Soybean microbiome composition and the impact of host plant resistance

Microbial communities play an important role in the growth and development of plants, including plant immunity and the decomposition of complex substances into absorbable nutrients. Hence, utilizing beneficial microbes becomes a promising strategy for the optimization of plant growth. The objective of this research was to explore the root bacterial profile across different soybean genotypes and the change in the microbial community under soybean cyst nematode (SCN) infection in greenhouse conditions using 16S rRNA sequencing. Soybean genotypes with soybean cyst nematode (SCN) susceptible and resistant phenotypes were grown under field and greenhouse conditions. Bulked soil, rhizosphere, and root samples were collected from each replicate. Sequencing of the bacterial 16S gene indicated that the bacterial profile of soybean root and soil samples partially overlapped but also contained different communities. The bacterial phyla Proteobacteria, Actinobacteria, and Bacteroidetes dominate the soybean root-enriched microbiota. The structure of bacteria was significantly affected by sample year (field) or time point (greenhouse). In addition, the host genotype had a small but significant effect on the diversity of the root microbiome under SCN pressure in the greenhouse test. These differences may potentially represent beneficial bacteria or secondary effects related to SCN resistance.

kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS

Genome-wide association studies (GWAS) have been widely used to identify genetic variation associated with complex traits. Despite its success and popularity, the traditional GWAS approach comes with a variety of limitations. For this reason, newer methods for GWAS have been developed, including the use of pan-genomes instead of a reference genome and the utilization of markers beyond single-nucleotide polymorphisms, such as structural variations and k-mers. The k-mers-based GWAS approach has especially gained attention from researchers in recent years. However, these new methodologies can be complicated and challenging to implement. Here, we present kGWASflow, a modular, user-friendly, and scalable workflow to perform GWAS using k-mers. We adopted an existing kmersGWAS method into an easier and more accessible workflow using management tools like Snakemake and Conda and eliminated the challenges caused by missing dependencies and version conflicts. kGWASflow increases the reproducibility of the kmersGWAS method by automating each step with Snakemake and using containerization tools like Docker. The workflow encompasses supplemental components such as quality control, read-trimming procedures, and generating summary statistics. kGWASflow also offers post-GWAS analysis options to identify the genomic location and context of trait-associated k-mers. kGWASflow can be applied to any organism and requires minimal programming skills. kGWASflow is freely available on GitHub (https://github.com/akcorut/kGWASflow) and Bioconda (https://anaconda.org/bioconda/kgwasflow).

Maize seed endophytes

Maize is a vital global crop, and each seed (kernel) hosts an ecosystem of microbes living inside it. However, we know very little about these endophytes and what their role is in plant production and physiology. In this Microreview, I summarize the major questions around maize seed endophytes, including what organisms are present, how they get there, whether and how they transmit across generations, and how they and the plant affect each other. Although several studies touch on each of these areas, ultimately there are far more questions than answers. Future priorities for research on maize seed endophytes should include understanding what adaptations allow microbes to be seed endophytes, how the host genetics and the environment affect these communities, and how maize seed endophytes ultimately contribute to the next generation of plants.

Yield prediction through integration of genetic, environment, and management data through deep learning

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall performance. BLUP models achieved the lowest average error, but deep learning models performed more consistently with similar average error. Optimizing deep neural network submodules for each data type improved model performance relative to optimizing the whole model for all data types at once. Examining the effect of interactions in the best-performing model revealed that including interactions altered the model's sensitivity to weather and management features, including a reduction of the importance scores for timepoints expected to have a limited physiological basis for influencing yield-those at the extreme end of the season, nearly 200 days post planting. Based on these results, deep learning provides a promising avenue for the phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors.

Effects of Inbreeding on Microbial Community Diversity of Zea mays

Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.

