Breeding without Breeding: Is a Complete Pedigree Necessary for Efficient Breeding?

Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called “Breeding without Breeding” (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB

An interlaboratory comparison on the characterization of a sub-micrometer polydisperse particle dispersion

The measurement of polydisperse protein aggregates and particles in biotherapeutics remains a challenge, especially for particles with diameters of ≈ 1 µm and below (sub-micrometer). This paper describes an interlaboratory comparison with the goal of assessing the measurement variability for the characterization of a sub-micrometer polydisperse particle dispersion composed of five sub-populations of poly(methyl methacrylate) (PMMA) and silica beads. The study included 20 participating laboratories from industry, academia, and government, and a variety of state-of-the-art particle-counting instruments. The received datasets were organized by instrument class to enable comparison of intralaboratory and interlaboratory performance. The main findings included high variability between datasets from different laboratories, with coefficients of variation from 13 % to 189 %. Intralaboratory variability was, on average, 37 % of the interlaboratory variability for an instrument class and particle sub-population. Drop-offs at either end of the size range and poor agreement on maximum counts of particle sub-populations were noted. The mean distributions from an instrument class, however, showed the size-coverage range for that class. The study shows that a poly-disperse sample can be used to assess performance capabilities of an instrument set-up (including hardware, software, and user settings) and provides guidance for the development of polydisperse reference materials.Drug Delivery Technolog

Perspectives on the use of transcriptomics to advance biofuels

As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.clos

Genetic Improvement of Racosperma spp. for Agroforestry in sub-Saharan African Countries

Racosperma auriculiformis (formerly Acacia auriculiformis) and R. mangium (formerly Acacia mangium), two woody leguminous plants, have been introduced in many sub-Saharan African countries for reforestation and agroforestry purposes. Nodulation with Rhizobium and vesicular- arbuscular (VA) mycorrhizal associations contribute much to the growth of both species, especially in soils poor in nutrients. Improved methods of enzyme extraction and horizontal starch gel electrophoresis were developed in order to study the mating system, the genetic diversity and its architecture within and among populations of both species. Analysis of the mating system revealed a predominantly outcrossing mode. The use of allozyme markers showed that populations were found with low apparent inbreeding and that diversity resided predominantly within populations. Early genecological tests showed that variation in quantitative characters follows patterns of geographic variation for both species. These tests permitted the selection of Papua New Guinea provenances as the most productive and adapted for use in agroforestry. Such a screening was also conducted for rooting ability, for its use in production of monospecific and hybrid varieties. To maximise plant productivity, a two-step selection procedure is suggested, the first step regarding the host plant and the second one the microsymbiont strains

Genetic Improvement of Racosperma spp. for Agroforestry in sub-Saharan African Countries

A book chapter/ conference paper on genetically engineering aggro-forestry in Sub-Saharan Africa.Racosperma auriculiformis (formerly Acacia auriculiformis) and R. mangium (formerly Acacia mangium), two woody leguminous plants, have been introduced in many sub-Saharan African countries for reforestation and agroforestry purposes. Nodulation with Rhizobium and vesicular- arbuscular (VA) mycorrhizal associations contribute much to the growth of both species, especially in soils poor in nutrients. Improved methods of enzyme extraction and horizontal starch gel electrophoresis were developed in order to study the mating system, the genetic diversity and its architecture within and among populations of both species. Analysis of the mating system revealed a predominantly outcrossing mode. The use of allozyme markers showed that populations were found with low apparent inbreeding and that diversity resided predominantly within populations. Early genecological tests showed that variation in quantitative characters follows patterns of geographic variation for both species. These tests permitted the selection of Papua New Guinea provenances as the most productive and adapted for use in agroforestry. Such a screening was also conducted for rooting ability, for its use in production of monospecific and hybrid varieties. To maximise plant productivity, a two-step selection procedure is suggested, the first step regarding the host plant and the second one the microsymbiont strains

Inferring the past from the present phylogeographic structure of North American forest trees Seeing the forest for the genes

The study of past historical events that have led to ecological changes is a recurrent topic in many disciplines. Given that many of these events have left a large and long-lasting evolutionary imprint on the extant population genetic structure of species, phylogeographic studies on modern taxa have been largely used to infer the impacts of these events and to complement previous paleoecological and paleobotanical surveys. In spite of the geographical and geological com- plexity of North America, converging patterns can be observed when comparing the available genetic data for forest trees. Such patterns include the co-location of genetic discontinuities among species and their coincidence with mountain ranges (e.g.;the Appalachians, the Rocky Mountains, the Sierra Nevada, or the Transverse Volcanic Belt) and with previously in- ferred glacial refugia. Using examples drawn from the available literature, we illustrate such shared features and present the contrasting phylogeographic patterns observed among the different regions of the continent. The various evolutionary consequences of historical events that can be deduced from these phylogeographic studies (e.g.;past bottlenecks, founder effects, allopatric divergence, or introgressive hybridization) are additionally discussed. The present challenges and future research prospects that are likely to further advance this field are finally outlined

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa.

Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational and abandoned gold mines, farms, and formal and informal settlements. In this study, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in the lower Wonderfonteinspruit and their response to various contaminant sources. The results showed that composition and structure of bacterial communities differed significantly (P<0.05) between less (downstream) and more (upstream) polluted sites. The taxonomic and functional gene dissimilarities significantly correlated with each other, while downstream sites had more distinct functional genes. The relative abundance of Proteobacteria, Bacteroidetes and Actinobacteria was higher at upstream sites, while Acidobacteria, Cyanobacteria, Firmicutes and Verrucomicrobia were prominent at downstream sites. In addition, upstream sites were rich in genera pathogenic and/or potentially pathogenic to humans. Multivariate and correlation analyses suggest that bacterial diversity was significantly (P<0.05) impacted by pH and heavy metals (cobalt, arsenic, chromium, nickel and uranium). A significant fraction (~14%) of the compositional variation was explained by a combination of anthropogenic inputs, of which mining (~6%) was the main contributor to bacterial community variation. Network analysis indicated that bacterial communities had non-random inter- and intra-phyla associations and that the main taxa showed both positive and negative linkages to environmental parameters. Our results suggest that species sorting, due to environmental parameters, was the main process that structured bacterial communities. Furthermore, upstream sites had higher relative abundances of genes involved in xenobiotic degradation, suggesting stronger removal of polycyclic aromatic hydrocarbons and other organic compounds. This study provides insights into the influences of anthropogenic land use on bacterial community structure and functions in the lower Wonderfonteinspruit