Genetic architecture of aerial and root traits in field-grown grafted grapevines is largely independent

Key message

QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent.

Abstract

Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv. Cabernet-Sauvignon × V. riparia cv. Gloire de Montpellier, used as rootstock, was phenotyped in grafted plants grown for 2 years in the field. Seven traits, related to aerial and root development, were quantified. Heritability ranged between 0.44 for aerial biomass to 0.7 for root number. Total root number was related to the number of fine roots, while root biomass was related to the number of coarse roots. Significant quantitative trait loci (QTLs) were identified for all the traits studied with some of them explaining approximately 20% of phenotypic variance. Only a single QTL co-localized for root and aerial biomass. Identified QTLs for aerial-to-root biomass ratio suggest that aerial and root traits are controlled independently. Genes known to be involved in auxin signaling pathways and phosphorus nutrition, whose orthologues were previously shown to regulate root development in Arabidopsis, were located in the confidence intervals of several QTLs. This study opens new perspectives for breeding rootstocks with improved root development capacities.

     

Semen quality of 4480 young cancer and systemic disease patients: baseline data and clinical considerations

Background

Except for testicular cancer and Hodgkin’s disease, baseline data on semen quality in case of cancers as well as systemic pathologies of the young adult are scarce or based on low sample size.

Methods

Semen quality in patients having testicular cancer (TGCT, n?=?2315), Hodgkin’s disease (HD, n?=?1175), non-Hodgkin’s lymphoma (NHL, n?=?439), leukemia (L, n?=?360), sarcoma (S, n?=?208), brain tumour (BT, n?=?40), Behcet’s disease (Behcet’s, n?=?68) or multiple sclerosis (MS, n?=?73) was studied and compared to that of 1448 fertile men candidates for sperm donation (CSD) and 208 partners of pregnant women (PPW). All samples were studied following the same methodology in a single laboratory. Post freezing and thawing semen characteristics were also studied.

Results

The percentage of normozoospermic men was only 37 % for L patients and lower than 60 % for TGCT, NHL, S and BT. The level of sperm production was differently decreased according to pathologies, the median total sperm count in TC and L patients being four times lower (p?<?0.01 when compared to CSD and PPW). The lowest percentage of progressively motile spermatozoa was found for L and BT patients (both, p?<?0.01 compared to CSD and PPW). The percentage of morphologically normal spermatozoa was also reduced in cancer patients, especially in BT patients. Progressive motility after thawing in patients was about half that observed among candidates for sperm donation. In almost half of the semen of patients with testicular cancer or leukemia, the total number of motile spermatozoa per straw was less than 0.5?×?10⁶ compared to 4.3?×?10⁶ in CSD.

Conclusions

The present data confirm on large series the deleterious impact of various cancers of the young adult on semen quality, establishing thus baseline data for future studies. Owing to the post-thaw quality of the frozen straws, future fertility projects for the majority of the patients studied (in case there is no post-treatment recovery of spermatogenesis) should necessitate an ICSI to provide the best chance of paternity whatever the fertility check-up in the female partner.

     

Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010

Although it is generally recognized that global biodiversity is declining, few studies have examined long‐term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5‐year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.     

Lipid-Protein Interactions in the Regulated Betaine Symporter BetP Probed by Infrared Spectroscopy

The Na⁺-coupled betaine symporter BetP senses changes in the membrane state and increasing levels of cytoplasmic K⁺ during hyperosmotic stress latter via its C-terminal domain and regulates transport activity according to both stimuli. This intriguing sensing and regulation behavior of BetP was intensively studied in the past. It was shown by several biochemical studies that activation and regulation depends crucially on the lipid composition of the surrounding membrane. In fact, BetP is active and regulated only when negatively charged lipids are present. Recent structural studies have revealed binding of phosphatidylglycerol lipids to functional important parts of BetP, suggesting a functional role of lipid interactions. However, a regulatory role of lipid interactions could only be speculated from the snapshot provided by the crystal structure. Here, we investigate the nature of lipid-protein interactions of BetP reconstituted in closely packed two-dimensional crystals of negatively charged lipids and probed at the molecular level with Fourier transform infrared (FTIR) spectroscopy. The FTIR data indicate that K⁺ binding weakens the interaction of BetP especially with the anionic lipid head groups. We suggest a regulation mechanism in which lipid-protein interactions, especially with the C-terminal domain and the functional important gating helices transmembrane helice 3 (TMH3) and TMH12, confine BetP to its down-regulated transport state. As BetP is also activated by changes in the physical state of the membrane, our results point toward a more general mechanism of how active transport can be modified by dynamic lipid-protein interactions.     

