Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Cost reduction in plant breeding and conservation programs depends largely on correctly defining the minimal sample size required for the trustworthy assessment of intra- and inter-cultivar genetic variation. White clover, an important pasture legume, was chosen for studying this aspect. In clonal plants, such as the aforementioned, an appropriate sampling scheme eliminates the redundant analysis of identical genotypes. The aim was to define an optimal sampling strategy, i.e., the minimum sample size and appropriate sampling scheme for white clover cultivars, by using AFLP data (283 loci) from three popular types. A grid-based sampling scheme, with an interplant distance of at least 40 cm, was sufficient to avoid any excess in replicates. Simulations revealed that the number of samples substantially influenced genetic diversity parameters. When using less than 15 per cultivar, the expected heterozygosity (He) and Shannon diversity index (I) were greatly underestimated, whereas with 20, more than 95% of total intra-cultivar genetic variation was covered. Based on AMOVA, a 20-cultivar sample was apparently sufficient to accurately quantify individual genetic structuring. The recommended sampling strategy facilitates the efficient characterization of diversity in white clover, for both conservation and exploitation

A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)

<p>Abstract</p> <p>Background</p> <p>Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (<it>Gossypium hirsutum </it>L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (<it>Li₂</it>) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, <it>Li₂</it>is a model system with which to study fiber elongation.</p> <p>Results</p> <p>Two near-isogenic lines of Ligon lintless-2 (<it>Li₂</it>) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC₅). An F₂population was developed from a cross between the two <it>Li₂</it>near-isogenic lines and used to develop a linkage map of the <it>Li₂</it>locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the <it>Li₂</it>locus region with two of the markers flanking the <it>Li₂</it>locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the <it>Li₂</it>mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the <it>Li₂</it>locus.</p> <p>Conclusions</p> <p>In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the <it>Li₂</it>locus on chromosome 18 and resided in a gene with similarity to a putative plectin-related protein. The complete linkage suggests that this expressed sequence may be the <it>Li₂</it>gene.</p

Ocean Acidification at High Latitudes: Potential Effects on Functioning of the Antarctic Bivalve Laternula elliptica

Ocean acidification is a well recognised threat to marine ecosystems. High latitude regions are predicted to be particularly affected due to cold waters and naturally low carbonate saturation levels. This is of concern for organisms utilising calcium carbonate (CaCO3) to generate shells or skeletons. Studies of potential effects of future levels of pCO2 on high latitude calcifiers are at present limited, and there is little understanding of their potential to acclimate to these changes. We describe a laboratory experiment to compare physiological and metabolic responses of a key benthic bivalve, Laternula elliptica, at pCO2 levels of their natural environment (430 µatm, pH 7.99; based on field measurements) with those predicted for 2100 (735 µatm, pH 7.78) and glacial levels (187 µatm, pH 8.32). Adult L. elliptica basal metabolism (oxygen consumption rates) and heat shock protein HSP70 gene expression levels increased in response both to lowering and elevation of pH. Expression of chitin synthase (CHS), a key enzyme involved in synthesis of bivalve shells, was significantly up-regulated in individuals at pH 7.78, indicating L. elliptica were working harder to calcify in seawater undersaturated in aragonite (ΩAr = 0.71), the CaCO3 polymorph of which their shells are comprised. The different response variables were influenced by pH in differing ways, highlighting the importance of assessing a variety of factors to determine the likely impact of pH change. In combination, the results indicate a negative effect of ocean acidification on whole-organism functioning of L. elliptica over relatively short terms (weeks-months) that may be energetically difficult to maintain over longer time periods. Importantly, however, the observed changes in L. elliptica CHS gene expression provides evidence for biological control over the shell formation process, which may enable some degree of adaptation or acclimation to future ocean acidification scenarios

Regional differentiation of New Zealand Pinot noir wine by wine professionals using canonical variate analysis

Pinot noir is the most widely planted red grape variety in New Zealand and is considered a premium product based on the price per volume. To date no studies have attempted to characterize the different styles of the four main Pinot noir producing regions: Central Otago, Marlborough, Martinborough, and Waipara. The intensities of aroma, flavor, and mouthfeel attributes of commercial regional wines from two vintages were investigated. Descriptive analysis was carried out by a panel consisting of experienced but untrained wine professionals. Canonical variate analysis showed that the four wine regions were differentiated according to aroma (barnyard, black cherry, herbal, raspberry, red cherry, oak, spice and violet), in-mouth flavor (fruit density/concentration and red fruit), and mouthfeel (balance, body, and finish length) attributes. Results show that Pinot noir wines from the four regions of New Zealand are stylistically different and that experienced but untrained wine professionals produce reliable results for this type of sensory analysis

