Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus

Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.

A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits

Background

Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits.

Results

The integrated consensus map covered a total of 1,987.2 cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46 cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease.

Conclusions

The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.

A reference linkage map for Eucalyptus

Background

Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method.

Results

The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM.

Conclusion

The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.

The fatty acid composition of the lymphocyte cell membrane. Influence on interactions with high endothelium and the expression of homing receptors

By incubating mouse lymphocytes in vitro with various fatty acids in an otherwise lipid-free medium, the lipid composition of the cell membrane was varied. These changes resulted in an altered adhesion pattern on High Endothelial Venules (HEV) using an in vitro adherence assay. Incubation with linoleic acid (18:2) resulted in an increased adherence of T and B lymphocytes, linolenic acid (18:3) had no influence and both arachidonic acid (20:4) and arachidic acid (20:0) resulted in a decreased adherence of the two cell types when the adherence assay was performed using HEV from peripheral lymph nodes. Using HEV from mucosa associated Peyer's patches, T and B cells incubated with arachidic acid or arachidonic acid were less able to adhere this type of HEV. After incubation with linoleic acid, T lymphocytes adhere better to the Peyer's patches HEV whereas B cells showed a decrease in adherence and linolenic acid resulted in a decreased adherence of only B lymphocytes. FACS analysis revealed that MEL-14 expression as well as the expression of LFA-1 was somewhat elevated in intensity on T and B lymphocytes after incubation with linoleic acid. In contrast, the intensity for MEL-14 had decreased after arachidic acid or arachidonic acid. In case of arachidic acid the LFA-1 expression had also decreased. No changes were found after incubation with linolenic acid. The results suggest a role for the lipid composition of the membrane in recirculation patterns of lymphocytes.

Electron kinetic effects in the nonlinear evolution of a driven ion-acoustic wave

The electron kinetic effects are shown to play an important role in the nonlinear evolution of a driven ion-acoustic wave. The numerical simulation results obtained (i) with a hybrid code, in which the electrons behave as a fluid and the ions are described along the particle-in-cell (PIC) method, are compared with those obtained (ii) with a full-PIC code, in which the kinetic effects on both species are retained. The electron kinetic effects interplay with the usual fluid-type nonlinearity to give rise to a broadband spectrum of ion-acoustic waves saturated at a low level, even in the case of a strong excitation. This low asymptotic level might solve the long-standing problem of the small stimulated Brillouin scattering reflectivity observed in laser-plasma interaction experiments.