The distribution of genetic diversity in a Brassica oleracea gene bank collection related to the effects on diversity of regeneration, as measured with AFLPs

The ex situ conservation of plant genetic resources in gene banks involves the selection of accessions to be conserved and the maintenance of these accessions for current and future users. Decisions concerning both these issues require knowledge about the distribution of genetic diversity within and between accessions sampled from the gene pool, but also about the changes in variation of these samples as a result of regenerations. These issues were studied in an existing gene bank collection of a cross-pollinating crop using a selection of groups of very similar Dutch white cabbage accessions, and additional groups of reference material representing the Dutch, and the global white cabbage gene pool. Six accessions were sampled both before and after a standard regeneration. 30 plants of each of 50 accessions plus 6 regeneration populations included in the study were characterised with AFLPs, using scores for 103 polymorphic bands. It was shown that the genetic changes as a result of standard gene bank regenerations, as measured by AFLPs, are of a comparable magnitude as the differences between some of the more similar accessions. The observed changes are mainly due to highly significant changes in allele frequencies for a few fragments, whereas for the majority of fragments the alleles occur in similar frequencies before and after regeneration. It is argued that, given the changes of accessions over generations, accessions that display similar levels of differentiation may be combined safely

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm

Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition

BACKGROUND: DNA homopolymer tracts, poly(dA).poly(dT) and poly(dG).poly(dC), are the simplest of simple sequence repeats. Homopolymer tracts have been systematically examined in the coding, intron and flanking regions of a limited number of eukaryotes. As the number of DNA sequences publicly available increases, the representation (over and under) of homopolymer tracts of different lengths in these regions of different genomes can be compared. RESULTS: We carried out a survey of the extent of homopolymer tract over-representation (enrichment) and over-proportional length distribution (above expected length) primarily in the single gene documents, but including some whole chromosomes of 27 eukaryotics across the (G+C)% composition range from 20 – 60%. A total of 5.2 × 10(7 )bases from 15,560 cleaned (redundancy removed) sequence documents were analyzed. Calculated frequencies of non-overlapping long homopolymer tracts were found over-represented in non-coding sequences of eukaryotes. Long poly(dA).poly(dT) tracts demonstrated an exponential increase with tract length compared to predicted frequencies. A novel negative slope was observed for all eukaryotes between their (G+C)% composition and the threshold length N where poly(dA).poly(dT) tracts exhibited over-representation and a corresponding positive slope was observed for poly(dG).poly(dC) tracts. Tract size thresholds where over-representation of tracts in different eukaryotes began to occur was between 4 – 11 bp depending upon the organism (G+C)% composition. The higher the GC%, the lower the threshold N value was for poly(dA).poly(dT) tracts, meaning that the over-representation happens at relatively lower tract length in more GC-rich surrounding sequence. We also observed a novel relationship between the highest over-representations, as well as lengths of homopolymer tracts in excess of their random occurrence expected maximum lengths. CONCLUSIONS: We discuss how our novel tract over-representation observations can be accounted for by a few models. A likely model for poly(dA).poly(dT) tract over-representation involves the known insertion into genomes of DNA synthesized from retroviral mRNAs containing 3' polyA tails. A proposed model that can account for a number of our observed results, concerns the origin of the isochore nature of eukaryotic genomes via a non-equilibrium GC% dependent mutation rate mechanism. Our data also suggest that tract lengthening via slip strand replication is not governed by a simple thermodynamic loop energy model

Crop wild relatives range shifts and conservation in Europe under climate change

Diversity and Distributions Published by John Wiley & Sons Ltd. Aim: Climate change is expected to have a great impact on the distribution of wild flora around the world. Wild plant species are an important component of the genetic resources for crop improvement, which is especially important in face of climate change impacts. Still, many crop wild relatives (CWRs) are currently threatened in their natural habitat and are poorly represented in gene bank collections. To guide in situ conservation measures and to prioritize species for ex situ conservation, predictions are needed about future species distributions as a result of climate change. Location: Europe. Methods: Using species occurrence data and present and future climatic information, we investigated the possible impacts of future climate change on the European distribution of a selection of CWRs red-listed in the Netherlands using a species distribution modelling framework. The representation of the CWRs in European protected areas was investigated for the current and future climatic conditions. The models were created based on an optimistic (RCP 2.6) and pessimistic (RCP 8.5) climate change scenario. Results: A shift in distribution range, mostly towards northern locations, was observed for all investigated species. A loss of distribution area of up to 61.10% (full dispersal assumption) and 68.91% (no dispersal) according to RCP 2.6 was observed for some species. A distribution area loss of up to 90.92% (full dispersal) and 98.36% (no dispersal) was predicted for the most affected species under the RCP 8.5. Based on the predicted distribution in protected areas, present occupation in nature reserves appeared to be no guarantee for the species’ future protection and persistence. Main conclusions: We conclude that in situ conservation measures, ignoring the effects of climate change, will not be effective for many CWRs and that large-scale ex situ conservation actions are needed to safeguard CWRs

Crop wild relatives range shifts and conservation in Europe under climate change

Diversity and Distributions Published by John Wiley and Sons Ltd. Aim: Climate change is expected to have a great impact on the distribution of wild flora around the world. Wild plant species are an important component of the genetic resources for crop improvement, which is especially important in face of climate change impacts. Still, many crop wild relatives (CWRs) are currently threatened in their natural habitat and are poorly represented in gene bank collections. To guide in situ conservation measures and to prioritize species for ex situ conservation, predictions are needed about future species distributions as a result of climate change. Location: Europe. Methods: Using species occurrence data and present and future climatic information, we investigated the possible impacts of future climate change on the European distribution of a selection of CWRs red-listed in the Netherlands using a species distribution modelling framework. The representation of the CWRs in European protected areas was investigated for the current and future climatic conditions. The models were created based on an optimistic (RCP 2.6) and pessimistic (RCP 8.5) climate change scenario. Results: A shift in distribution range, mostly towards northern locations, was observed for all investigated species. A loss of distribution area of up to 61.10% (full dispersal assumption) and 68.91% (no dispersal) according to RCP 2.6 was observed for some species. A distribution area loss of up to 90.92% (full dispersal) and 98.36% (no dispersal) was predicted for the most affected species under the RCP 8.5. Based on the predicted distribution in protected areas, present occupation in nature reserves appeared to be no guarantee for the species’ future protection and persistence. Main conclusions: We conclude that in situ conservation measures, ignoring the effects of climate change, will not be effective for many CWRs and that large-scale ex situ conservation actions are needed to safeguard CWRs