Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines,as compared to the maize USDA genebank

Key message

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs.

Abstract

Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees–Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees–Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.

     

Identification, sequencing and mutagenesis of the gene for a d-carbamoylase from Agrobacterium radiobacter

Abstract A clone positive for d-carbamoylase activity (2.7 kb Hin dIII- Bam H1 DNA fragment) was obtained by screening a genomic library of Agrobacterium radiobacter in Escherichia coli . This DNA fragment contains an open reading frame of 912 bp which is predicted to encode a peptide of 304 amino acids with a calculated molecular mass of 34247 Da. The d-carbamoylase gene. named cauA , was placed under the control of T7 RNA-dependent promoter and expressed in E. coli BL21 (DE3). After induction with isopropyl-thio-β-d-galactopyranoside, the synthesis of d-carbamoylase in E. coli reached about 40% of the total protein. The expressed protein was shown to possess a molecular mass, on SDS-PAGE, of 36 kDa and showed an enhanced allowed us to establish that a Pro¹⁴→Leu¹⁴ exchange leads to an inactive enzyme species, while a Cys²⁷⁹→Ser²⁷⁹ exchange did not impair the functional properties of the enxyme.     

Optimization of integrated alkaline–extrusion pretreatment of barley straw for sugar production by enzymatic hydrolysis

In this work, an integrated one-step alkaline–extrusion process was tested as pretreatment for sugar production from barley straw (BS) biomass. The influence of extrusion temperature (T) and the ratio NaOH/BS dry matter (w/w) (R) into the extruder on pretreatment effectiveness was investigated in a twin-screw extruder at bench scale. A 2³ factorial design of experiments was used to analyze the effect of process conditions [T: 50–100 °C; R: 2.5–7.5% (w/w)] on composition and enzymatic digestibility of pretreated substrate (extrudate). The optimum conditions for a maximum glucan to glucose conversion were determined to be R = 6% and T = 68 °C. At these conditions, glucan yield reached close to 90% of theoretical, while xylan conversion was 71% of theoretical. These values are 5 and 9 times higher than that of the untreated material, which supports the great potential of this one-step combined pre-treatment technology for sugar production from lignocellulosic substrates. The absence of sugar degradation products is a relevant advantage over other traditional methods for a biomass to ethanol production process since inhibitory effect of such product on sugar fermentation would be prevented.     

Bonelli's Eagle Hieraaetus fasciatus juvenile dispersal: hourly and daily movements tracked by GPS

Capsule Birds cover daily distances not normally exceeding 20 km during the initial phase of dispersal, with the daily peak of movement/activity in the afternoon.     

Seasonal variation of circulating plasma carotenoids in Mediterranean Great Tit males Parus major

Capsule Mediterranean Great Tits showed a marked increase in levels of circulating carotenoids during moult and autumn.

Aims To study seasonal variation in plasma carotenoid content during a whole annual cycle for Great Tits Parus major inhabiting a Mediterranean woodland.

Methods We used a sample of 71 adult male Great Tits captured in NE Spain during a whole year. Data were organized into four seasons (winter, breeding, moult and autumn). We sampled blood to extract plasma. Carotenoid plasma concentrations were analysed by High-performance liquid chromatography (HPLC).

Results Lutein and zeaxanthin content varied seasonally, with a marked increase in levels during moult and autumn. Within the moulting period, levels increased gradually as the season progressed. This pattern differed significantly from that previously described in northern European populations, where high values appear mainly in the breeding season. Carotenoid concentrations (lutein: 1.2?±?0.25, zeaxanthin: 0.07?±?0.03?µg mL^?1) were also lower than in northern Europe.

Conclusion Mediterranean Great Tits show a very different pattern of circulating carotenoids and lower levels than northern European populations. The increasing pattern of carotenoid availability found within the moulting period raises the need to control for the effect of sampling date when analysing data on carotenoid concentrations at different times of year.     

Grazing history influences biodiversity: a case study on ground-dwelling arachnids (Arachnida: Araneae, Opiliones) in the Natural Park of Alpi Marittime (NW Italy)

