A Simple Method for Automated Allele Binning in Microsatellite Markers

Idury, Ramana M.; Cardon, Lon R.

doi:10.1101/gr.7.11.1104

Cited by 96 publications

(78 citation statements)

References 8 publications

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“…O genitor não genotipado foi o clone 7. Na obtenção da dissimilaridade genética entre os 20 genitores, os tamanhos de fragmentos em pares de bases dos marcadores do tipo microssatélite foram padronizados utilizando-se o software "Allelobin" (Idury & Cardon, 1997). Esse software utiliza um procedimento de categorização de alelos em classes, definidos com base em quadrados mínimos, para eliminar o problema de padronização com uso de critérios pessoais.…”

Section: Methodsunclassified

Potencial de híbridos entre clones-elite de eucalipto por meio de marcadores microssatélites

Aguiar

Ferreira²,

Aguiar³

et al. 2007

Pesq. agropec. bras.

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Resumo -O objetivo deste trabalho foi avaliar o potencial dos marcadores microssatélites em predizer o comportamento dos híbridos entre clones-elite de eucalipto da empresa Aracruz Celulose. Foram utilizados 21 clones-elite, cruzados conforme o esquema de dialelo balanceado. Os 137 híbridos obtidos, além dos 21 pais e 11 híbridos repetidos, foram avaliados em três locais: Aracruz, São Mateus e Caravelas, em delineamento de blocos incompletos 13x13 com 40 repetições. As parcelas foram constituídas de uma planta, espaçadas 3x3 m. Os caracteres circunferência à altura do peito (CAP) e densidade básica da madeira foram avaliados aos dois anos de idade. Os dados foram submetidos à análise dialélica e, posteriormente, foi obtida a correlação entre a divergência genética dos genitores, obtida por meio dos marcadores microssatélites, e as estimativas dos parâmetros do dialelo. A divergência genética apresentou coeficientes de correlação significativos apenas com a capacidade específica de combinação para CAP e com a média dos híbridos para CAP. A predição por meio de marcadores microssatélites possui baixa precisão para poder ser utilizada em substituição aos cruzamentos dialélicos.Termos para indexação: Eucalyptus, análise dialelo, divergência genética, melhoramento genético. Potential of hybrids among elite clones of eucalypt by microsatellite markersAbstract -The objective of this work was to evaluate the potential of microsatellite markers to predict the performance of hybrids among elite clones of eucalypt from Aracruz Celulose. Twenty one elite clones were crossed in a full-diallel mating scheme. One hundred and thirty seven hybrids, 21 parents and 11 repeated hybrids were evaluated in three sites: Aracruz, São Mateus and Caravelas, in an experimental design of incomplete blocks 13x13 with 40 replicates, comprising single plant plot and spaced 3x3 m. The characters evaluated were the circumference at breast height (CBH) and the wood basic density, two years after the planting. Means were submitted to diallel analysis and, later, the correlation between the genetic divergence of parents by microsatellite markers and the estimative of diallel parameters were obtained. The genetic divergence was correlated with the specific combining ability to CBH height and with the means of hybrids to the same character. The other coefficients of correlation with the genetic divergence were not significantly different from zero. The prediction by microsatellite markers is of little accuracy to be utilized in place of diallel estimates.

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Section: Methodsunclassified

Potencial de híbridos entre clones-elite de eucalipto por meio de marcadores microssatélites

Aguiar

Ferreira²,

Aguiar³

et al. 2007

Pesq. agropec. bras.

