High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.     

Inference for Proportions in a 2 × 2 Contingency Table: HPD or not HPD?

Summary Highest posterior density intervals are common in Bayesian inference, but as noted by Agresti and Min (2005, Biometrics 61, 515–523) they are not invariant under transformations. Agresti and Min suggested central or “tail” intervals as preferable in the context of the relative risk and odds ratio. A modification to this is proposed for extreme outcomes, as invariance is maintained when replacing central intervals by one‐sided intervals. Bayes–Laplace priors for the binomial parameters appear preferable here, compared to Jeffreys priors, contrary to Agresti and Min's suggestion based on frequentist coverage.     

Structural basis for the lower affinity of the insulin-like growth factors for the insulin receptor

Insulin and the insulin-like growth factors (IGFs) bind with high affinity to their cognate receptor and with lower affinity to the noncognate receptor. The major structural difference between insulin and the IGFs is that the IGFs are single chain polypeptides containing A-, B-, C-, and D-domains, whereas the insulin molecule contains separate A- and B-chains. The C-domain of IGF-I is critical for high affinity binding to the insulin-like growth factor I receptor, and lack of a C-domain largely explains the low affinity of insulin for the insulin-like growth factor I receptor. It is less clear why the IGFs have lower affinity for the insulin receptor. In this study, 24 insulin analogues and four IGF analogues were expressed and analyzed to explore the role of amino acid differences in the A- and B-domains between insulin and the IGFs in binding affinity for the insulin receptor. Using the information obtained from single substituted analogues, four multiple substituted analogues were produced. A "quadruple insulin" analogue ([Phe(A8), Ser(A10), Thr(B5), Gln(B16)]Ins) showed affinity as IGF-I for the insulin receptor, and a "sextuple insulin" analogue ([Phe(A8), Ser(A10), Thr(A18), Thr(B5), Thr(B14), Gln(B16)]Ins) showed an affinity close to that of IGF-II for the insulin receptor, whereas a "quadruple IGF-I" analogue ([His(4), Tyr(15), Thr(49), Ile(51)]IGF-I) and a "sextuple IGF-II" analogue ([His(7), Ala(16), Tyr(18), Thr(48), Ile(50), Asn(58)]IGF-II) showed affinities similar to that of insulin for the insulin receptor. The mitogenic potency of these analogues correlated well with the binding properties. Thus, a small number of A- and B-domain substitutions that map to the IGF surface equivalent to the classical binding surface of insulin weaken two hotspots that bind to the insulin receptor site 1.     

Alanine scanning of a putative receptor binding surface of insulin-like growth factor-I

Current evidence supports a binding model in which the insulin molecule contains two binding surfaces, site 1 and site 2, which contact the two halves of the insulin receptor. The interaction of these two surfaces with the insulin receptor results in a high affinity cross-linking of the two receptor alpha subunits and leads to receptor activation. Evidence suggests that insulin-like growth factor-I (IGF-I) may activate the IGF-I receptor in a similar mode. So far IGF-I residues structurally corresponding to the residues of the insulin site 1 together with residues in the C-domain of IGF-I have been found to be important for binding of IGF-I to the IGF-I receptor (e.g. Phe(23), Tyr(24), Tyr(31), Arg(36), Arg(37), Val(44), Tyr(60), and Ala(62)). However, an IGF-I second binding surface similar to site 2 of insulin has not been identified yet. In this study, we have analyzed whether IGF-I residues corresponding to the six residues of the insulin site 2 have a role in high affinity binding of IGF-I to the IGF-I receptor. Six single-substituted IGF-I analogues were produced, each containing an alanine substitution in one of the following positions (corresponding insulin residues in parentheses): Glu(9) (His(B10)), Asp(12) (Glu(B13)), Phe(16) (Leu(B17)), Asp(53) (Ser(A12)), Leu(54) (Leu(A13)), and Glu(58) (Glu(A17)). In addition, two analogues with 2 and 3 combined alanine substitutions were also produced (E9A,D12A IGF-I and E9A,D12A,E58A IGF-I). The results show that introducing alanine in positions Glu(9), Asp(12), Phe(16), Leu(54), and Glu(58) results in a significant reduction in IGF-I receptor binding affinity, whereas alanine substitution at position 53 had no effect on IGF-I receptor binding. The multiple substitutions resulted in a 33-100-fold reduction in IGF-I receptor binding affinity. These data suggest that IGF-I, in addition to the C-domain, uses surfaces similar to those of insulin in contacting its cognate receptor, although the relative contribution of the side chains of homologous residues varies.     

Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice

We have developed a transiently-expressed transposase (TET)-mediated Dissociation (Ds) insertional mutagenesis system for generating stable insertion lines in rice which will allow localized mutagenesis of a chromosomal region. In this system, a Ds containing T-DNA construct was used to produce Ds launch pad lines. Callus tissues, from single-copy Ds/T-DNA lines, were then transiently infected with Agrobacterium harbouring an immobile Ac (iAc) construct, also containing a green fluorescent protein gene (sgfpS65T) as the visual marker. We have regenerated stable Ds insertion lines at a frequency of 9–13% using selection for Ds excision and GFP counter selection against iAc and nearly half of them were unique insertion lines. Double transformants (iAc/Ds) were also obtained and their progeny yielded ~10% stable insertion lines following excision and visual marker screening with 50% redundancy. In general, more than 50% of the Ds reinsertions were within 1 cM of the launch pad. We have produced a large number of single-copy Ds/T-DNA launch pads distributed over the rice chromosomes and have further refined the Ds/T-DNA construct to enrich for “clean” single-copy T-DNA insertions. The availability of single copy “clean” Ds/T-DNA launch pads will facilitate chromosomal region-directed insertion mutagenesis. This system provides an opportunity for distribution of gene tagging tasks among collaborating laboratories on the basis of chromosomal locations. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Presence of the Chytrid Fungus Batrachochytrium dendrobatidis in Populations of the Critically Endangered Frog Mannophryne olmonae in Tobago, West Indies

The emerging infectious disease chytridiomycosis is prevalent in Central and South America, and has caused catastrophic declines of amphibian populations in the Neotropics. The responsible organism, Batrachochytrium dendrobatidis, has been recorded on three West Indian islands, but the whole of the Caribbean region is predicted to offer a suitable environment for the disease. Monitoring the spread of chytridiomycosis is thus a priority in this region, which has exceptionally high levels of amphibian endemism. PCR analysis of 124 amphibian skin swabs in Tobago (Republic of Trinidad and Tobago) demonstrated the presence of B. dendrobatidis in three widely separated populations of the frog Mannophryne olmonae, which is listed as Critically Endangered on the basis of recent population declines. Chytridiomycosis is presently endemic in this species, with a prevalence of about 20% and no associated clinical disease. Increased susceptibility to chytridiomycosis from climate change is unlikely in amphibian populations in Tobago, as this island does not have high montane environments, but remains a possibility in the sister island of Trinidad. Preventing the spread of chytridiomycosis within and between these and other Caribbean islands should be a major goal of practical conservation measures for amphibians in the region.     

Does more mean less? The value of information for conservation planning under sea level rise

Many studies have explored the benefits of adopting more sophisticated modelling techniques or spatial data in terms of our ability to accurately predict ecosystem responses to global change. However, we currently know little about whether the improved predictions will actually lead to better conservation outcomes once the costs of gaining improved models or data are accounted for. This severely limits our ability to make strategic decisions for adaptation to global pressures, particularly in landscapes subject to dynamic change such as the coastal zone. In such landscapes, the global phenomenon of sea level rise is a critical consideration for preserving biodiversity. Here, we address this issue in the context of making decisions about where to locate a reserve system to preserve coastal biodiversity with a limited budget. Specifically, we determined the cost‐effectiveness of investing in high‐resolution elevation data and process‐based models for predicting wetland shifts in a coastal region of South East Queensland, Australia. We evaluated the resulting priority areas for reserve selection to quantify the cost‐effectiveness of investment in better quantifying biological and physical processes. We show that, in this case, it is considerably more cost effective to use a process‐based model and high‐resolution elevation data, even if this requires a substantial proportion of the project budget to be expended (up to 99% in one instance). The less accurate model and data set failed to identify areas of high conservation value, reducing the cost‐effectiveness of the resultant conservation plan. This suggests that when developing conservation plans in areas where sea level rise threatens biodiversity, investing in high‐resolution elevation data and process‐based models to predict shifts in coastal ecosystems may be highly cost effective. A future research priority is to determine how this cost‐effectiveness varies among different regions across the globe.     

Conserving biodiversity efficiently: what to do, where, and when

Conservation priority-setting schemes have not yet combined geographic priorities with a framework that can guide the allocation of funds among alternate conservation actions that address specific threats. We develop such a framework, and apply it to 17 of the world's 39 Mediterranean ecoregions. This framework offers an improvement over approaches that only focus on land purchase or species richness and do not account for threats. We discover that one could protect many more plant and vertebrate species by investing in a sequence of conservation actions targeted towards specific threats, such as invasive species control, land acquisition, and off-reserve management, than by relying solely on acquiring land for protected areas. Applying this new framework will ensure investment in actions that provide the most cost-effective outcomes for biodiversity conservation. This will help to minimise the misallocation of scarce conservation resources.