Interspecific hybridization between Coffea arabica L. and tetraploid C. canephora P. Ex Fr. II. Meiosis in F1 hybrids and back crosses to C. Arabica

Summary Melosis was studied in Coffea arabica, in induced tetraploid C. canephora, in their F₁ hybrid (arabusta hybrid) and in backcross generations of the hybrid with C. arabica as recurrent parent. Irregularities were observed, consisting of univalents (especially in the arabusta hybrid), multivalents (especially in tetraploid C. canephora) and uneven distribution of chromosomes at first anaphase. Chromosome distribution was improved by backcrossing. Meiotic irregularities wer negatively correlated with pollen fertility.     

: a software to evaluate model performance

The software (Integrated Resources for Evaluating Numerical Estimates) is a data analysis tool designed to provide easy access to statistical techniques for use in model evaluation. Mostly, non-replicated model estimates (E_i) are compared against non-replicated measurements (M_i). The software also allows comparing individual estimates against replicated measurements (or vice versa) and replicated estimates against replicated measurements. The evaluation of model performance is essentially based on the difference E_i−M_i, or on the correlation–regression of E_i vs. M_i (or vice versa). In addition, model evaluation by probability distributions, pattern analysis, or fuzzy-based aggregation statistics is allowed. Graphics are included in most analytical tasks. The results are displayed in separate spreadsheets and can be exported into MS Excel workbooks.     

Reduced chromosome association between the short arms of 5H homologues in Hordeum vulgare L. at metaphase I

Rod or ring bivalents at metaphase I (MI) reflect whether crossing-over has occurred on one or both pairs of chromosome arms, respectively, during meiotic prophase (pachytene). In cultivated barley ( Hordeum vulgare ) the highest frequencies of rod bivalents were found for satellite chromosomes (either 5H or 6H). To distinguish between chromosome 5H and 6H associations, a recombinant line derived from an H. vulgare × H. bulbosum hybrid with a hemizygous introgression from H. bulbosum on the short arm of chromosome 6H was probed with 45S rDNA and pSc119.2 using fluorescent in situ hybridization and compared with non-recombinant H. vulgare. The frequencies of rod bivalents, caused by failure of the short arms of 5H chromosomes (5HS) to associate during meiosis in the recombinant line, were similar to the frequencies of rod bivalents involving the satellite chromosomes in H. vulgare. Hence, rod bivalent formation in H. vulgare satellite chromosomes is probably based on reduced association of 5HS, corresponding to a low frequency of genetic recombination. 5HS is, therefore, more likely to show linkage disequilibrium than the other chromosome arms.     

Development and application of functional markers in maize

Summary Functional markers (FMs) are derived from polymorphic sites within genes causally involved in phenotypic trait variation (Andersen, J.R. & T. Lübberstedt, 2003. Trends Plant Sci 8: 554–560). FM development requires allele sequences of functionally characterized genes from which polymorphic, functional motifs affecting plant phenotype can be identified. In maize and other species with low levels of linkage disequilibrium, association studies have the potential to identify sequence motifs, such as a few nucleotides or insertions/deletions, affecting trait expression. In one of the pioneering studies, nine sequence motifs in the dwarf8 gene of maize were shown to be associated with variation for flowering time (Thornsberry, J.M., M.M. Goodman, J. Doebley, S. Kresovich, D. Nielsen & E.S. Buckler, 2001. Nat Genet 28: 286–289). Proof of sequence motif function can be obtained by comparing isogenic genotypes differing in single sequence motifs. At current, the most appropriate approach for this purpose in crops is targeting induced local lesions in genomes (TILLING) (McCallum, C.M., L. Comai, E.A. Greene & S. Henikoff, 2000. Nat Biotechnol 18: 455–457). In central Europe, maize is mainly grown as forage crop, with forage quality as major trait, which can be determined as proportion of digestible neutral detergent fiber (DNDF). Brown midrib gene knock out mutations have been shown to be beneficial for forage quality but disadvantageous for overall agronomic performance. Two brown midrib genes (bm1 and bm3) have been shown to be involved in monolignol biosynthesis. These two and additional lignin biosynthesis genes have been isolated based on sequence homology. Additional candidate genes putatively affecting forage quality have been identified by expression profiling using, e.g., isogenic bm lines. Furthermore, we identified an association between a polymorphism at the COMT locus and DNDF in a collection of European elite inbred lines.     

Chromosome association and pollen fertility in some interspecific hybrids of Lilium

Summary Meiotic observations in PMCs were made in eight kinds of interspecific hybrids in Lilium. Three hybrids, 6134-S × L. cernuum. L. regale × L. leichtlinii maximowiczii and L. auratum platyphyllum × L. henryi showed respectively the mean chromosome association frequencies of 1.4_II, 0.8_II and 1.5_II per cell at MI which were the lowest values hitherto reported in Lilium hybrids. In L. longiflorum × L. henryi, 33.3° of the cells had 1 or 2 multivalents of three to five chromosomes in addition to uni- and bivalents. 12° bivalents and 12 univalents were invariably observed in the triploid hybrid L. longiflorum × L. cernuum. The hybrids between the species belonging to the different sections of the genus generally showed high pollen sterility, with some exceptions. A more or less remote genomic homology was found between the different sections in Lilium.     

The association of sexuality with plant traits and tuber yield in white yam

Summary One 3-to 5-year clonal and two recent seedling-derived populations of white yam cultivars were grown and studied for the association of sex, flowering intensity, number of fruits and seed yield with vegetative characters and tuber yield. Yield was lowest in non-flowering plants and increased in the following order: male, monoecious and female plants; with females yielding almost twice as much as the non-flowering plants. The plants produced from small tuber setts, with higher leaf virus infection, low plant leafiness either had low flowering intensity, fewer fruits and seeds or even failed to flower. The sequence and timing of vegetative and reproductive processes in relation to the difference in yield between male and female plants is discussed. There is a strong indication that the intensity of flowering and fruiting is lower in plants from previous vegetative propagation compared to recent seedling-serived clones.     

Estimating floristic integrity in tallgrass prairie

Indices are needed in habitat conservation and restoration to provide repeatable measures relevant to conservation goals. A monitoring and research program was established at Nachusa Grasslands in north-central Illinois (USA) to assess progress in tallgrass prairie restoration and reconstruction efforts and evaluate the effectiveness of indices used to measure community-level properties related to vegetation integrity. Indices selected for comparison included standard diversity measures (e.g., Shannon-Weiner Index, Evenness, Species Richness) and indices developed specifically to estimate vegetation integrity. These latter indices included two unweighted diversity indices, the Species Richness Index and Native Richness Index, and two indices weighted by characteristics of species composition, the Floristic Quality Index (FQI) and its component Mean Coefficient of Conservatism (Mean C). A coefficient of conservatism (CC) is an integer ranging from 0 to 10 assigned a priori to each taxon in a regional flora that estimates the fidelity of a species to natural areas (non-native and most ruderal species are assigned 0 or low values, respectively; species known primarily from natural areas are assigned higher values). All indices compared in this study were calculated using vegetation data collected from equal-sized sampling grids stratified across seven prairie units. The units included remnants and plantings representing a wide range of habitat quality. The FQI and Mean C explained the most variation among sites and were most effective at distinguishing recognized qualitative differences indicating they can be more informative than traditional species-diversity measures in assessing floristic integrity within community types. The FQI and Mean C are applicable to both quantitative ecological monitoring and plotless survey methods.     

Spatial structure of multispecies distributions in southern California, USA

Analysis of the spatial distribution of all species of conservation importance within a region is necessary to augment reserve selection strategies and habitat management in biodiversity conservation. In this study, we analyzed the spatial aggregation, spatial association, and vegetation types of point occurrence data collected from museum and herbaria records for rare, special concern, threatened, and endangered species of plants, reptiles, mammals, and birds in western Riverside County in southern California, USA. All taxa showed clumped distributions, with aggregation evident below 14 km for plants, 12 km for reptiles, 2 km for mammals, and 10 km for birds. In addition, all combinations of the different species groups showed high positive spatial association. The Santa Rosa Plateau exhibited the highest number of rare, special concern, threatened, and endangered species, and shrubland (coastal sage and chaparral) was the vegetation type inhabited by the most species. Local land use planning, zoning and reserve design should consider the spatial aggregation within and between species to determine the appropriate scale for conservation planning. The higher spatial association between species groups in this study may indicate interdependence between different species groups or shared habitat requirements. It is important to maintain diverse communities due to potential interdependence. The results of the study indicate that concentrating preservation efforts on areas with the highest number of species of concern and the restoration of native shrublands are the most appropriate actions for multiple species habitat conservation in this area.     

Novel SNP in 5' flanking region of EDG1 associated with marbling in Japanese Black beef cattle

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation , sphingolipid G-protein-coupled receptor , 1 ( EDG1 ) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.-312A > G in the 5' untranslated region (UTR) and c.*446G > A in the 3' UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G > A and g.1471620G > T , in the 5' flanking region of the EDG1 between low-marbled and high-marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G > A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G > T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G > T SNP might have an impact on EDG1 expression and also marbling.