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Phenotypic plasticity is the property of a genotype to produce different phenotypes under different environmental conditions. Understanding genetic and environmental factors behind phenotypic plasticity helps answer some longstanding biology questions and improve phenotype prediction. In this study, we investigated the phenotypic plasticity of flowering time and plant height with a set of diverse sorghum lines evaluated across 14 natural field environments. An environmental index was identified to quantitatively connect the environments. Reaction norms were then obtained with the identified indices for genetic dissection of phenotypic plasticity and performance prediction. Genome-wide association studies (GWAS) detected different sets of loci for reaction-norm parameters (intercept and slope), including 10 new genomic regions in addition to known maturity (Ma1) and dwarfing genes (Dw1, Dw2, Dw3, Dw4 and qHT7.1). Cross-validations under multiple scenarios showed promising results in predicting diverse germplasm in dynamic environments. Additional experiments conducted at four new environments, including one from a site outside of the geographical region of the initial environments, further validated the predictions. Our findings indicate that identifying the environmental index enriches our understanding of gene-environmental interplay underlying phenotypic plasticity, and that genomic prediction with the environmental dimension facilitates prediction-guided breeding for future environments., (© 2024 The Author(s). Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Leaf chlorophyll concentration was measured for 84 publicly available maize hybrids grown under three nitrogen fertilizer treatments in two contrasting environments in Nebraska. The effect of nitrogen treatment on chlorophyll response was found to be significant (p < 0.05) for both locations. In Scottsbluff, chlorophyll concentrations increased significantly with increasing nitrogen rate, while no significant difference was found between medium and high nitrogen in Lincoln. Within equivalent nitrogen treatments, chlorophyll was more abundant in Lincoln than Scottsbluff for nearly every hybrid. Hybrid response was not consistent between environments, with approximately 11% of variance explained by genotype by environment interaction., Competing Interests: The authors declare that there are no conflicts of interest present., (Copyright: © 2024 by the authors.)

A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation., (© 2022. The Author(s).)

Classical genetic studies have identified many cases of pleiotropy where mutations in individual genes alter many different phenotypes. Quantitative genetic studies of natural genetic variants frequently examine one or a few traits, limiting their potential to identify pleiotropic effects of natural genetic variants. Widely adopted community association panels have been employed by plant genetics communities to study the genetic basis of naturally occurring phenotypic variation in a wide range of traits. High-density genetic marker data-18M markers-from 2 partially overlapping maize association panels comprising 1,014 unique genotypes grown in field trials across at least 7 US states and scored for 162 distinct trait data sets enabled the identification of of 2,154 suggestive marker-trait associations and 697 confident associations in the maize genome using a resampling-based genome-wide association strategy. The precision of individual marker-trait associations was estimated to be 3 genes based on a reference set of genes with known phenotypes. Examples were observed of both genetic loci associated with variation in diverse traits (e.g., above-ground and below-ground traits), as well as individual loci associated with the same or similar traits across diverse environments. Many significant signals are located near genes whose functions were previously entirely unknown or estimated purely via functional data on homologs. This study demonstrates the potential of mining community association panel data using new higher-density genetic marker sets combined with resampling-based genome-wide association tests to develop testable hypotheses about gene functions, identify potential pleiotropic effects of natural genetic variants, and study genotype-by-environment interaction., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize ( Zea mays L .) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and n=622 plant loci were identified that are linked to the abundance of n=104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments toward harnessing the full potential of root-associated microbial symbionts in maize production., Competing Interests: MM, GX, ML, GL, CS, BS, JH, JA, YG, JS, JY No competing interests declared, (© 2022, Meier et al.)

