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Wadl P.A.,University of Tennessee at Knoxville | Szyp-Borowska I.,Forest Research Institute | Piorecki N.,Arboretum and Institute of Physiography | Piorecki N.,University of Rzeszow | And 3 more authors.
Scientia Horticulturae | Year: 2014

Cornelian cherry (Cornus mas L.) is indigenous to central and southeastern Europe and is an ecologically and economically important shrub or small tree. The aim of this study was to develop molecular tools for assessing genetic diversity and provide unique molecular identification of C. mas samples from central Europe and United States. A microsatellite-enriched library was used to develop nine polymorphic microsatellite loci. The loci amplified perfect and imperfect repeats with 2 to 11 alleles detected per locus. Observed heterozygosity ranged from 0.00 to 0.71 and expected heterozygosity ranged from 0.00 to 0.82. Additionally, cross species transfer to Cornus eydeana was observed. The multilocus allelic data was used to cluster 37 C. mas samples and 1 C. eydeana sample based on the allele sharing distance matrix. The similarity coefficient ranged from 0.05 to 0.73 among all genotypes. All C. mas individuals clustered into two main clades, with the single C. eydeana sample used to root the dendrogram. All samples in group I belong to the botanical form Macrocarpa and originated from Austria, Poland, or Ukraine, whereas group II included samples that originated from Poland, Romania, and the United States. Five loci (CM007, CM010, CM031, CM037, and CM043) were used to develop a molecular identification key that successfully delineated all samples. The loci described in this study will facilitate further investigations of genetic diversity, gene flow, and genetic structure among populations of C. mas. © 2014 Elsevier B.V. Source


Zaidi S.S.-E.-A.,National Institute for Biotechnology and Genetic Engineering NIBGE | Zaidi S.S.-E.-A.,Pakistan Institute of Engineering and Applied Sciences | Shafiq M.,National Institute for Biotechnology and Genetic Engineering NIBGE | Shafiq M.,Pakistan Institute of Engineering and Applied Sciences | And 5 more authors.
PLoS ONE | Year: 2016

Cotton leaf curl disease (CLCuD) is the major biotic constraint to cotton production on the Indian subcontinent, and is caused by monopartite begomoviruses accompanied by a specific DNA satellite, Cotton leaf curl Multan betasatellite (CLCuMB). Since the breakdown of resistance against CLCuD in 2001/2002, only one virus, the "Burewala" strain of Cotton leaf curl Kokhran virus (CLCuKoV-Bur), and a recombinant form of CLCuMB have consistently been identified in cotton across the major cotton growing areas of Pakistan. Unusually a bipartite isolate of the begomovirus Tomato leaf curl virus was identified in CLCuD-affected cotton recently. In the study described here we isolated the bipartite begomovirus Tomato leaf curl New Delhi virus (ToLCNDV) from CLCuD-affected cotton. To assess the frequency and geographic occurrence of ToLCNDV in cotton, CLCuD-symptomatic cotton plants were collected from across the Punjab and Sindh provinces between 2013 and 2015. Analysis of the plants by diagnostic PCR showed the presence of CLCuKoV-Bur in all 31 plants examined and ToLCNDV in 20 of the samples. Additionally, a quantitative real-time PCR analysis of the levels of the two viruses in co-infected plants suggests that coinfection of ToLCNDV with the CLCuKoV-Bur/CLCuMB complex leads to an increase in the levels of CLCuMB, which encodes the major pathogenicity (symptom) determinant of the complex. The significance of these results are discussed. © 2016, Public Library of Science. All rights reserved. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Source


Buriev Z.T.,Academy of Sciences of Uzbekistan | Saha S.,U.S. Department of Agriculture | Abdurakhmonov I.Y.,Academy of Sciences of Uzbekistan | Jenkins J.N.,U.S. Department of Agriculture | And 3 more authors.
Theoretical and Applied Genetics | Year: 2010

MIC-3 is a recently identified gene family shown to exhibit increased root-specific expression following nematode infection of cotton plants that are resistant to root-knot nematode. Here, we cloned and sequenced MIC-3 genes from selected diploid and tetraploid cotton species to reveal sequence differences at the molecular level and identify chromosomal locations of MIC-3 genes in Gossypium species. Detailed sequence analysis and phylogenetic clustering of MIC-3 genes indicated the presence of multiple MIC-3 gene members in Gossypium species. Haplotypes of a MIC-3 gene family member were discovered by comparative analysis among consensus sequences across genotypes within an individual clade in the phylogram to overcome the problem of duplicated loci in the tetraploid cotton. Deficiency tests of the SNPs delimited six At-genome members of the MIC-3 family clustered to chromosome arm 4sh, and one Dt-genome member to chromosome 19. Clustering was confirmed by long-PCR amplification of the intergenic regions using At-genome-specific MIC-3 primer pairs. The clustered distribution may have been favored by selection for responsiveness to evolving disease and/or pest pressures, because large variants of the MIC-3 gene family may have been recovered from small physical areas by recombination. This could give a buffer against selection pressure from a broad range of pest and pathogens in the future. To our knowledge, these are the first results on the evolution of clustering and genome-specific haplotype members of a unique cotton gene family associated with resistant response against a major pathogen. © Springer-Verlag 2009. Source


Perera O.P.,U.S. Department of Agriculture | Blanco C.A.,U.S. Department of Agriculture | Ballard L.,Genomics and Bioinformatics Research Unit | Silva-Brandao K.L.,University of Sao Paulo | And 2 more authors.
Southwestern Entomologist | Year: 2011

Polymorphic genetic markers were identified and characterized using a partial genomic library of the tobacco budworm, Heliothis virescens (Fabricius), enriched for simple sequence repeats (SSR) and nucleotide sequences of expressed sequence tags (EST). Nucleotide sequences of 192 clones from the partial genomic library yielded 147 unique SSRs while EST evaluations identified 280 SSR-containing sequences. All anonymous SSRs and 192 EST-SSRs were evaluated to select loci that produced the best quality peaks without stutter peaks. Six anonymous markers and nine EST-derived markers were selected to evaluate a sample of 96 insects collected from Stoneville, MS. The observed number of alleles ranged from two to eight, with an average of 5.87 (SE ± 0.53). The polymorphic information content (PIC) value averaged 0.446 (SE ± 0.052). Significant deviations from Hardy-Weinberg expectations were detected at eight loci. We speculate that these loci are under selection in the population of tobacco budworm used in the study. No significant linkage disequilibrium was detected at any of the loci. Proportions of anonymous and EST-SSR markers validated after extensive evaluation were 4.08 and 4.68%, respectively. One anonymous SSR marker (HvMS117) and all nine EST markers were transferable to the bollworm, Helicoverpa zea (Boddie). Copyright © 2011 BioOne All rights reserved. Source


Duitama J.,Agrobiodiversity research area | Silva A.,Agrobiodiversity research area | Sanabria Y.,Louisiana State University | Cruz D.F.,Agrobiodiversity research area | And 10 more authors.
PLoS ONE | Year: 2015

Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops. © 2015 Public Library of Science. All rights reserved. Source

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