Screening species and cultivars for their tolerance to acidic soil conditions.

The major phytotoxins in acid soils are aluminium and manganese. Tolerances to Al and to excessive Mn are independently inherited and Al and Mn solubilities in soils vary. In this work, the response of pasture grasses and legumes to soil acidity was studied on three soils with different Al and Mn concentrations. One provides moderate concentrations of Al with little Mn; one provides high concentrations of both Al and Mn and another provides a very high concentration of Mn at relatively low concentrations of Al. The response of a plant cultivar to changes in the soil acidity induced by lime or acid additions reflects the degree of Al and/or Mn stress provided by a particular soil, and the ability of the cultivar to tolerate those stresses. Examples are given of the way cultivars with different tolerances to Al and Mn toxicity respond to changes in acidity on the soils with different Al and Mn solubility characteristics. The utility of this screening technique to define the tolerance of cultivars to acidity on classically different soils is highlighted.     

Root-zone constraints and plant-based solutions for dryland salinity

Limitations to agricultural productivity imposed by the root-zone constraints in Australian dryland soils are severe and need redemption to improve the yields of grain crops and thereby meet world demand. Physical, chemical and biological constraints in soil horizons impose a stress on the plant and restrict plant growth and development. Hardsetting, crusting, compaction, salinity, sodicity, acidity, alkalinity, nutrient deficiencies and toxicities due to boron, carbonates and aluminium are the major factors that cause these constraints. Further, subsoils in agricultural regions in Australia have very low organic matter and biological activity. Dryland salinity is currently given wide attention in the public debate and government policies in Australia, but they only focus on salinity induced by shallow groundwater. However, the occurrence of transient salinity in root-zone layers in the regions where water tables are deep is an important issue with potential for larger economic loss than water table-induced seepage salinity. Root-zone constraints pose a challenge for salinity mitigation in recharge as well as discharge zones. In recharge zones, reduced water movement in sodic horizons results in salt accumulation in the root zone resulting in chemical and physical constraints that reduce transpiration that, in turn, upsets salt balance and plant growth. High salinity in soil and groundwater restricts the ability of plants to reduce water table in discharge zones. Thus plant-based strategies must address different kinds of limitations in soil profiles, both in recharge and discharge zones. In this paper we give an overview of plant response to root-zone constraints but with an emphasis on the processes of salt accumulation in the root-zone of soils. We also examine physical and chemical methods to overcome subsoil limitations, the ability of plants to adapt to and ameliorate these constraints, soil modification by management of agricultural and forestry ecosystems, the use of biological activity, and plant breeding for resistance to the soil constraints. We emphasise that soil scientists in cooperation with agronomists and plant breeders should design site-specific strategies to overcome multiple soil constraints, with vertical and lateral variations, and to develop plant-based solutions for dryland salinity.     

Novel polymorphic microsatellite loci for the protogynous hermaphrodite slinger sea bream (Chrysoblephus puniceus, Sparidae)

As a result of the global decline of fish stocks, an increasing number of fish species are becoming targets of heavy exploitation, often concomitantly with a lack of biological knowledge on their structure and demographics. Here we present 11 new polymorphic microsatellite loci, isolated from the slinger sea bream (Chrysoblephus puniceus, Sparidae), a relatively recent target of coastal fisheries in eastern South Africa. Levels of genetic diversity were assessed in 39 individuals collected from the KwaZulu-Natal coast (Park Rynie, South Africa). Observed and expected heterozygosities varied between 0.39 and 0.97 and between 0.53 and 0.96, respectively. One locus (SL35) showed significant heterozygote deficiency and linkage disequilibrium was detected between SL35 and SL1. Importantly, five of these microsatellites cross-amplify in Cheimerius nufar, a sympatric species also subjected to exploitation.     

Microsatellite and mtDNA analysis of the population structure of grey seals (Halichoerus grypus) from three breeding areas in the Baltic Sea

The growing number of grey seals in the Baltic Sea has led to a dramatic increase in interactions between seals and fisheries. The conflict has become such a problem that hunting was introduced in Finland in 1998 and the Swedish Environment Protection Agency recommended a cull of grey seals starting in 2001. Culling has been implemented despite the lack of data on population structure. Low levels of migration between regions would mean that intensive culling in specific geographic areas would have disproportionate effects on local population structure and genetic diversity. We used eight microsatellite loci and a 489 bp section of the mtDNA control region to examine the genetic variability and differentiation between three breeding sites in the Baltic Sea and two in the UK. We found high levels of genetic variability in all sampled Baltic groups for both the microsatellites and the control region. There were highly significant differences in microsatellite allele frequencies between all three Baltic breeding sites and between the Baltic sites and the UK sites. However, there were no significant differences in mtDNA control region haplotypes between the Baltic sites. This genetic substructure of the Baltic grey seal populations should be taken into consideration when managing the seal population to prevent the hunting regime from having an adverse effect on genetic diversity by setting hunting quotas separately for the different subpopulations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Outlier SNP markers reveal fine‐scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome‐wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large‐ and fine‐scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F_CT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F_CT range 0.275–0.705) and fine‐scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.     

SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus)

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.     

Direct assessment of mineral phosphorus availability to tropical crops using 32P labelled compounds

The availability to plants of phosphorus (P) derived from sparingly soluble iron and aluminium phosphates was directly assessed with ³²P labelled compounds in two glasshouse trials.In the first experiment, the comparative availability of all mineral phosphate (P) compounds to maize increased with time (14 to 42 days post emergence) and plant total P uptake, but P source did not affect the growth or total plant uptake of P. The comparative availability of the amorphous AlPO₄ (Al-P), crystalline AlPO₄ (variscite), amorphous FePO₄ (Fe-P), and crystalline FePO₄ (strengite) compared to KH₂PO₄ (=100) was 53.1, 3.4, 38.9, and 1.9%, respectively. In the second experiment, the availability of Fe-P, strengite, and KH₂PO₄ to several topical crop species was examined. There was no difference between maize, sorghum, mungbean, cowpea or soybean in their ability to utilise Fe-P or KH₂PO₄, although maize utilised strengite more than the other species. The major difference between these species in their ability to acquire P appears to be a difference in ability to locate soluble soil P rather than differences in their ability to access different pools of soil P.The advantages of using neutron irradiation to directly measure P absorption from mineral P compounds over traditional methodologies is discussed.     

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.