Identification of small effect quantitative trait loci of plant architectural, flowering, and early maturity traits in reciprocal interspecific introgression population in cotton

Plant architecture, flowering time and maturity traits are important determinants of yield and fiber quality of cotton. Genetic dissection of loci determining these yield and quality components is complicated by numerous loci with alleles conferring small differences. Therefore, mapping populations segregating for smaller numbers and sizes of introgressed segments is expected to facilitate dissection of these complex quantitative traits. At an advanced stage in the development of reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum cultivar 'Acala Maxxa' (GH) and G. barbadense 'Pima S6' (GB), we undertook mapping of plant architectural traits, flowering time and maturity. A total of 284 BC₄F₁ and BC₄F₂ progeny rows, 120 in GH and 164 in GB background, were evaluated for phenotype, with only 4 and 3 (of 7) traits showing significant differences among progenies. Genotyping by sequencing yielded 3,186 and 3,026 SNPs, respectively, that revealed a total of 27 QTLs in GH background and 22 in GB, for plant height, days to flowering, residual flowering at maturity and maturity. More than of 90% QTLs identified in both backgrounds had small effects (%PV < 10), supporting the merit of this population structure to reduce background noise and small effect QTLs. Germplasm developed in this study may serve as potential pre-breeding material to develop improved cotton cultivars.

Genomic and Chemical Diversity of Commercially Available High-CBD Industrial Hemp Accessions

High consumer demand for cannabidiol (CBD) has made high-CBD hemp (Cannabis sativa) an extremely high-value crop. However, high demand has resulted in the industry developing faster than the research, resulting in the sale of many hemp accessions with inconsistent performance and chemical profiles. These inconsistencies cause significant economic and legal problems for growers interested in producing high-CBD hemp. To determine the genetic and phenotypic consistency in available high-CBD hemp varieties, we obtained seed or clones from 22 different named accessions meant for commercial production. Genotypes (∼48,000 SNPs) and chemical profiles (% CBD and THC by dry weight) were determined for up to 8 plants per accession. Many accessions-including several with the same name-showed little consistency either genetically or chemically. Most seed-grown accessions also deviated significantly from their purported levels of CBD and THC based on the supplied certificates of analysis. Several also showed evidence of an active tetrahydrocannabinolic acid (THCa) synthase gene, leading to unacceptably high levels of THC in female flowers. We conclude that the current market for high-CBD hemp varieties is highly unreliable, making many purchases risky for growers. We suggest options for addressing these issues, such using unique names and developing seed and plant certification programs to ensure the availability of high-quality, verified planting materials.

Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain

Vitamin A deficiency remains prevalent in parts of Asia, Latin America, and sub-Saharan Africa where maize (Zea mays) is a food staple. Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percentage of phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide an in-depth genome-level understanding of the genetic and molecular control of carotenoids in plants. In addition, these findings provide a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.

Genome-Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet

Developed genome-wide SNP marker data for kodo, proso, and little millet Marker data used to analyze genetic diversity Heritability results of various traits used to validate genetic data Millets are a diverse group of small-seeded grains that are rich in nutrients but have received relatively little advanced plant breeding research. Millets are important to smallholder farmers in Africa and Asia because of their short growing season, good stress tolerance, and high nutritional content. To advance the study and use of these species, we present genome-wide marker datasets and population structure analyses for three minor millets: kodo millet (Paspalum scrobiculatum L.), little millet (Panicum sumatrense Roth), and proso millet (Panicum miliaceum L.).We generated genome-wide marker data sets for 190 accessions of each species with genotyping-by-sequencing (GBS). After filtering, we retained between 161 and 165 accessions of each species, with 3461, 2245, and 1882 single-nucleotide polymorphisms (SNPs) for kodo, little, and proso millet, respectively. Population genetic analysis revealed seven putative subpopulations of kodo millet and eight each of proso millet and little millet. To confirm the accuracy of this genetic data, we used public phenotype data on a subset of these accessions to estimate the heritability of various agronomically relevant phenotypes. Heritability values largely agree with the prior expectation for each phenotype, indicating that these SNPs provide an accurate genome-wide sample of genetic variation. These data represent one of first genome-wide population genetics analyses-and the most extensive-in these species and the first genomic analyses of any sort for little millet and kodo millet. These data will be a valuable resource for researchers and breeders trying to improve these crops for smallholder farmers.

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.

Mapping a male-fertility restoration locus for the A4 cytoplasmic-genic male-sterility system in pearl millet using a genotyping-by-sequencing-based linkage map

BACKGROUND

Pearl millet (Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) R. Br) is an important cereal and fodder crop in hot and arid environments. There is great potential to improve pearl millet production through hybrid breeding. Cytoplasmic male sterility (CMS) and the corresponding nuclear fertility restoration / sterility maintenance genes (Rfs) are essential tools for economic hybrid seed production in pearl millet. Mapping the Rf genes of the A₄ CMS system in pearl millet would enable more efficient introgression of both dominant male-fertility restoration alleles (Rf) and their recessive male-sterility maintenance counterparts (rf).

RESULTS

A high density linkage map based on single nucleotide polymorphism (SNP) markers was generated using an F₂ mapping population and genotyping-by-sequencing (GBS). The parents of this cross were 'ICMA 02777' and 'ICMR 08888', which segregate for the A₄ Rf locus. The linkage map consists of 460 SNP markers distributed mostly evenly and has a total length of 462 cM. The segregation ratio of male-fertile and male-sterile plants (3:1) based on pollen production (presence/absence) indicated monogenic dominant inheritance of male-fertility restoration. Correspondingly, a major quantitative trait locus (QTL) for pollen production was found on linkage group 2, with cross-validation showing a very high QTL occurrence (97%). The major QTL was confirmed using selfed seed set as phenotypic trait, though with a lower precision. However, these QTL explained only 14.5% and 9.9% of the phenotypic variance of pollen production and selfed seed set, respectively, which was below expectation. Two functional KASP markers were developed for the identified locus.

CONCLUSION

This study identified a major QTL for male-fertility restoration using a GBS-based linkage map and developed KASP markers which support high-throughput screening of the haploblock. This is a first step toward marker-assisted selection of A₄ male-fertility restoration and male-sterility maintenance in pearl millet.

Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations

In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments. Totals of 3186 and 3026 polymorphic single-nucleotide polymorphisms (SNPs) in GH and GB backgrounds, respectively, were identified and used for trait mapping. Small-effect QTL (<10% variance explained) made up 87 and 100% of QTL in GH and GB backgrounds, respectively. In both species, favorable alleles were found with effects being masked or neutralized by unfavorable alleles, with greater scope for improvement of GH than GB by introgressive breeding. A total of three stable QTL-two in GH background for fiber elongation (ELO) and micronaire (MIC) and one in GB background for upper-half mean length (UHM)-were identified in two out of three environments. Curiously, only four QTL-three for UHM and one for ELO-showed the expected opposite effects in reciprocal backgrounds, perhaps reflecting the combined consequences of epistasis, small phenotypic effects, and low coverage of some genomic regions. Along with new information for marker-assisted breeding, this study adds to knowledge that can be used to unravel complex genetic networks governing fiber quality traits.

Genetic Analysis of Gossypium Fiber Quality Traits in Reciprocal Advanced Backcross Populations

In mapping populations segregating for many loci, the large amount of variation among genotypes often masks small-effect quantitative trait loci (QTL). This problem can be reduced by development of populations with fewer chromosome segments segregating. Here, we report early QTL detection in reciprocal advanced backcross populations from crosses between elite Gossypium hirsutum L. 'Acala Maxxa' (GH) and G. barbadense L. 'Pima S6' (GB). A total of 297 BCF and BCF progeny rows-127 segregating for GB chromosome segments in GH background and 170 segregating for GH chromosome segments in GB background-were evaluated in three environments. Totals of 3186 and 3026 polymorphic single-nucleotide polymorphisms (SNPs) in GH and GB backgrounds, respectively, were identified and used for trait mapping. Small-effect QTL (<10% variance explained) made up 87 and 100% of QTL in GH and GB backgrounds, respectively. In both species, favorable alleles were found with effects being masked or neutralized by unfavorable alleles, with greater scope for improvement of GH than GB by introgressive breeding. A total of three stable QTL-two in GH background for fiber elongation (ELO) and micronaire (MIC) and one in GB background for upper-half mean length (UHM)-were identified in two out of three environments. Curiously, only four QTL-three for UHM and one for ELO-showed the expected opposite effects in reciprocal backgrounds, perhaps reflecting the combined consequences of epistasis, small phenotypic effects, and low coverage of some genomic regions. Along with new information for marker-assisted breeding, this study adds to knowledge that can be used to unravel complex genetic networks governing fiber quality traits.

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

Tocopherols, tocotrienols, and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot Arabidopsis thaliana, which has green, photosynthetic seeds, but our understanding of tocochromanol accumulation in major crops, whose seeds are nonphotosynthetic, remains limited. To understand the genetic control of tocochromanols in grain, we conducted a joint linkage and genome-wide association study in the 5000-line U.S. maize (Zea mays) nested association mapping panel. Fifty-two quantitative trait loci for individual and total tocochromanols were identified, and of the 14 resolved to individual genes, six encode novel activities affecting tocochromanols in plants. These include two chlorophyll biosynthetic enzymes that explain the majority of tocopherol variation, which was not predicted given that, like most major cereal crops, maize grain is nonphotosynthetic. This comprehensive assessment of natural variation in vitamin E levels in maize establishes the foundation for improving tocochromanol and vitamin E content in seeds of maize and other major cereal crops.

Maize YABBY Genes drooping leaf1 and drooping leaf2 Regulate Plant Architecture

Leaf architecture directly influences canopy structure, consequentially affecting yield. We discovered a maize (Zea mays) mutant with aberrant leaf architecture, which we named drooping leaf1 (drl1). Pleiotropic mutations in drl1 affect leaf length and width, leaf angle, and internode length and diameter. These phenotypes are enhanced by natural variation at the drl2 enhancer locus, including reduced expression of the drl2-Mo17 allele in the Mo17 inbred. A second drl2 allele, produced by transposon mutagenesis, interacted synergistically with drl1 mutants and reduced drl2 transcript levels. The drl genes are required for proper leaf patterning, development and cell proliferation of leaf support tissues, and for restricting auricle expansion at the midrib. The paralogous loci encode maize CRABS CLAW co-orthologs in the YABBY family of transcriptional regulators. The drl genes are coexpressed in incipient and emergent leaf primordia at the shoot apex, but not in the vegetative meristem or stem. Genome-wide association studies using maize NAM-RIL (nested association mapping-recombinant inbred line) populations indicated that the drl loci reside within quantitative trait locus regions for leaf angle, leaf width, and internode length and identified rare single nucleotide polymorphisms with large phenotypic effects for the latter two traits. This study demonstrates that drl genes control the development of key agronomic traits in maize.

Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers

Pearl millet [ (L.) R. Br; also (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines 'Tift 99DB' and 'Tift 454'. DNA from 186 RILs, the parents, and the F was used for 96-plex KI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to leaf spot [ (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community.

Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection

Foxtail millet [Setaria italica (L.) P. Beauv.] is one among the most ancient crops of dryland agriculture. It is the second most important crop among millets grown for grains or forage. Foxtail millet germplasm resources provide reservoirs of novel alleles and genes for crop improvement that have remained mostly unexplored. We genotyped a set of 190 foxtail millet germplasm accessions (including 155 accessions of the foxtail millet core collection) using genotyping-by-sequencing (GBS) for rapid single nucleotide polymorphisms (SNP) characterization to study population genetics and structure, which enable allele mining through association mapping approaches. After filtering a total 350,000 raw SNPs identified across 190 germplasm accessions for minor allele frequency (MAF), coverage for samples and coverage for sites, we retained 181 accessions with 17,714 high-quality SNPs with ≥5% MAF. Genetic structure analyses revealed that foxtail millet germplasm accessions are structured along both on the basis of races and geographic origin, and the maximum proportion of variation was due to among individuals within populations. Accessions of race indica were less diverse and are highly differentiated from those of maxima and moharia. Genome-wide linkage disequilibrium (LD) analysis showed on an average LD extends up to ∼150 kbp and varied with individual chromosomes. The utility of the data for performing genome-wide association studies (GWASs) was tested with plant pigmentation and days to flowering and identified significant marker-trait associations. This SNP data provides a foundation for exploration of foxtail millet diversity and for mining novel alleles and mapping genes for economically important traits.

Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population

Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and are at the basis of crop yield and adaptation. We performed high-throughput metabolite analyses on over 12,000 samples from the nested association mapping population to identify genetic variation in C and N metabolism in maize (Zea mays ssp. mays). All samples were grown in the same field and used to identify natural variation controlling the levels of 12 key C and N metabolites, namely chlorophyll a, chlorophyll b, fructose, fumarate, glucose, glutamate, malate, nitrate, starch, sucrose, total amino acids, and total protein, along with the first two principal components derived from them. Our genome-wide association results frequently identified hits with single-gene resolution. In addition to expected genes such as invertases, natural variation was identified in key C4 metabolism genes, including carbonic anhydrases and a malate transporter. Unlike several prior maize studies, extensive pleiotropy was found for C and N metabolites. This integration of field-derived metabolite data with powerful mapping and genomics resources allows for the dissection of key metabolic pathways, providing avenues for future genetic improvement.

Genome-wide association of carbon and nitrogen metabolism in the maize nested association mapping population

Carbon (C) and nitrogen (N) metabolism are critical to plant growth and development and are at the basis of crop yield and adaptation. We performed high-throughput metabolite analyses on over 12,000 samples from the nested association mapping population to identify genetic variation in C and N metabolism in maize (Zea mays ssp. mays). All samples were grown in the same field and used to identify natural variation controlling the levels of 12 key C and N metabolites, namely chlorophyll a, chlorophyll b, fructose, fumarate, glucose, glutamate, malate, nitrate, starch, sucrose, total amino acids, and total protein, along with the first two principal components derived from them. Our genome-wide association results frequently identified hits with single-gene resolution. In addition to expected genes such as invertases, natural variation was identified in key C4 metabolism genes, including carbonic anhydrases and a malate transporter. Unlike several prior maize studies, extensive pleiotropy was found for C and N metabolites. This integration of field-derived metabolite data with powerful mapping and genomics resources allows for the dissection of key metabolic pathways, providing avenues for future genetic improvement.

The Genetic Makeup of a Global Barnyard Millet Germplasm Collection

Barnyard millet (Echinochloa spp.) is an important crop for many smallholder farmers in southern and eastern Asia. It is valued for its drought tolerance, rapid maturation, and superior nutritional qualities. Despite these characteristics there are almost no genetic or genomic resources for this crop in either cultivated species [E. colona (L.) Link and E. crus-galli (L.) P. Beauv.]. Recently, a core collection of 89 barnyard millet accessions was developed at the genebank at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). To enhance the use of this germplasm and genomic research in barnyard millet improvement, we report the genetic characterization of this core collection using whole-genome genotyping-by-sequencing. We identified several thousand single-nucleotide polymorphisms segregating in the core collection, and we use them to show patterns of population structure and phylogenetic relationships among the accessions. We determine that there are probably four population clusters within the E. colona accessions and three such clusters within E. crus-galli. These clusters match phylogenetic relationships but by and large do not correspond to classification into individual races or clusters based on morphology. Geospatial data available for a subset of samples indicates that the clusters probably originate from geographic divisions. In all, these data will be useful to breeders working to improve this crop for smallholder farmers. This work also serves as a case study of how modern genomics can rapidly characterize crops, including ones with little to no prior genetic data.

Association mapping across numerous traits reveals patterns of functional variation in maize

Phenotypic variation in natural populations results from a combination of genetic effects, environmental effects, and gene-by-environment interactions. Despite the vast amount of genomic data becoming available, many pressing questions remain about the nature of genetic mutations that underlie functional variation. We present the results of combining genome-wide association analysis of 41 different phenotypes in ∼ 5,000 inbred maize lines to analyze patterns of high-resolution genetic association among of 28.9 million single-nucleotide polymorphisms (SNPs) and ∼ 800,000 copy-number variants (CNVs). We show that genic and intergenic regions have opposite patterns of enrichment, minor allele frequencies, and effect sizes, implying tradeoffs among the probability that a given polymorphism will have an effect, the detectable size of that effect, and its frequency in the population. We also find that genes tagged by GWAS are enriched for regulatory functions and are ∼ 50% more likely to have a paralog than expected by chance, indicating that gene regulation and gene duplication are strong drivers of phenotypic variation. These results will likely apply to many other organisms, especially ones with large and complex genomes like maize.

