, a modified biotin-streptavidin capture method was used to detect 13 microsatellite markers in the genome of M. horridula. The polymorphism of each locus was assessed in 24 samples collected from four populations. The number of alleles per locus ranged from 2 to 7 (mean: 3.2). The observed and expected heterozygosities ranged from 0.0833 to 0.9167 and 0.0816 to 0.8050, respectively. Additionally, nine of the 13 microsatellite markers were successfully amplified in three other congeneric species. These polymorphic SSR markers could be useful for studying the population genetics of M. horridula and for assessing genetic variation in this and congenerc...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetic structure; Heterozygosity; Meconopsis horridula; Microsatellite markers; Polymorphism.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000300026
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Characterization of casein gene complex and genetic diversity analysis in indian goats Inra
Rout, P.K.; Kumar, A.; Mandal, A.; Laloë, D.; Singh, S.K.; Roy, R..
Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at aS1-CN (CSN1S1), b-CN (CSN2), aS2-CN (CSN1S2), j-CN (CSN3), b-LG, and a-LA loci. Indian goats exhibited aS1-casein A allele in higher frequency in the majority of breeds except Ganjam and...
Tipo: Journal Article Palavras-chave:  Casein haplotype; Genetic polymorphism; Genetic structure; Goat.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD201140d0a011&uri=/notices/prodinra1/2011/06/
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Combining US and Brazilian Microsatellite Data for a meta-analysis of sheep (Ovis aries) breed diversity: facilitating the FAO Global Plan of Action for Conserving Animal Genetic Resources. Repositório Alice
PAIVA, S. R.; MARIANTE, A. da S.; BLACKBURN, H. D..
bitstream/item/183403/1/esr101.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genetic structure; Merging data sets; Molecular markers.
Ano: 2011 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/909125
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Comparative genetic structure in pines: evolutionary and conservation consequences RChHN
DELGADO,PATRICIA; CUENCA,ARGELIA; ESCALANTE,ANA E.; MOLINA-FREANER,FRANCISCO; PIÑERO,DANIEL.
Pines have been the focus of several studies that estimate population genetic parameters using both allozymes and chloroplast single sequence repeats (SSRs). Also, the genus has also been recently studied using molecular systematics so that we now have a more clear understanding of their evolutionary history. With this background we studied comparatively the genetic structure in pines. Expected heterozygosity is particularly constant with a 99 % confidence interval between 0.19 and 0.23 in species that have been studied until now using allozymes. There is a significant proportion of species (9/41) that show high population differentiation estimates (Fst = or larger than 0.15) and five of these have large and wingless seeds probably associated with low...
Tipo: Journal article Palavras-chave: Pinus; Genetic structure; Outcrossing rates; Microsatellites; Allozymes.
Ano: 2002 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-078X2002000100004
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Conservação genética de populações de Cryptocarya moschata Nees (Lauraceae) na Mata Atlântica do estado de São Paulo Rev. Bras. Bot.
MORAES,PEDRO LUÍS RODRIGUES DE; MONTEIRO,REINALDO; VENCOVSKY,ROLAND.
Através da análise de 18 locos isoenzimáticos polimórficos, foram estimadas as freqüências alélicas referentes a 214 indivíduos adultos de quatro populações naturais de Cryptocarya moschata de duas regiões do estado de São Paulo. Com base nas heterozigosidades observadas e esperadas, foram obtidas estimativas das estatísticas F de Wright. Para fins de comparação, utilizou-se também o método da análise da variância para estimação dos parâmetros correspondentes F = FIT, <FONT FACE="Symbol">q</font>P= FST e f = FIS. Os dois métodos forneceram resultados bastante concordantes: <img src="http:/img/fbpe/rbb/v22s2/f.gif" alt="f.gif (76 bytes)">IT = 0,142; <img src="http:/img/fbpe/rbb/v22s2/f.gif" alt="f.gif (76 bytes)">ST = 0,140; <img...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetic structure; Effective population size; Gene flow; Cryptocarya moschata.
Ano: 1999 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-84041999000500004
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Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oysters (Crassostrea gigas) revealed by genome-wide SNP data ArchiMer
Vendrami, David L. J.; Houston, Ross D.; Gharbi, Karim; Telesca, Luca; Gutierrez, Alejandro P.; Gurney-smith, Helen; Hasegawa, Natsuki; Boudry, Pierre; Hoffman, Joseph I..
Cultivated bivalves are important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium-density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed...
Tipo: Text Palavras-chave: Aquaculture; Crassostrea gigas; Genetic structure; High-density genotyping array; Inbreeding; Pacific oyster; Restriction site-associated DNA (RAD) sequencing; Single nucleotide polymorphism (SNP).
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00484/59561/62557.pdf
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Developing a common bean core collection suitable for association mapping studies Genet. Mol. Biol.
Perseguini,Juliana Morini Küpper Cardoso; Silva,Gliciane Micaele Borges; Rosa,João Ricardo Bachega Feijó; Gazaffi,Rodrigo; Marçal,Jéssica Fernanda; Carbonell,Sérgio Augusto Morais; Chiorato,Alisson Fernando; Zucchi,Maria Imaculada; Garcia,Antonio Augusto Franco; Benchimol-Reis,Luciana Lasry.
Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Molecular markers; Genetic diversity; Genetic structure; Microsatellites; Phaseolus vulgaris L.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000100067
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Discriminating populations of Paleosuchus trigonatus (Caimaninae: Alligatoridae) through microsatellite markers retrieved by next generation sequencing. Repositório Alice
MUNIZ, F. de L.; XIMENES, A. M.; BITTENCOURT, P. S.; RANGEL, S. M. H.; CAMPOS, Z. M. da S.; HRBEK, T.; FARIAS, I. P..
bitstream/item/182017/1/Discriminating-Zilca.pdf
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Cross-amplification; Genetic structure; Madeira River; Xingu River; Paleosuchus trigonatus.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1091695
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Estructura genética de poblaciones de Oligonychus perseae y Oligonychus punicae (Acari: Tetranychidae) en huertos de aguacate. Colegio de Postgraduados
Guzmán Valencia, Stephanie.
La identidad y estructura genética de poblaciones de Oligonychus punicae y O. perseae (Acari: Tetranychidae) fue estudiada en siete localidades productoras de aguacate Persea americana var. Hass. La identidad de los ácaros fue determinada morfológica y molecularmente mediante la secuenciación de una fracción del gen Citocromo Oxidasa subunidad I (COI). La variación genética intraespecífica de diferentes poblaciones de ambas especies de ácaros fue estudiada mediante la secuenciación de las regiones ITS1 e ITS2 del rADN. El análisis filogenético de las secuencias parciales del gen COI separó adecuadamente las dos especies de ácaros, confirmando los resultados de la identificación morfológica. El análisis de las secuencias de las regiones ITS1 e ITS2 del...
Palavras-chave: COI; ITS1; ITS2; Estructura genética; Entomología y Acarología; Maestría; Genetic structure.
Ano: 2012 URL: http://hdl.handle.net/10521/1765
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Evidence of two lineages of the dengue vector Aedes aegypti in the Brazilian Amazon, based on mitochondrial DNA ND4 gene sequences Genet. Mol. Biol.
Lima Júnior,Raimundo Sousa; Scarpassa,Vera Margarete.
Genetic variation was estimated in ten samples populations of Aedes aegypti from the Brazilian Amazon, by using a 380 bp fragment of the mitochocondrial NADH dehydrogenase subunit 4 (ND4) gene. A total of 123 individuals were analyzed, whereby 13 haplotypes were found. Mean genetic diversity was slightly high (h = 0.666 ± 0.029; π = 0.0115 ± 0.0010). Two AMOVA analyses indicated that most of the variation (~70%-72%) occurred within populations. The variation found among and between populations within the groups disclosed lower, but even so, highly significant values. F ST values were not significant in most of the comparisons, except for the samples from Pacaraima and Rio Branco. The isolation by distance (IBD) model was not significant (r = 0.2880; p =...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Aedes aegypti; Dengue vector; Genetic structure; Gene flow; Brazilian Amazon; Genetic lineages.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000200032
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Genetic charecterization of cotton landraces found in the Paraíba and Rio Grande do Norte states. Repositório Alice
MENEZES, I. P. P. DE; HOFFMANN, L. V.; BARROSO, P. A. V..
The objective of this study was to estimate genetic diversity of cotton mocó planted in Paraíba and Rio Grande do Norte using microsatellite markers, since mocó landraces are a valuable source of genetic diversity. A set of 38 accessions - 21 plants from Rio Grande do Norte and 17 from Paraiba - was analyzed using 24 pairs of cotton microsatellite primers, which amplified 20 polymorphic loci. The average inbreeding was 0.432, and was slightly higher in individuals from Paraíba than from Rio Grande do Norte. Genetic diversity (Nei´s unbiased estimator) between individuals from each state?s populations had similar values (HT = 0.327 and 0.302 in Paraíba and Rio Grande do Norte, respectively), indicating that comparable variability has been maintained....
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Cotton; Genetic structure; Microsatellite markers; Gossypium hirsutum.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1041495
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Genetic differentiation among Brazilian populations of Euschistus heros (Fabricius) (Heteroptera: Pentatomidae) based on RAPD analysis Neotropical Entomology
Sosa-Gomez,Daniel R.; Delpin,Katiaíres E.; Almeida,Alvaro M.R.; Hirose,Edson.
The Neotropical Brown Stink Bug (NBSB), Euschistus heros (Fabricius), has a wide distribution in Brazilian soybean fields, being more important in the central region of the country. The species is the main target of insecticide applications for stink bug pest control. We determined the variability among and within populations of the NBSB by random amplification of polymorphic DNA (RAPD) analysis. Samples of NBSB were collected in soybean fields from Ubiratã (PR), Londrina (PR), Centenário do Sul (PR), Cândido Mota (SP), Ponta Porã (MS) and Sapezal (MT). Genomic DNA was extracted from the head to minimize DNA contamination by endoparasites. DNA was amplified with 10 mer primers. Fifteen primers produced 246 bands. The genetic similarity matrix was obtained,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: RAPD; Molecular marker; Genetic structure; Gene flow.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1519-566X2004000200009
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Genetic diversity in cultivated carioca common beans based on molecular marker analysis Genet. Mol. Biol.
Perseguini,Juliana Morini Küpper Cardoso; Chioratto,Alisson Fernando; Zucchi,Maria Imaculada; Colombo,Carlos Augusto; Carbonell,Sérgio Augusto Moraes; Mondego,Jorge Mauricio Costa; Gazaffi,Rodrigo; Garcia,Antonio Augusto Franco; Campos,Tatiana de; Souza,Anete Pereira de; Rubiano,Luciana Benchimol.
A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats - SSRs and amplified fragment length polymorphisms - AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger's modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were...
Tipo: Info:eu-repo/semantics/article Palavras-chave: AFLPs; Genetic structure; Genetic variability; Phaseolus vulgaris L.; SSRs.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000100017
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