Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping.

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

Identification of genomic loci regulating grain iron content in aus rice under two irrigation management systems.

Iron (Fe) deficiency is one of the common causes of anaemia in humans. Improving grain Fe in rice, therefore, could have a positive impact for humans worldwide, especially for those people who consume rice as a staple food. In this study, 225-269 accessions of the Bengal and Assam Aus Panel (BAAP) were investigated for their accumulation of grain Fe in two consecutive years in a field experiment under alternative wetting and drying (AWD) and continuous flooded (CF) irrigation. AWD reduced straw Fe by 40% and grain Fe by 5.5-13%. Genotype differences accounted for 35% of the variation in grain Fe, while genotype by irrigation interaction accounted for 12% of the variation in straw and grain Fe in year 1, with no significant interactions detected in year 2. Twelve rice accessions were identified as having high grain Fe for both years regardless of irrigation treatment, half of which were from BAAP aus subgroup 3 which prominently comes from Bangladesh. On average, subgroup 3 had higher grain Fe than the other four subgroups of aus. Genome-wide association mapping identified 6 genomic loci controlling natural variation of grain Fe concentration in plants grown under AWD. For one QTL, nicotianamine synthase OsNAS3 is proposed as candidate for controlling natural variation of grain Fe in rice. The BAAP contains three haplotypes of OsNAS3 where one haplotype (detected in 31% of the individuals) increased grain Fe up to 11%. Haplotype analysis of this gene in rice suggests that the ability to detect the QTL is enhanced in the BAAP because the high Fe allele is balanced in aus, unlike indica and japonica subgroups.

Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation.

KEY MESSAGE: Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from the aus subpopulation. Rice (Oryza sativa L.) is a globally important cereal crop. Sodium (Na+) and potassium (K+) are the major monovalent ions which affect rice growth, and exploring their uptake mechanisms will be useful for understanding rice biology. Since the balance of Na+ and K+ plays a significant role in adaptation of rice to salinity, that biology might inform the search for tolerance. In this study, the Na+ and K+ concentration and Na+/K+ ratio in grains and shoots were analyzed in the Bengal and Assam Aus Panel grown in field conditions under continuously flooded (CF) and alternate wetting and drying (AWD) irrigation. Overall, AWD irrigation significantly reduced the Na+ concentration and increased the K+ concentration in shoots and grains compared to the plants grown under CF. Genome-wide association mapping was conducted on Na+, K+ concentration and Na+/K+ ratio with 2 million SNPs using an efficient mixed model. Only QTLs which contained more than two significant SNPs (p < 0.0001) and where at least one of these significant SNPs passed a 10% false discovery rate were reported. A total of 106 QTLs were identified as being associated with Na+ concentration and Na+/K+ ratio across all traits and field conditions, with 48 QTLs found in multiple traits and/or water conditions. Four notable QTLs (one each on chromosomes 1 and 11, two on chromosome 2) and the haplotype variants of four candidate genes (OsHKT1;5, OsNHX2, LOC_Os02g32490 and OsFAD2_1) are discussed. The QTLs/candidate genes identified here could be useful for breeding rice that accumulates lower concentrations of sodium.

Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach.

Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.

Genetic loci regulating arsenic content in rice grains when grown flooded or under alternative wetting and drying irrigation.

BACKGROUND: Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic. RESULTS: AWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1% in year 1 and 2 respectively and shoot arsenic by 27.0% compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic. All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL. CONCLUSIONS: This study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10% in all high yielding cultivars studied.

Genome Wide Association Mapping of Grain and Straw Biomass Traits in the Rice Bengal and Assam Aus Panel (BAAP) Grown Under Alternate Wetting and Drying and Permanently Flooded Irrigation.

Growing demand for staple crops like rice will need to be achieved predominately through agricultural intensification and more efficient use of inputs. To meet this demand it is essential that the genetic diversity within rice is fully utilized. The aus subpopulation is considered an underappreciated resource within that diversity. A new rice panel, the Bengal and Assam Aus Panel (BAAP) of 266 aus accessions was generated with ∼2 million informative SNPs obtained using skim sequencing at ∼4× depth. The BAAP was grown in the field in Bangladesh in the 'boro' season under both continuously flooded and Alternate Wetting and Drying (AWD) irrigation during 2013 and 2014 in Mymensingh and during 2014 in Madhupur. Heading date, grain mass, straw biomass and harvest index were measured. The majority (94%) of BAAP accessions flowered within a relatively small window of 10 days. The AWD irrigation treatment generally caused an increase in grain mass, but no significant genotype by treatment interactions were detected for this trait. Shoot biomass was the only trait that showed evidence of genotype by treatment interaction. The average LD (Linkage Disequilibrium) decay across the genome was 243 Kbp. Genome wide association mapping revealed 115 quantitative trait loci (QTLs). There was little evidence of QTLs specific to the irrigation treatment, and only a few QTLs co-localized with known genes. However, some QTLs were detected across multiple sites and years. These QTLs should be targets for breeding, and include a region around 2.2 Mbp on chromosome 1, a large region in the middle of chromosome 7 and two regions on chromosome 11 (∼10 Mbp and ∼29 Mbp). The BAAP appears to be a valuable addition to the growing collection of GWA mapping populations of rice.

Biomass and elemental concentrations of 22 rice cultivars grown under alternate wetting and drying conditions at three field sites in Bangladesh.

As the global population grows, demand on food production will also rise. For rice, one limiting factor effecting production could be availability of fresh water, hence adoption of techniques that decrease water usage while maintaining or increasing crop yield are needed. Alternative wetting and drying (AWD) is one of these techniques. AWD is a method by which the level of water within a rice field cycles between being flooded and nonflooded during the growth period of the rice crop. The degree to which AWD affects cultivars differently has not been adequately addressed to date. In this study, 22 rice cultivars, mostly landraces of the aus subpopulation, plus some popular improved indica cultivars from Bangladesh, were tested for their response to AWD across three different field sites in Bangladesh. Grain and shoot elemental concentrations were determined at harvest. Overall, AWD slightly increased grain mass and harvest index compared to plants grown under continually flooded (CF) conditions. Plants grown under AWD had decreased concentrations of nitrogen in their straw compared to plants grown under CF. The concentration of elements in the grain were also affected when plants were grown under AWD compared to CF: Nickel, copper, cadmium and iron increased, but sodium, potassium, calcium, cobalt, phosphorus, molybdenum and arsenic decreased in the grains of plants grown under AWD. However, there was some variation in these patterns across different sites. Analysis of variance revealed no significant cultivar × treatment interaction, or site × cultivar × treatment interaction, for any of the plant mass traits. Of the elements analyzed, only grain cadmium concentrations were significantly affected by treatment × cultivar interactions. These data suggest that there is no genetic adaptation amongst the cultivars screened for response to AWD, except for grain cadmium concentration and imply that breeding specifically for AWD is not needed.

Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity.

OBJECTIVE: Roseburia hominis is a flagellated gut anaerobic bacterium belonging to the Lachnospiraceae family within the Firmicutes phylum. A significant decrease of R. hominis colonization in the gut of ulcerative colitis patients has recently been demonstrated. In this work, we have investigated the mechanisms of R. hominis-host cross talk using both murine and in vitro models. DESIGN: The complete genome sequence of R. hominis A2-183 was determined. C3H/HeN germ-free mice were mono-colonized with R. hominis, and the host-microbe interaction was studied using histology, transcriptome analyses and FACS. Further investigations were performed in vitro and using the TLR5KO and DSS-colitis murine models. RESULTS: In the bacterium, R. hominis, host gut colonization upregulated genes involved in conjugation/mobilization, metabolism, motility, and chemotaxis. In the host cells, bacterial colonization upregulated genes related to antimicrobial peptides, gut barrier function, toll-like receptors (TLR) signaling, and T cell biology. CD4+CD25+FoxP3+ T cell numbers increased in the lamina propria of both mono-associated and conventional mice treated with R. hominis. Treatment with the R. hominis bacterium provided protection against DSS-induced colitis. The role of flagellin in host-bacterium interaction was also investigated. CONCLUSION: Mono-association of mice with R. hominis bacteria results in specific bidirectional gene expression patterns. A set of genes thought to be important for host colonization are induced in R. hominis, while the host cells respond by strengthening gut barrier function and enhancing Treg population expansion, possibly via TLR5-flagellin signaling. Our data reveal the immunomodulatory properties of R. hominis that could be useful for the control and treatment of gut inflammation.

Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal.

BACKGROUND: Genetic diversity among rice cultivars from Bangladesh and North East India was assessed using a custom 384-SNP microarray assay. A total of 511 cultivars were obtained from several sources, choosing landraces likely to be from the aus subpopulation and modern improved cultivars from Bangladesh. Cultivars from the OryzaSNP set and Rice Diversity Panel 1 (RDP1) were also included for reference. RESULTS: The population analysis program STRUCTURE was used to infer putative population groups in the panel, revealing four groups: indica (76 cultivars), japonica (55) and two distinct groups within the aus subpopulation (aus-1 = 99, aus-2 = 151). Principal Component Analysis was used to confirm the four population groups identified by STRUCTURE. The analysis revealed cultivars that belonged to neither aus-1 nor aus-2 but which are clearly aus based on the combined probabilities of their membership of the two aus groups which have been termed aus-admix (96). Information obtained from the panel of 511 cultivars was used to assign rice groups to 74 additional landraces obtained from Assam and West Bengal. While both the aus-1 and aus-2 groups were represented approximately equally in India, aus-2 (which includes cultivar N 22) was more common in Bangladesh, but was not found at all in West Bengal. CONCLUSIONS: Examining the distribution of landrace names within theaus-1 and aus-2 groups suggests that aus-1 is associated with the term "boro", a word used to describe a winter growing season in Bangladesh and Assam. The information described here has been used to select a population of 300 cultivars for Genome Wide Association studies of the aus rice subpopulation.

Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis.

We report here the complete genome sequence of the human gut symbiont Roseburia hominis A2-183(T) (= DSM 16839(T) = NCIMB 14029(T)), isolated from human feces. The genome is represented by a 3,592,125-bp chromosome with 3,405 coding sequences. A number of potential functions contributing to host-microbe interaction are identified.

Community-driven development for computational biology at Sprints, Hackathons and Codefests.

BACKGROUND: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. RESULTS: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. CONCLUSIONS: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

Associations between proteins and RNA-RNA duplexes are important in post-transcriptional regulation of gene expression. The CLASH (Cross-linking, Ligation and Sequencing of Hybrids) technique captures RNA-RNA interactions by physically joining two RNA molecules associated with a protein complex into a single chimeric RNA molecule. These events are relatively rare and considerable effort is needed to detect a small number of chimeric sequences amongst millions of non-chimeric cDNA reads resulting from a CLASH experiment. We present the "hyb" bioinformatics pipeline, which we developed to analyse high-throughput cDNA sequencing data from CLASH experiments. Although primarily designed for use with AGO CLASH data, hyb can also be used for the detection and annotation of chimeric reads in other high-throughput sequencing datasets. We examined the sensitivity and specificity of chimera detection in a test dataset using the BLAST, BLAST+, BLAT, pBLAT and Bowtie2 read alignment programs. We obtained the most reliable results in the shortest time using a combination of preprocessing with Flexbar and subsequent read-mapping using Bowtie2. The "hyb" software is distributed under the GNU GPL (General Public License) and can be downloaded from https://github.com/gkudla/hyb.

Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1.

BACKGROUND: The cellulosome is a multi-enzyme machine, which plays a key role in the breakdown of plant cell walls in many anaerobic cellulose-degrading microorganisms. Ruminococcus flavefaciens FD-1, a major fiber-degrading bacterium present in the gut of herbivores, has the most intricate cellulosomal organization thus far described. Cellulosome complexes are assembled through high-affinity cohesin-dockerin interactions. More than two-hundred dockerin-containing proteins have been identified in the R. flavefaciens genome, yet the reason for the expansion of these crucial cellulosomal components is yet unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have explored the full spectrum of 222 dockerin-containing proteins potentially involved in the assembly of cellulosome-like complexes of R. flavefaciens. Bioinformatic analysis of the various dockerin modules showed distinctive conservation patterns within their two Ca(2+)-binding repeats and their flanking regions. Thus, we established the conceptual framework for six major groups of dockerin types, according to their unique sequence features. Within this framework, the modular architecture of the parent proteins, some of which are multi-functional proteins, was evaluated together with their gene expression levels. Specific dockerin types were found to be associated with selected groups of functional components, such as carbohydrate-binding modules, numerous peptidases, and/or carbohydrate-active enzymes. In addition, members of other dockerin groups were linked to structural proteins, e.g., cohesin-containing proteins, belonging to the scaffoldins. CONCLUSIONS/SIGNIFICANCE: This report profiles the abundance and sequence diversity of the R. flavefaciens FD-1 dockerins, and provides the molecular basis for future understanding of the potential for a wide array of cohesin-dockerin specificities. Conserved differences between dockerins may be reflected in their stability, function or expression within the context of the parent protein, in response to their role in the rumen environment.

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network.

New 'omics' technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information that accompanies data-intense technologies. NuGO, the European Nutrigenomics Organization, the major collaborating network in molecular nutritional sciences, is supporting the application of modern information technologies in this area. We have developed and implemented a concept for data management and computing infrastructure that supports collaboration between nutrigenomics researchers. The system fills the gap between "private" storing with occasional file sharing by email and the use of centralized databases. It provides flexible tools to share data, also during experiments, while preserving ownership. The NuGO Information Network is a decentral, distributed system for data exchange based on standard web technology. Secure access to data, maintained by the individual researcher, is enabled by web services based on the the BioMoby framework. A central directory provides information about available web services. The flexibility of the infrastructure allows a wide variety of services for data processing and integration by combining several web services, including public services. Therefore, this integrated information system is suited for other research collaborations.

An NAD(+)-dependent glutamate dehydrogenase cloned from the ruminal ciliate protozoan, Entodinium caudatum.

An NAD(+)-dependent glutamate dehydrogenase (GDH; EC 1.4.1.24) was cloned from the ruminal ciliate protozoan, Entodinium caudatum. The gene had high sequence similarity to GDH genes from the Bacteroides (class)--a class of bacteria which is highly represented in the rumen. When expressed in Escherichia coli the enzyme had a high affinity for ammonia and alpha-ketoglutarate (apparent K(m) of 2.33 and 0.71 mM, respectively) and a low affinity for glutamate (apparent K(m) of 98 mM). GDH activity and GDH mRNA concentration were increased by incubating washed E. caudatum cells with ammonia and antibiotics. These results suggest that the GDH is an anabolic enzyme catalysing the assimilation of ammonia by E. caudatum in the rumen and that the gene was probably acquired by lateral gene transfer from a ruminal bacterium.