Entering the second century of maize quantitative genetics

Maize is the most widely grown cereal in the world. In addition to its role in global agriculture, it has also long served as a model organism for genetic research. Maize stands at a genetic crossroads, as it has access to all the tools available for plant genetics but exhibits a genetic architecture more similar to other outcrossing organisms than to self-pollinating crops and model plants. In this review, we summarize recent advances in maize genetics, including the development of powerful populations for genetic mapping and genome-wide association studies (GWAS), and the insights these studies yield on the mechanisms underlying complex maize traits. Most maize traits are controlled by a large number of genes, and linkage analysis of several traits implicates a 'common gene, rare allele' model of genetic variation where some genes have many individually rare alleles contributing. Most natural alleles exhibit small effect sizes with little-to-no detectable pleiotropy or epistasis. Additionally, many of these genes are locked away in low-recombination regions that encourage the formation of multi-gene blocks that may underlie maize's strong heterotic effect. Domestication left strong marks on the maize genome, and some of the differences in trait architectures may be due to different selective pressures over time. Overall, maize's advantages as a model system make it highly desirable for studying the genetics of outcrossing species, and results from it can provide insight into other such species, including humans.

OLE RNA protects extremophilic bacteria from alcohol toxicity

OLE (Ornate, Large, Extremophilic) RNAs represent a recently discovered non-coding RNA class found in extremophilic anaerobic bacteria, including certain human pathogens. OLE RNAs exhibit several unusual characteristics that indicate a potentially novel function, including exceptionally high expression and localization to cell membranes via interaction with a protein partner called OLE-associated protein (OAP). In the current study, new genetic and phenotypic characteristics of OLE RNA from Bacillus halodurans C-125 were established. OLE RNA is transcribed at high levels from its own promoter under normal growth conditions and the transcript is exceptionally stable compared to most other RNAs. Expression is increased by ∼7-fold when cells are exposed to near lethal concentrations of short-chain alcohols such as ethanol or methanol. Strains wherein the genes for OLE and/or OAP are deleted are more susceptible to growth inhibition by alcohol and also become more sensitive to cold. Normal growth characteristics can be restored by expressing the genes for OLE and OAP from plasmids or from elsewhere on the chromosome. Our findings confirm a functional link between OLE and OAP and reveal the importance of a large non-coding RNA in the response to alcohol-induced stress.

Improved genetic transformation methods for the model alkaliphile Bacillus halodurans C-125

AIMS

Bacillus halodurans C-125 is a Gram-positive bacterium that was the first alkaliphilic species to have its genome completely sequenced. Despite its many years as a model for alkaliphily and source of industrially important enzymes, genetic manipulation of B. halodurans C-125 remains difficult, and therefore, we sought to develop a robust method to allow routine transformation of this organism.

METHODS AND RESULTS

A plasmid artificial modification system (PAM system, Yasui et al. 2008) for B. halodurans C-125 was created that increases transformation efficiency by 10- to 1000-fold. Also, recovering transformed protoplasts on succinate nutrient agar (SNA) yields faster, more robust colony recovery than on the traditional recovery medium. Combining these two techniques often allows recovery of transformants in as little as 48 h.

CONCLUSIONS

Use of the B. halodurans C-125 PAM system and SNA greatly improves the efficiency and speed of protoplast transformation of B. halodurans C-125.

SIGNIFICANCE AND IMPACT OF THE STUDY

These techniques allow routine genetic manipulation of B. halodurans C-125, a model alkaliphilic bacterium with important industrial properties.

Association of OLE RNA with bacterial membranes via an RNA-protein interaction

Ornate, large, extremophilic (OLE) RNAs are large, non-coding transcripts characterized by their ornate secondary structure and presence predominantly in Gram-positive, extremophilic bacteria. A gene for an OLE-associated protein (OAP) is almost always located immediately downstream of the OLE gene. OAP has no extensive homology to other proteins and is predicted to form multiple transmembrane domains. We show that this protein forms a ribonucleoprotein complex with OLE RNA using at least 2:1 protein : RNA stoichiometry. A series of truncated OLE RNA constructs was used to establish that most of the RNA can be deleted without eliminating protein binding. Two primary binding sites are present within the RNA, although additional binding determinants exist and extensive structural stabilization is induced by OAP. RNA fluorescence in situ hybridization (FISH) was used in Escherichia coli to demonstrate that ribonucleoprotein complex formation localizes the RNA near cell membranes of this heterologous system. Therefore, the majority of the complex structure formed by OLE RNA may perform a biochemical function that requires membrane localization.

