Population Genetic Structure and Conservation of the Lesser White-Fronted GooseAnser erythropus

The lesser white-fronted goose is a sub-Arctic species with a currently fragmented breeding range, which extends from Fennoscandia to easternmost Siberia. The population started to decline at the beginning of the last century and, with a current world population estimate of 25,000 individuals, it is the most threatened of the Palearctic goose species. Of these, only 30–50 pairs breed in Fennoscandia. A fragment of the control region of mtDNA was sequenced from 110 individuals from four breeding, one staging and two wintering areas to study geographic subdivisions and gene flow. Sequences defined 15 mtDNA haplotypes that were assigned to two mtDNA lineages. Both the mtDNA lineages were found from all sampled localities indicating a common ancestry and/or some level of gene flow. Analyses of molecular variance showed significant structuring among populations ( _ST 0.220, P < 0.001). The results presented here together with ecological data indicate that the lesser white-fronted goose is fragmented into three distinctive subpopulations, and thus, the conservation status of the species should be reconsidered.     

The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance

Genome-wide association (GWA) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean. More rarely, loci have also been detected based on variance differences between genotypes. Several hypotheses have been proposed to explain the possible genetic mechanisms leading to such variance signals. However, little is known about what causes these signals, or whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association reveals that the vGWA emerges from the effects of three independent genetic polymorphisms that all are in strong LD with the markers displaying the genetic variance-heterogeneity. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation or “missing heritability”. Two of the three polymorphisms underlying the genetic variance-heterogeneity are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of MOT1. Use of a T-DNA knockout allele highlights Copper Transporter 6; COPT6 (AT2G26975) as a strong candidate gene for this association. Our results show that an extended LD across a complex locus including multiple functional alleles can lead to a variance-heterogeneity between genotypes in natural populations. Further, they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations.     

Ecosystem responses to woody plant encroachment in a semiarid savanna rangeland

Woody plant encroachment alters the structure and function of rangeland ecosystems. The objective of this study was to explore the association between woody plant encroachment and various ecosystem properties (i.e. vascular plant species diversity, richness, evenness, soil organic matter, herbaceous biomass, leaf litter and bare ground cover) in a semiarid savanna rangeland, and also to test whether the relationships were influenced by woody species composition, elevation and site. We carried out a vegetation survey in four rangeland sites in the lower Omo region of southwestern Ethiopia, and regressed each one of the ecosystem properties, separately, against woody plant density, elevation and site using multiple linear regressions. We found that vascular plant species diversity, richness and evenness increased with woody plant density, most likely due to increased spatial heterogeneity and soil microclimate improvement. Bare ground cover increased significantly, whereas herbaceous biomass and soil organic matter did not respond to woody encroachment. In a subsequent investigation, we used a redundancy analysis to assess whether ecosystem properties were influenced by the identity of encroaching woody plant species. Species diversity and richness responded positively to Lannea triphylla, whereas leaf litter responded positively to Grewia tenax and G. villosa. Our findings suggest that woody plant encroachment in a semiarid rangeland does alter ecosystem properties. However, its impact is highly variable, influenced by a set of factors including the level of encroachment and identity of encroaching woody species.     

Symbiotic N2-fixation by the cover crop Pueraria phaseoloides as influenced by litter mineralization

The perennial legume Pueraria phaseoloides is widely used as a cover crop in rubber and oil palm plantations. However, very little knowledge exists on the effect of litter mineralization from P. phaseoloides on its symbiotic N₂-fixation. The contribution from symbiotic N₂-fixation (Ndfa) and litter N (Ndfl) to total plant N in P. phaseoloides was determined in a pot experiment using a ¹⁵N cross-labeling technique. For determination of N₂-fixation the non-fixing plant Axonopus compressus was used as a reference. The experiment was carried out in a growth chamber during 9 weeks with a sandy soil and 4 rates of ground litter (C/N=16,2.8% N). P. phaseoloides plants supplied with the highest amount of litter produced 26% more dry matter and fixed 23% more N than plants grown in soil with no litter application, but the percentage of Ndfa decreased slightly, but significantly, from 87 to 84%. The litter N uptake was directly proportional to the rate of application and constituted 10% of total plant N at the highest application rate. Additionally, a positive correlation was found between litter N uptake and the amount of fixed N₂. The total recovery of litter N in plants averaged 26% at harvest (shoot + root) and was not affected by the quantity added. A parallel incubation experiment also showed that, as an average of all litter levels, 26% of the litter N was present in the inorganic N pool. The amounts of fertilizer and soil N taken up by plants decreased with litter application, probably due to microbial immobilization and denitrification. It is concluded that, within the litter levels studied, litter mineralization will result in a higher amount of N₂-fixed by P. phaseoloides.     

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation.