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(1600K 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 17K,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.

Livestock induces strong spatial heterogeneity of soil CO2, N2O and CH4 emissions within a semi-arid sylvo-pastoral landscape in West Africa

Greenhouse gas （GHG） emissions from the surface soils and surface water receiving animal excreta may be important components of the GHG balance of terrestrial ecosystems, but the associated processes are poorly documented in tropical environments, especially in tropical arid and semi-arid areas. A typical sylvo-pastoral landscape in the semi-arid zone of Senegal, West Africa, was investigated in this study. The study area （706 km2 of managed pastoral land） was a circular zone with a radius of 15 km centered on a borehole used to water livestock. The landscape supports a stocking rate ranging from 0.11 to 0.39 tropical livestock units per hectare depending on the seasonal movements of the livestock. Six landscape units were investigated （land in the vicinity of the borehole, natural ponds, natural rangelands, forest plantations, settlements, and enclosed plots）. Carbon dioxide （CO2）, nitrous oxide （N2O） and methane （CH4） fluxes were measured with static chambers set up at 13 sites covering the six landscape units, and the 13 sites are assumed to be representative of the spatial heterogeneity of the emissions. A total of 216 fluxes were measured during the one-year study period （May 2014 to April 2015）. At the landscape level, soils and surface water emitted an average 19.8 t C-CO2 eq/（hm2.a） （CO2： 82%, N2O： 15%, and CH4： 3%）, but detailed results revealed notable spatial heterogeneity of GHG emissions. CO2 fluxes ranged from 1148.2 （±91.6） mg/（m2.d） in rangelands to 97,980.2 （±4,861.7） mg/（m2.d） in surface water in the vicinity of the borehole. N2O fluxes ranged from 0.6 （±0.1） mg/（m2.d） in forest plantations to 22.6 （±10.8） mg/（m2.d） in the vicinity of the borehole. CH4 fluxes ranged from -3.2 （±0.3） mg/（m2.d） in forest plantations to 8788.5 （±2295.9） mg/（m2.d） from surface water in the vicinity of the borehole. This study identified GHG emission ＂hot spots＂ in the landscape. Emissions from the surface soils were significantly higher in the landscape units most frequently used by the animals, i.e., in the vicinity of the borehole and settlements; and emissions measured from surface water in the vicinity of the borehole and from natural ponds were on average about 10 times higher than soil emissions.

Manufacture of a Low Oxalate Mitsumame-Type Dessert Using Rhubarb Juice and Calcium Salts

Rhubarb (Rheum rhabarbarum) juice was used to make a Japanese soft mitsumame-type dessert sweet. The dessert was prepared from extracted rhubarb juice, which was cooked with sugar, agar and guar gum, then allowed to set in sweet moulds. The total, soluble and insoluble oxalates were determined in the ingredients and the final products using HPLC chromatography. To reduce the soluble oxalate content of the dessert while retaining the colour and taste of the final product, increments of CaCl2 and CaCO3 were added to the test dessert mixes. The addition of CaCl2 reduced the pH from 3.55 ± 0.03 to pH 3.09 ± 0.02 while addition of CaCO3 increased the pH from 3.55 ± 0.03 to 4.96 ± 0.01. In both cases, the incremental addition of calcium reduced the soluble oxalate content of the sweets by converting it to insoluble oxalate.

Perceptions of the Role Played by Aquaculture and the Services It Provides for Territories: Complementarity of Survey Types

This article discusses the perception of ecosystem services for French and Brazilian pond fish farming. Its aim is to study the extent to which the industry and its stakeholders are aware of the existence of such services in order to be able to prioritize them with respect to social well-being. This identification phase is seldom discussed. It requires that survey questionnaires be designed so as to improve understanding of these perceptions. The surveys undertaken combined both open questions where the interviewees expressed their perceptions spontaneously and closed questions where they were invited to rank a pre-established list of the relevant services. These surveys involved 133 fish farmers and 93 stakeholders. The results show that perceptions differ by question type, and confirm the significance of the questionnaire design and the importance of combining several kinds of approach.

CRISPR/Cas9-Targeted Knockout of Rice Susceptibility Genes OsDjA2 and OsERF104 Reveals Alternative Sources of Resistance to Pyricularia oryzae

Rice genes OsDjA2 and OsERF104,encoding a chaperone protein and an APETELA2/ethylene-responsive factor,respectively,are strongly induced in a compatible interaction with blast fungus,and also have function in plant susceptibility validated through gene silencing.Here,we reported the CRISPR/Cas9 knockout of OsDjA2 and OsERF104 genes resulting in considerable improvement of blast resistance.A total of 15 OsDjA2(62.5%)and 17 OsERF104(70.8%)T_(0)transformed lines were identified from 24 regenerated plants for each target and used in downstream experiments.Phenotyping of homozygous T1 mutant lines revealed not only a significant decrease in the number of blast lesions but also a reduction in the percentage of diseased leaf area,compared with the infected control plants.Our results supported CRISPR/Cas9-mediated target mutation in rice susceptibility genes as a potential and alternative breeding strategy for building resistance to blast disease.

Relationship between Carbon Isotope Discrimination and Grain Yield in Spring Wheat Cultivated under Different Water Regimes

In C3 plants, carbon isotope discrimination （A） has been proposed as an indirect selection criterion for grain yield. Reported correlations between A and grain yield however, differ highly according to the analyzed organ or tissue, the stage of sampling, and the environment and water regime. In a first experiment carried out in spring wheat during two consecutive seasons in the dry conditions of northwest Mexico （Ciudad Obregon, Sonora）, different water treatments were applied, corresponding to the main water regimes available to spring wheat worldwide, and the relationships between A values of different organs and grain yield were examined. Under terminal （post-anthesis） water stress, grain yield was positively associated with A in grain at maturity and in leaf at anthesis, confirming results previously obtained under Mediterranean environments. Under early （pre-anthesis） water stress and residual moisture stress, the association between grain A and yield was weaker and highly depended on the quantity of water stored in the soil at sowing. No correlation was found between A and grain yield under optimal irrigation. The relationship between A and grain yield was also studied during two consecutive seasons in 20 bread wheat cultivars in the Ningxia region （Northern China）, characterized by winter drought （pre-anthesis water stress）. Wheat was grown under rainfed conditions in two locations （Guyuan and Pengyang） and under irrigated conditions in another two （Yinchuan and Huinong）. In Huinong, the crop was also exposed to salt stress. Highly significant positive associations were found between leaf and grain A and grain yields across the environments. The relationship between A and yield within environments highly depended on the quantity of water stored in the soil at sowing, the quantity and distribution of rainfall during the growth cycle, the presence of salt in the soil, and the occurrence of irrigation before anthesis. These two experiments confirmed the value of A as an indirect selection criterion for yield and a phenotyping tool under post-anthesis water stress （including limited irrigation）.

Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS

GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures.It allows long-term access to datasets following the FAIR principles:Findable,Accessible,Interoperable,and Reusable,by using a flexible and original approach.It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration,storage,and querying.It takes advantage of international standards including the Crop Ontology,MIAPPE,and the Breeding API.GnpIS allows handling data for a wide range of species and experiment types,including multiannual perennial plants experimental network or annual plant trials with either raw data,i.e.,direct measures,or computed traits.It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data.This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data.Our repository follows the Open Science data publication principles by ensuring citability of each dataset.Finally,GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types.GnpIS can therefore contribute to emerging international federations of information systems.

PDX1.1-dependent biosynthesis of vitamin B6 protects roots from ammonium-induced oxidative stress

Despite serving as a major inorganic nitrogen source for plants,ammonium causes toxicity at elevated con-centrations,inhibiting root elongation early on.While previous studies have shown that ammonium-inhibited root development relates to ammonium uptake and formation of reactive oxygen species(ROS)in roots,it remains unclear about the mechanisms underlying the repression of root growth and how plants cope with this inhibitory effect of ammonium.In this study,we demonstrate that ammonium-induced apo-plastic acidification co-localizes with Fe precipitation and hydrogen peroxide(H_(2)O_(2))accumulation along the stele of the elongation and differentiation zone in root tips,indicating Fe-dependent ROS formation.By screening ammonium sensitivity in T-DNA insertion lines of ammonium-responsive genes,we identified PDX1.1,which is upregulated by ammonium in the root stele and whose product catalyzes de novo biosyn-thesis of vitamin B6.Root growth of pdx1.1 mutants is hypersensitive to ammonium,while chemical complementation or overexpression of PDX1.1 restores root elongation.This salvage strategy requires non-phosphorylated forms of vitamin B6 that are able to quench ROS and rescue root growth from ammo-nium inhibition.Collectively,these results suggest that PDX1.1-mediated synthesis of non-phosphorylated B6 vitamers acts as a primary strategy to protect roots from ammonium-dependent ROS formation.

Easy MPE:Extraction of Quality Microplot Images for UAV-Based High-Throughput Field Phenotyping

Microplot extraction(PE)is a necessary image processing step in unmanned aerial vehicle-(UAV-)based research on breeding fields.At present,it is manually using ArcGIS,QGIS,or other GIS-based software,but achieving the desired accuracy is timeconsuming.We therefore developed an intuitive,easy-to-use semiautomatic program for MPE called Easy MPE to enable researchers and others to access reliable plot data UAV images of whole fields under variable field conditions.The program uses four major steps:(1)binary segmentation,(2)microplot extraction,(3)production of∗.shp files to enable further file manipulation,and(4)projection of individual microplots generated from the orthomosaic back onto the raw aerial UAV images to preserve the image quality.Crop rows were successfully identified in all trial fields.The performance of the proposed method was evaluated by calculating the intersection-over-union(IOU)ratio between microplots determined manually and by Easy MPE:the average IOU(±SD)of all trials was 91%(±3).

A chromosome-level,haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate wholegenome assembly

Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly proneto partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report herethe first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that thediploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequentlyobserved. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gbwith a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequenciesand the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linkinggene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complexmolecular regulation of endoreplication along the chromosomes. This high-quality, anchored assemblyrepresents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidationof this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a userfriendly integrated web portal that enables centralized access to high-throughput genomic and other omicsdata and interoperable use of bioinformatics tools.

iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community

sequenced genome of a multicellular organism (Arabidopsis Genome, 2000) completed just after those of the nematode Caenorhabditis elegans (C. elegans Sequencing Consortium, 1998) and the fruit fly Drosophila melanogaster (Adams et al., 2000). Availability of a full whole-genome sequence for the reference plant opened to plant biologists what is commonly called the post-genomic era.