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We present the development of a genomic library using RADseq (restriction site associated DNA sequencing) protocol for marker discovery that can be applied on evolutionary studies of the sugarcane borer Diatraea saccharalis, an important South American insect pest. A RADtag protocol combined with Illumina paired-end sequencing allowed de novo discovery of 12 811 SNPs and a high-quality assembly of 122.8M paired-end reads from six individuals, representing 40 Gb of sequencing data. Approximately 1.7 Mb of the sugarcane borer genome distributed over 5289 minicontigs were obtained upon assembly of second reads from first reads RADtag loci where at least one SNP was discovered and genotyped. Minicontig lengths ranged from 200 to 611 bp and were used for functional annotation and microsatellite discovery. These markers will be used in future studies to understand gene flow and adaptation to host plants and control tactics. [ABSTRACT FROM AUTHOR]

With 1 figure and 1 table Curcuma longa L. is a sterile, triploid, vegetatively-propagated crop cultivated mainly in Southeast Asia. When dried rhizomes are ground, the resulting yellow powder is used by the food industry as a natural food dye. Moreover, many pharmacological compounds have broadened the commercial application of the crop. However, conventional breeding is difficult and hence, improvement has been limited to germplasm selection. To better utilize the germplasm collections and facilitate genotype selection, a total of 17 polymorphic microsatellite loci were developed using a CT/GT/CTT enriched genomic library. All microsatellites resulted in amplified PCR products, showing a banding pattern of 2-11 polymorphic bands per locus, enabling genotype discrimination. These results can be used in further studies aimed at characterizing C. longa genetic resource collections and also to improve breeding strategies. [ABSTRACT FROM AUTHOR]

Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out. Le Brachiaria humidicola (Rendle) Schweick. est une graminée des climats chauds fréquemment employée comme plante fourragère dans les tropiques. Des accessions de cette espèce ont été collectés en Afrique de l'Est et massivement introduites dans les Amériques au cours des années 1980. Plusieurs de ces accessions sont représentées au sein d'une collection de ressources génétiques maintenue par le Brazilian Agricultural Research Corporation. Cependant, l'apomixie, la ploïdie et des connaissances limitées des bases génétiques des accessions de cette collection ont restreint les efforts de sélection. Les objectifs de ce travail étaient d'identifier la variabilité génétique au sein de la collection brésilienne du B. humidicola au moyen de microsatellites et de comparer les résultats avec les informations suivantes : 1) le lieu de collection des accessions ; 2) le mode de reproduction et le niveau de ploïdie ; et 3) la diversité génétique mesurée sur la base des caractères morphologiques. La collection de ressources génétiques examinée forme quatre groupes majeurs très distincts. La seule accession à reproduction sexuée se distinguait des quatre autres groupes. Le degré de différenciation génétique n'était corrélé ni avec la distance géographique ni avec la distance génétique mesurée sur la base des caractères morphologiques. De plus, la structure génétique identifiée au sein de la collection ne correspond pas à des différences quant aux niveaux de ploïdie. Les allèles présents uniquement au sein d'accessions sexuées ou apomictiques ont été identifiés et une évaluation ultérieure de l'association entre ces locus et l'aposporie serait utile. [ABSTRACT FROM AUTHOR]

Abstract Aim: To study the response of the bacterial community to bioremediation of a soil with an aged contamination of crude oil. Methods and Results: The bacterial community in laboratory soil columns during a 72-day biostimulation treatment was followed by analysing the number of total cultivable hydrocarbon-degrading bacteria, soil respiratory activity and the 16S–23S rDNA internal transcribed spacer homoduplex heteroduplex polymorphisms (ITS-HHP) of total soil bacterial DNA. ITS-HHP permits an estimate of both length and sequence polymorphism in a 16S–23S rDNA spacer population, using to advantage the homoduplex and heteroduplex fragments that are generated during PCR. The treatment, made by air sparging and biostimulation with a mineral nutrient and surfactant solution, resulted in a 39·5% decrease of the total hydrocarbon content. Within 4 days of treatment onset the bacterial community underwent a first phase of activation that led to a substantial increase in the observable diversity. Subsequently, after a 12-day period of stability, another activation phase was observed with further shifts of the community structure and an increase in the abundance and diversity of catechol-2,3-dioxygenase (C23O) genes. Conclusions: The overall data suggest an important contribution of uncultivable bacteria to the soil bioremediation, since, during the second activation phase, the increases of the respiratory activity, bacterial diversity and C23O gene abundance and diversity were not accompanied by a corresponding increase of the cultivable bacteria number. Significance and Impact of the Study: This study shows that successive phases of activation of bacterial populations occur during a bioremediation treatment of oil-polluted soil. [ABSTRACT FROM AUTHOR]