Alpine pastures are typical examples of “high nature value farmlands”, representing important habitats harbouring unique biological communities. Disturbance induced by overgrazing influences significantly ecosystem processes, in which invertebrates play a major role. To develop new models of sustainable management of pastures, more knowledge is needed of the animal communities, essential to the ecological functioning of pasture ecosystems. The apparent poor ecological state of several pastures in the Natural Regional Park of Alpi Marittime (NW-Italy) lead us to evaluate the influence of grazing history on biodiversity, using spider and harvestmen assemblages as key groups. Four different pastoral types characterized by four different grazing histories were identified using the Daget-Poissonet method. Spiders and harvestmen were collected by means of pitfall traps. Arachnid assemblages were characterized in terms of composition, abundance, species richness, richness of endemic species and taxonomic relatedness. Generalized linear mixed models (GLMM) were used to test differences among assemblages occurring in each pastoral type. Furthermore, we tested differences in terms of plant communities (species richness and percentage of zoogenic species). Specificity and fidelity of every spider and harvestmen species within pastoral types were explored by the IndVal (Indicator Value) procedure. Fifty-eight species of spiders and seven species of harvestmen were collected (2,304 individuals). Pastoral types related to intensive grazing were characterized by the dominance of diurnal wanderer spiders (namely Lycosidae) while, conversely, nocturnal wanderers (mainly Gnaphosidae) were more abundant in extensive pastoral types. Results show that both species richness and spider abundance were higher in abandoned areas of extensive grazing, while endemic assemblages were richer in extensive grazed areas, which also hosted the most diverse plant community. Furthermore, most of the indicator species of spiders of this type were endemic, characterized by more demanding ecological requirements.     

Role of exotic tree stands on the current distribution and social behaviour of Swainson's hawk, Buteo swainsoni in the Argentine Pampas

Aim The Argentine Pampas was extensively and abruptly altered by European colonization. Between 1880 and 1885 the indigenous human inhabitants were completely displaced, and native grasslands were replaced by exotic pasture plants and crops. One of the most important ecological changes in the Pampas landscape, the introduction of tall exotic tree species, has received little attention, and its effect on wildlife has never been assessed. We have made an intensive survey of habitat use of Swainson's hawk, Buteo swainsoni in its most important non‐breeding quarters, the Pampas of Argentina, aiming to characterize the sites used by hawks for communal roosting. Location Pampas grasslands, Argentina. Methods We surveyed 30,000 km of roads by car during the austral summer from 2001 to 2004, covering the main non‐breeding area occupied by Swainson's hawks. Their roost sites were located by direct observation of birds roosting in tree stands close to the roads, by surveying potential roost sites around places where groups of pre‐ and post‐roosting hawks were recorded, and by gathering information from local farmers. Results Swainson's hawks exclusively used stands of exotic tree species for roosting. Eucalyptus viminalis was present in all 34 roosts surveyed, and in 59% of them it was the only species present. The remaining exotic tree species were the Siberian elm, Ulmus pumila, pines (Pinus spp.) and cypress (Cupressus spp.). Flock sizes at roost sites were unusually high for a raptor, with an average of 658 individuals (range 8–5000 hawks, n = 27 flocks). Main conclusions The introduction of exotic trees may have resulted in the expansion of the suitable habitat for Swainson's hawks, permitting a recent colonization of the Argentine Pampas. Tree stands may have also changed the communal roosting behaviour of this raptor, by virtue of their providing new structural elements in a region that almost completely lacked trees prior to European occupation.     

Mate Choice in Captive American Kestrels,Falco sparverius,Parasitized by a Nematode,Trichinella pseudospiralis

The American kestrel (Falco sparverius) — Trichinella pseudospiralis host-parasite association was used as a laboratory model to study the effect of a nematode infection on (1) mate choice of female kestrels and (2) competitive abilities of male kestrels during the breeding season. Females were given the opportunity to choose between infected and uninfected males. There was no significant difference in the proportion of females that chose uninfected (n = 18) over infected (n = 16) males. Eight of 11 competitions between infected and uninfected males exposed to a caged female and a nest box were dominated by uninfected males. Female kestrels seemed to base their choices on the intensity of display effort by the males; the experimental level of infection did not affect male courtship behaviour. Although T. pseudospiralis is known to debilitate American kestrels, parasitized males in mate-choice tests may have diverted energy from less important functions to court the females.     

Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

The effect of MHC polymorphism on individual fitness variation in the wild remains equivocal; however, much evidence suggests that heterozygote advantage is a major determinant. To understand the contribution of MHC polymorphism to individual disease resistance or susceptibility in natural populations, we investigated two MHC class II B loci, DQB and DRB, in the New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened species which is unusually susceptible to death by bacterial infection at an early age; it has suffered three bacterial induced epizootics resulting in high mortality levels of young pups since 1997. The MHC DQB and DRB haplotypes of dead NZSL pups with known cause of death (bacteria, enteritis or trauma) were sequenced and reconstructed, compared to pups that survived beyond 2 months of age, and distinct MHC DRB allele frequency and genotype differences were identified. Two findings were striking: (i) one DRB allele was present only in dead pups, and (ii) one heterozygous DRB genotype, common in live pups, was absent from dead pups. These results are consistent with some functional relationship with these variants and suggest heterozygote advantage is operating at DRB. We found no association between heterozygosity and fitness at 17 microsatellite loci, indicating that general heterozygosity is not responsible for the effect on fitness detected here. This result may be a consequence of recurrent selection by multiple pathogen assault over recent years and highlights the importance of heterozygote advantage at MHC as a potential mechanism for fitness differences in wild populations.