A review of the role of assistive technology for people with dementia in the hours of darkness

Assistive Technology (AT) has been utilized to support people with dementia (PwD) and their carers in the home. Such support can extend the time that PwD can remain safely at home and reduce the burden on the tertiary healthcare sector. Technology can assist people in the hours of darkness as well as during the day. The objective of this literature review is to evaluate reported healthcare technologies appropriate to night time care. This paper summarises and categorises the current evidence base. In all, 131 abstracts were returned from a database search, yielding fifty four relevant papers which were considered in detail. While night-time specific studies identified very few papers (4 papers, 7%), most of the more general AT findings could be adopted to benefit night-time assistance. Studies have used technology for prompting and reminding as loss of time and forgetfulness are major problems; for monitoring daily activities in a sensor enriched environment and utilised location aware technologies to provide information to enhance safety. Technology also supports a range of therapies to alleviate symptoms. Therapies include the delivery of music and familial pictures for reminiscing, the use of light therapy to enhance wellbeing and the provision of mental tasks to stimulate the brain and maintain activity levels.

Telemedicine applications for the regional paediatric cardiology service in Northern Ireland

The regional paediatric cardiology centre in Northern Ireland has a telemedicine network linking the neonatal units of three district general hospitals using ISDN and IP-compliant equipment. We have previously reported the use of ISDN transmission at 128 kbit/s for remote echocardiography. In a series of 61 patients, a total of 59 transmitted scans were of sufficient diagnostic quality to confirm or exclude the presence of major congenital heart disease (CHD). There were three diagnostic errors (7%). Subsequently, we have examined the use of ISDN transmission at 384 kbit/s. Echocardiographic studies were carried out on 21 patients and all were followed up. Fourteen patients (67%) had CHD confirmed. There were two diagnostic errors (10%). Our experience of transmitting live echocardiographic images suggests that ISDN at 384 kbit/s provides the optimum balance between the clarity of the transmitted images and costs. We expect that IP videoconferencing will offer similar quality but at a lower running cost, and are currently assessing it in a pilot study. All sites within our network will remain capable of ISDN transmission until the efficacy and reliability of IP transmission has been demonstrated in a controlled trial. The clinical telemedicine service has led to the earlier diagnosis of and instigation of appropriate treatment for CHD.

A knowledge-based multimedia telecare system to improve the provision of formal and informal care for the elderly and disabled

We have developed a knowledge-based multimedia telecare system, based on a multimedia PC connected by ISDN at 128 kbit/s. The user display is a television. Multimedia material is accessed through a browser-based interface. A remote-control handset is used as the main means of interaction, to ensure ease of use and overcome any initial reservations resulting from 'technophobia' on the part of the informal carer. The system was used in 13 family homes and four professional sites in Northern Ireland. The evaluations produced positive comments from the informal carers. There are plans to expand the use of the system.

Perception of different frequencies of cranial transcutaneous electrical nerve stimulation in normal and HIV-positive individuals

Sine-wave transcutaneous electrical nerve stimulation (TENS) of varying frequencies applied across the cranium (ear to ear) has been demonstrated to evoke three different noncutaneous sensations in three discrete, nonoverlapping frequency bands in normal, healthy subjects. This report describes two studies which evaluate perception of these cranial TENS-evoked, frequency-dependent sensations in normal and HIV-positive individuals. In Exp. I, all of 50 normal, healthy subjects reported perceiving the same three noncutaneous sensations in the same three nonoverlapping frequency bands as long as stimulated and over repeated trials. In Exp. II, 34 HIV-positive individuals (14 asymptomatic, 9 ARC, 11 AIDS) who were free of neurological symptoms differed significantly from 10 normal, healthy controls, and from the norms observed in Exp. I, on perception of the three different TENS-evoked sensations. Also, inability to maintain perception of the stimulus over repeated trials, observed only in the HIV-positive individuals, increased significantly with severity of HIV infection.