Single Nucleotide Polymorphism Genotyping and Distribution of Coxiella burnetii Strains from Field Samples in Belgium

The genotypic characterization of Coxiella burnetii provides useful information about the strains circulating at the farm, region, or country level and may be used to identify the source of infection for animals and humans. The aim of the present study was to investigate the strains of C. burnetii circulating in caprine and bovine Belgian farms using a single nucleotide polymorphism (SNP) technique. Direct genotyping was applied to different samples (bulk tank milk, individual milk, vaginal swab, fetal product, and air sample). Besides the well-known SNP genotypes, unreported ones were found in bovine and caprine samples, increasing the variability of the strains found in the two species in Belgium. Moreover, multiple genotypes were detected contemporarily in caprine farms at different years of sampling and by using different samples. Interestingly, certain SNP genotypes were detected in both bovine and caprine samples, raising the question of interspecies transmission of the pathogen.     

ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis

The tagging‐via‐substrate approach designed for the capture of mammal prenylated proteins was adapted to Arabidopsis cell culture. In this way, proteins are in vivo tagged with an azide‐modified farnesyl moiety and captured thanks to biotin alkyne Click‐iT® chemistry with further streptavidin‐affinity chromatography. Mass spectrometry analyses identified four small GTPases and ASG2 (ALTERED SEED GERMINATION 2), a protein previously associated to the seed germination gene network. ASG2 is a conserved protein in plants and displays a unique feature that associates WD40 domains and tetratricopeptide repeats. Additionally, we show that ASG2 has a C‐terminal CaaX‐box that is farnesylated in vitro. Protoplast transfections using CaaX prenyltransferase mutants show that farnesylation provokes ASG2 nucleus exclusion. Moreover, ASG2 interacts with DDB1 (DAMAGE DNA BINDING protein 1), and the subcellular localization of this complex depends on ASG2 farnesylation status. Finally, germination and root elongation experiments reveal that asg2 and the farnesyltransferase mutant era1 (ENHANCED RESPONSE TO ABSCISIC ACID (ABA) 1) behave in similar manners when exposed to ABA or salt stress. To our knowledge, ASG2 is the first farnesylated DWD (DDB1 binding WD40) protein related to ABA response in Arabidopsis that may be linked to era1 phenotypes.     

Review and advancement of the marine biotic resource use metric in seafood LCAs: a case study of Norwegian salmon feed

Purpose

Seafood life cycle assessment (LCA) studies have adopted the primary production required (PPR) indicator to account for the impact of these production systems (e.g., capture fisheries or aquaculture) on the ecosystems they harvest wild inputs from. However, there exists a large diversity in the application of methods to calculate PPR, and current practice often does not consider species- and ecosystem-specific factors. Here, we critically examine current practice and propose a refined method for applying the PPR metric in seafood LCAs.

Methods

We surveyed seafood LCAs that quantify PPR, or its derivatives, to examine the diversity of practice. We then defined and applied a refined method to a case study of the average Norwegian salmon feed in 2012. This refined method incorporates species-specific fishmeal and oil yields, source ecosystem-specific transfer efficiencies and expresses results as a percentage of total ecosystem production that PPR represents. Results were compared to those using previously applied methods based on the literature review, and the impact of uncertainty and natural variability of key input parameters was also assessed using Monte Carlo simulation.

Results and discussion

From the literature review, most studies do not incorporate species-specific fishmeal and oil yields or ecosystem-specific transfer efficiencies when calculating PPR. Our proposed method, which incorporated source species- and ecosystem-specific values for these parameters, provides far greater resolution of PPR than when employing global average values. When alternative methods to calculate PPR were applied to marine inputs to Norwegian salmon feeds, resulting PPR values were similar for some sources of fishmeal and oil. For other species, such as Atlantic herring from ecosystems with low transfer efficiencies, there was a large divergence in resulting PPR values. For combined inputs to Norwegian salmon feeds in 2012, the refined method resulted in a total PPR value that is three times higher than would result using the currently standard method signaling that previous LCA research may have substantially underestimated the marine biotic impacts of fishery products.

Conclusions

While there exists a great diversity of practice in the application of the PPR indicator in seafood LCA, the refined method should be adopted for future LCA studies to be more specific to the context of the study.