Genomic Prediction of Arsenic Tolerance and Grain Yield in Rice: Contribution of Trait-Specific Markers and Multi-Environment Models

Many rice-growing areas are affected by high concentrations of arsenic(As). Rice varieties that prevent As uptake and/or accumulation can mitigate As threats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability(PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic(1600 K SNPs) and phenotypic(grain As content, grain yield and days to flowering) data of the Bengal and Assam Aus Panel. Under the base-line single-environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grain As content, respectively; the three prediction methods(Bayesian Lasso, genomic best linear unbiased prediction and reproducing kernel Hilbert spaces) were considered to perform similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17 K, without negative effect on PA of genomic predictions. Single-environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for genotype × environment interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest predictive ability(0.831 for grain As) with much higher efficiency for computing time. These findings pave the way for breeding for As-tolerance in the progenies of biparental crosses involving members of the Bengal and Assam Aus Panel. Genomic prediction can also be applied to breeding for other complex traits under multiple environments.     

Using fishers' anecdotes, naturalists' observations and grey literature to reassess marine species at risk: the case of the Gulf grouper in the Gulf of California, Mexico

Designing fishing policies without knowledge of past levels of target species abundance is a dangerous omission for fisheries management. However, as fisheries monitoring started long after exploitation of many species began, this is a difficult issue to address. Here we show how the ‘shifting baseline’ syndrome can affect the stock assessment of a vulnerable species by masking real population trends and thereby put marine animals at serious risk. Current fishery data suggest that landings of the large Gulf grouper (Mycteroperca jordani, Serranidae) are increasing in the Gulf of California. However, reviews of historical evidence, naturalists’ observations and a systematic documentation of fishers’ perceptions of trends in the abundance of this species indicate that it has dramatically declined. The heyday for the Gulf grouper fishery occurred prior to the 1970s, after which abundance dropped rapidly, probably falling to a few percent of former numbers. This decline happened long before fishery statistics were formally developed. We use the case of the Gulf grouper to illustrate how other vulnerable tropical and semi‐tropical fish and shellfish species around the world may be facing the same fate as the Gulf grouper. In accordance with other recent studies, we recommend using historical tools as part of a broad data‐gathering approach to assess the conservation status of marine species that are vulnerable to over‐exploitation.     

Antifungal activity of strawberry fruit volatile compounds against Colletotrichum acutatum

Eight volatile products characterizing strawberry aroma, which is generated from the oxidative degradation of linoleic and linolenic acids by a lipoxygenase (LOX) pathway, were examined because of their antifungal activity against Colletotrichum acutatum, one of the causal agents of strawberry anthracnose. In this study, the effects of aldehydes, alcohols, and esters on mycelial growth and conidia development were evaluated. (E)-Hex-2-enal was found to be the best inhibitor of mycelial growth [MID (minimum inhibitory doses)=33.65 microL L(-1)] and of spore germination (MID=6.76 microL L(-1)), while hexyl acetate was the least effective of all volatile compounds tested (MID=6441.89 microL L(-1) for mycelial growth and MID=1351.35 microL L(-1) for spore germination). Furthermore, the antifungal activity of (E)-hex-2-enal on susceptibility of strawberry fruits to C. acutatum was also confirmed. The presence of these molecules in jars containing strawberry fruits inoculated with a suspension of spores inhibited the fungus growth and prevented the appearance of symptoms. Moreover, a study of the effects of (E)-hex-2-enal on conidial cells of C. acutatum was evaluated by transmission electron microscopy. This volatile compound altered the structures of the cell wall and plasma membrane, causing disorganization and lysis of organelles and, eventually, cell death.     

Effects of fragmentation on pollinator assemblage, pollen limitation and seed production of Mediterranean myrtle (Myrtus communis)

Pollinator assemblages may shift as a consequence of the destruction and fragmentation of natural habitats. The scarcity of mates and pollinators can lead plant populations to suffer from pollen limitation and a decrease in reproductive performance within fragmented areas. We studied the shift in pollinator assemblages along with pollen limitation and seed production patterns in the Mediterranean shrub Myrtus communis. Our study included six populations contrasting in patch and population size (Large vs. Small) within a fragmented landscape characterized by ∼1% of potential forest coverage. The breeding system in Myrtus communis was self-compatible, but compared with natural pollination, fruit set increased with pollen addition (quantity limited), and seed set (brood size) increased with outcross pollen addition (quality limited). While the pollinator assemblage in Large patches was taxonomically diverse, it was almost monopolized by honeybees in Small patches, where visitation rates were highest and wild bee species were almost absent. In general, Small populations were less pollen limited for fruit set than Large populations, particularly those that received the highest rates of honeybee visits. However, despite differences in fragmentation and pollinators between Large and Small populations, seed production patterns (brood size and seed mass) were rather similar among them, in agreement with similar pollen limitation levels found for brood size. A higher susceptibility of native pollinators to the presence of honeybee hives was found in Small patches, suggesting that the pollinator assemblage may be severely altered when fragmentation occurs in combination with beekeeping. We discuss its implications and effects on plant reproduction in fragmented areas.     

Development and evaluation of a highly sensitive and specific blocking enzyme-linked immunosorbent assay and polymerase chain reaction assay for diagnosis of bovine leukemia virus infection in cattle

OBJECTIVE: To develop a blocking ELISA for detection of bovine leukemia virus (BLV) antibodies that is comparable to a radioimmunoprecipitation (RIP) assay, to evaluate use of this ELISA for identification of BLV-infected herds, and to develop a polymerase chain reaction (PCR) assay for direct diagnosis of infection with BLV. SAMPLE POPULATION: Serum samples and pooled bulk-tank milk samples from cattle. PROCEDURE: The blocking ELISA was developed, using BLV gp51 as antigen, captured by a selected bovine polyclonal serum. A nested PCR was conducted with primers specific for a segment of the pol region of the BLV genome. RESULTS: Sensitivity and specificity of the ELISA were comparable to those of the RIP assay. Use of the ELISA on pooled milk samples allowed identification of herds in which prevalence of BLV infection among lactating cows was as low as 2.5%. Pooled milk samples from BLV-free herds did not react in the ELISA. All cattle that had positive results for the nested PCR had BLV antibodies, but cattle with consistantly low antibody titers required examination of sequential DNA samples to detect viral sequences. None of the 63 antibody-negative cattle had positive results for the PCR. CONCLUSIONS AND CLINICAL RELEVANCE: This ELISA is a highly specific and sensitive assay for the detection of BLV antibodies in serum and milk samples of cattle. Examination of pooled milk samples with the ELISA provides a reliable, practical, and economic procedure for identification of BLV-infected herds. The nested PCR also constitutes a specific procedure for direct diagnosis of infection with BLV.