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“…Thus, the software AlleloBin (Prasanth et al 2006) was used to classify observed microsatellite allele sizes into representative discrete alleles using the least-square minimization algorithm of Idury and Cardon (1997). All statistical analyses were performed on the adjusted data.…”

Section: Data Scoring and Analysesmentioning

confidence: 99%

Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers

et al. 2010

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Corresponding author e-mail: e_mutegi.1@yahoo.com 2 3 AbstractUnderstanding the extent and partitioning of diversity within and among crop landraces and their wild/ weedy relatives constitutes the first step in conserving and unlocking their genetic potential. This study aimed to characterize the genetic structure and relationships within and between cultivated and wild sorghum at country scale in Kenya, and to elucidate some of the underlying evolutionary mechanisms. We analyzed a total of 439 individuals comprising 329 cultivated and 110 wild sorghums using 24 microsatellite markers. We observed a total of 295 alleles across all loci and individuals, with 257 different alleles being detected in the cultivated sorghum gene pool and 238 alleles in the wild sorghum gene pool.We found that the wild sorghum gene pool harboured significantly more genetic diversity than its domesticated counterpart, a reflection that domestication of sorghum was accompanied by a genetic bottleneck. Overall, our study found close genetic proximity between cultivated sorghum and its wild progenitor, with the extent of crop-wild divergence varying among cultivation regions. The observed genetic proximity may have arisen primarily due to historical and/or contemporary gene flow between the two congeners, with differences in farmers' practices explaining inter-regional gene flow differences. This suggests that deployment of transgenic sorghum in Kenya may lead to escape of transgenes into wildweedy sorghum relatives. In both cultivated and wild sorghum, genetic diversity was found to be structured more along geographical level than agro-climatic level. This indicated that gene flow and genetic drift contributed to shaping the contemporary genetic structure in the two congeners. Spatial autocorrelation analysis revealed a strong spatial genetic structure in both cultivated and wild sorghums at the country scale, which could be explained by medium-to long-distance seed movement.

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“…4.0 (Life Technologies, USA). The raw data were converted into discrete allele sizes using the leastsquare minimisation algorithm implemented in AlleloBin software (Idury & Cardon 1997).…”

Section: Microsatellite Analysesmentioning

confidence: 99%

Comparison of range-wide chloroplast microsatellite and needle trait variation patterns in Pinus mugo Turra (dwarf mountain pine)

Żukowska¹,

Boratyńska²,

Wachowiak³

2017

iForest

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In this study, range-wide genetic variation was analysed in 553 Pinus mugo Turra (dwarf mountain pine) individuals from 21 locations using 11 chloroplast microsatellites. Our main goal was to assess the spatial distribution of neutral genetic variation. We also used data from a previous study on the morphological variation of needles from 18 stands of P. mugo. In total, 22 needle characteristics were reanalysed and compared to microsatellite data to describe the distribution of morphological variation in the context of neutral genetic variation. We hypothesised that the chloroplast microsatellite and needle trait variation patterns would not entirely overlap. The results indicate the recent divergence of P. mugo populations derived from a formerly larger distribution. We identified 4 genetic and 3 morphological clusters whose spatial distribution overlapped only to some extent. The distribution of genetic variation showed a south-north pattern with signs of admixture in the Alps and Carpathians. Two south-westernmost stands from Italy were evidently isolated from the others. In contrast, morphological variation tended to display a west-east pattern. A separate group based on needle traits was formed mostly by eastern stands and was not observed by microsatellite analysis. In addition, a few needle characteristics significantly correlated with longitude and climate variables. These findings suggest that eastern populations of P. mugo may be of different origin and/or that some needle characteristics may be adaptively important in these locations. The potential roles of past demographic events, phenotypic plasticity and local adaptation in shaping the patterns of genetic and morphological variation in P. mugo are discussed.

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A Simple Method for Automated Allele Binning in Microsatellite Markers

Cited by 96 publications

References 8 publications

Potencial de híbridos entre clones-elite de eucalipto por meio de marcadores microssatélites

Potencial de híbridos entre clones-elite de eucalipto por meio de marcadores microssatélites

Genetic structure and relationships within and between cultivated and wild sorghum (Sorghum bicolor (L.) Moench) in Kenya as revealed by microsatellite markers

Comparison of range-wide chloroplast microsatellite and needle trait variation patterns in Pinus mugo Turra (dwarf mountain pine)

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