Vascular malformation: case report and literature review

The therapeutic outcome of congenital vascular malformations generally parallels the complexity of the lesion. The less extensive malformations that are prone to regression may be observed. Larger lesions that produce facial asymmetry or have diffuse extremity involvement require a more aggressive approach. Even with the limitations of current treatment methods these extensive malformations can usually be controlled thus affording the patient a better life.

Legionnaires' disease and the sick-building syndrome

In October 1985, six cases of legionnaires' disease were associated with a police headquarters building. Four were amongst staff who worked in or visited the communications wing of the headquarters and two cases occurred in the local community. A case-control study implicated the operations room of the communications wing as the main area associated with infection. This wing was air-conditioned and smoke tracer studies showed that drift from the exhaust as well as from the base of the cooling tower entered the main air-intake which serviced the air-conditioning system. Legionella pneumophila serogroup 1 subgroup pontiac was isolated from water and sludge in the cooling tower pond. Contaminated drift from the top of the cooling tower was probably responsible for the two community cases. An additional discovery was that symptoms suggestive of the sick-building syndrome were associated with working in this wing.

Pulmonary involvement in primary biliary cirrhosis

Four patients with primary biliary cirrhosis (PBC) and Sjogren's syndrome presented with pulmonary disease manifested by fever, cough, and dyspnea. One patient had obstructive lung disease secondary to an autoimmune process documented by immunofluorescent staining of lung parenchyma. The other three patients had interstitial lung disease, pulmonary nodules, and multiple granulomas of the lung, respectively. Primary biliary cirrhosis is a complex autoimmune syndrome involving a disorder of the secretory immune system and its epithelial end organs. These four cases suggest that, in addition to biliary, lacrimal, intestinal, renal tubular, and salivary epithelium, lung tissue also is a possible site for autoimmune involvement in PBC.

Faecal carriage of Clostridium perfringens

The numbers and serotypes of Clostridium perfringens present in the faeces of three groups of hospital patients and young healthy laboratory workers were examined in studies lasting between 10 and 13 weeks. In one hospital some long-stay geriatric patients carried relatively high numbers of C. perfringens (greater than 10(7)/g) most of the time and it was not unusual in any one week for the majority of these patients to carry the same serotype(s). However, the numbers of C. perfringens in the faeces of young long-stay patients in the same hospital were in the range of 10(3)-10(4)/g and carriage of common serotypes was not observed. These results were similar to the findings with the young laboratory workers. This investigation indicates that two of the laboratory criteria often used in the investigation of C. perfringens food poisoning, i.e. faecal counts of greater than or equal to 10(5) C. perfringens/g and patients carrying the same serological type need to be interpreted with caution with suspected outbreaks involving some groups of geriatric long-stay hospital patients.

Sixty latissimus dorsi flaps

In clinical experiences with 60 cases, we have found the latissimus dorsi to be a reliable and versatile flap. We describe its use for a functional muscle transfer (in restoration of elbow flexion and repair of abdominal wall defects), for arm and shoulder coverage, for breast reconstruction, and as a free flap.

Paratyphoid in man and cattle

Salmonella paratyphi B, phage type Taunton, caused generalized subclinical infection of cows and cases of human enteric fever at a dairy farm. The cattle were probably infected from a stream receiving the sewage effluent of a village in which a chronic carrier lived. At the same time as the farm outbreak a water-borne outbreak of human paratyphoid fever occurred in villages several miles away. The water supply was chlorinated and no failure of its treatment had been detected. S. paratyphi B, type Taunton, was isolated from the septic tank of a cottage near the water source and from soil over a break in the effluent pipe. Several inhabitants of the cottage worked at the infected dairy farm and one showed serological evidence of infection.Attention is drawn to the lack of statutory powers which could be applied to prevent the spread of the disease from the dairy herd and to the hazards of simple chlorination in the absence of additional safeguards of a water supply liable to pollution by surface water.