A comparison of cardinal temperatures estimated by linear and nonlinear models for germination and bulb growth of forage brassicas

Forage brassicas are widely used as a supplementary feed in temperate pasture systems but there is a lack of quantitative data about their growth and development. Furthermore, numerous models are available to estimate cardinal temperatures but there is uncertainty about whether linear or nonlinear models should be used. Initially a germination experiment was used to describe the rate response of nine forage brassicas to temperature. Three models were compared to estimate cardinal temperatures and the two best models were used for thermal time (Tt) accumulation for three groups of forage brassicas. Cardinal temperatures, defined as the base (Tb), optimum (Topt) and maximum (Tm), differed among groups of species for the bilinear and Lactin models but were similar within a group of species for these models. In most cases, cardinal temperatures estimated by the bilinear and Lactin models for the B. rapa group ranged from 3 to 4 °C for Tb, 31 °C for Topt and 41 to 48 °C for Tm. For the B. napus and B. napus biennis groups these temperatures ranged from 0 to 3 °C for Tb, 29 to 33 °C for Topt and 38 °C for Tm. The B. oleracea group had temperatures from 0 to 1 °C for Tb, 25 to 27 °C for Topt and 35 °C for Tm. A second data set based on hypocotyl thickening was used to estimate the base temperature (Tb) for bulb growth of turnips and swedes. Both models estimated an average Tb of 4.2 °C for bulb turnips and an average of 3.7 °C for swedes. The Lactin model was considered the most adequate model to describe temperature responses where as, in some cases, the bilinear model had to be modified to account for changes in the rate of development. More importantly, an appropriate range of test temperatures was crucial for the estimation of reliable cardinal temperatures, independent of the model used

Recovery of ovulation rate in ewes following their removal from an oestrogenic lucerne forage

Grazing ewes on lucerne crops that contain elevated coumestrol concentrations before and during their mating period can decrease ovulation rate, which results in fewer multiple birth lambs. In this experiment, the ovulation rate of ewes grazing a moderately oestrogenic (29.1 ± 2.88 mg coumestrol/kg DM) lucerne crop for 6 weeks was compared with those transferred to grass pasture for 1 or 3 weeks, and a Control group on grass throughout. Ordinal regression predicted an exponential relationship with a sharp initial increase in ovulation rate from 0 to 14 days on grass that levelled off when ewes were on grass for durations greater than 3 weeks. Of importance, moderate coumestrol levels in lucerne remained throughout the experiment, and liveweight was unaffected by grazing treatment. This experiment quantified the decrease in risk of impaired lambing performance due to moderately oestrogenic lucerne consumption in relation to time on grass before ovulation. Specifically, removal of ewes from lucerne 2 weeks before ovulation mitigated the risk of decreased lambing performance

A Simulation of Sheep Crossbreeding Systems: a Risk Analysis

A static simulation study was performed to develop algorithms and a model for predicting crossbred performance. The model was built using @Risk software using quantitative risk analysis. Estimates of crossbreeding parameters were fitted with normal distribution functions as the model inputs. Sets of available population means were used as model target values. The standard deviations of the predicted means from the target values for all structured crossbreeding systems using up to 4 breeds were compared to predefined risk threshold criteria. This appeared to be a good approach to estimating robust, balanced trait parameters

Prediction of coumestrol content in unirrigated lucerne crops using weather variables

Elevated coumestrol levels in lucerne (Medicago sativa L.) can reduce the reproductive performance of ewes. A model to predict coumestrol content of lucerne between summer and late autumn was developed to assess the risk of a crop having elevated levels. Data from previous studies have shown fungal damage to be the major contributor to coumestrol levels, but the fungal infestation levels that can cause a risk to reproduction in sheep are difficult to quantify. A number of variables were tested and the sum of rainfall and days where relative humidity was over 95% at 0900 h was found to have the best fit with coumestrol content of lucerne crops. The model was then tested with independent data from the literature and field. A decision tree is proposed as a practical user-friendly guide to predict whether coumestrol content is above or below a risk threshold of 25 mg/kg DM