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Determining the genetic control of root system architecture (RSA) in plants via large-scale genome-wide association study (GWAS) requires high-throughput pipelines for root phenotyping. We developed Core Root Excavation using Compressed-air (CREAMD), a high-throughput pipeline for the cleaning of field-grown roots, and Core Root Feature Extraction (COFE), a semiautomated pipeline for the extraction of RSA traits from images. CREAMD-COFE was applied to diversity panels of maize ( Zea mays ) and sorghum ( Sorghum bicolor ), which consisted of 369 and 294 genotypes, respectively. Six RSA-traits were extracted from images collected from >3,300 maize roots and >1,470 sorghum roots. Single nucleotide polymorphism (SNP)-based GWAS identified 87 TAS (trait-associated SNPs) in maize, representing 77 genes and 115 TAS in sorghum. An additional 62 RSA-associated maize genes were identified via expression read depth GWAS. Among the 139 maize RSA-associated genes (or their homologs), 22 (16%) are known to affect RSA in maize or other species. In addition, 26 RSA-associated genes are coregulated with genes previously shown to affect RSA and 51 (37% of RSA-associated genes) are themselves transe-quantitative trait locus for another RSA-associated gene. Finally, the finding that RSA-associated genes from maize and sorghum included seven pairs of syntenic genes demonstrates the conservation of regulation of morphology across taxa., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Background: Hyperspectral reflectance data in the visible, near infrared and shortwave infrared range (VIS-NIR-SWIR, 400-2500 nm) are commonly used to nondestructively measure plant leaf properties. We investigated the usefulness of VIS-NIR-SWIR as a high-throughput tool to measure six leaf properties of maize plants including chlorophyll content (CHL), leaf water content (LWC), specific leaf area (SLA), nitrogen (N), phosphorus (P), and potassium (K). This assessment was performed using the lines of the maize diversity panel. Data were collected from plants grown in greenhouse condition, as well as in the field under two nitrogen application regimes. Leaf-level hyperspectral data were collected with a VIS-NIR-SWIR spectroradiometer at tasseling. Two multivariate modeling approaches, partial least squares regression (PLSR) and support vector regression (SVR), were employed to estimate the leaf properties from hyperspectral data. Several common vegetation indices (VIs: GNDVI, RENDVI, and NDWI), which were calculated from hyperspectral data, were also assessed to estimate these leaf properties., Results: Some VIs were able to estimate CHL and N (R 2  > 0.68), but failed to estimate the other four leaf properties. Models developed with PLSR and SVR exhibited comparable performance to each other, and provided improved accuracy relative to VI models. CHL were estimated most successfully, with R 2 (coefficient of determination) > 0.94 and ratio of performance to deviation (RPD) > 4.0. N was also predicted satisfactorily (R 2  > 0.85 and RPD > 2.6). LWC, SLA and K were predicted moderately well, with R 2 ranging from 0.54 to 0.70 and RPD from 1.5 to 1.8. The lowest prediction accuracy was for P, with R 2  < 0.5 and RPD < 1.4., Conclusion: This study showed that VIS-NIR-SWIR reflectance spectroscopy is a promising tool for low-cost, nondestructive, and high-throughput analysis of a number of leaf physiological and biochemical properties. Full-spectrum based modeling approaches (PLSR and SVR) led to more accurate prediction models compared to VI-based methods. We called for the construction of a leaf VIS-NIR-SWIR spectral library that would greatly benefit the plant phenotyping community for the research of plant leaf traits., Competing Interests: Competing interestsThe authors declare that they have no competing interests.

Modern maize was domesticated from Zea mays parviglumis, a teosinte, about 9000 years ago in Mexico. Genes thought to have been selected upon during the domestication of crops are commonly known as domestication loci. The ramosa1 (ra1) gene encodes a putative transcription factor that controls branching architecture in the maize tassel and ear. Previous work demonstrated reduced nucleotide diversity in a segment of the ra1 gene in a survey of modern maize inbreds, indicating that positive selection occurred at some point in time since maize diverged from its common ancestor with the sister species Tripsacum dactyloides and prompting the hypothesis that ra1 may be a domestication gene. To investigate this hypothesis, we examined ear phenotypes resulting from minor changes in ra1 activity and sampled nucleotide diversity of ra1 across the phylogenetic spectrum between tripsacum and maize, including a broad panel of teosintes and unimproved maize landraces. Weak mutant alleles of ra1 showed subtle effects in the ear, including crooked rows of kernels due to the occasional formation of extra spikelets, correlating a plausible, selected trait with subtle variations in gene activity. Nucleotide diversity was significantly reduced for maize landraces but not for teosintes, and statistical tests implied directional selection on ra1 consistent with the hypothesis that ra1 is a domestication locus. In maize landraces, a noncoding 3'-segment contained almost no genetic diversity and 5'-flanking diversity was greatly reduced, suggesting that a regulatory element may have been a target of selection.

We report here the detection of Bartonella quintana, after putative bite transmission, in pre-enrichment blood cultures from a woman and from two feral barn cats. Prospective molecular epidemiological studies are necessary to characterize the risk of human Bartonella quintana infection following cat bites.

In contrast to the large body of literature regarding Bartonella henselae in humans and cats, there is little information about B. henselae as an infectious agent in dogs. Due to the paucity of information regarding the B. henselae serology in dogs, we performed a cross-sectional serosurvey using B. henselae antigen in order to compare the seroprevalence between sick and healthy dogs from the south-eastern USA. Ninety-nine sera were collected from clinically healthy dogs. Three hundred and one sera from sick dogs were submitted to North Carolina State University for serologic screening against a panel of arthropod-transmitted organisms. Serological tests were performed using B. henselae (Bh), Rickettsia rickettsii (Rr), Ehrlichia canis (Ec), Bartonella vinsonii subspecies berkhoffii (Bvb), Babesia canis (Bc) and Borrelia burgdorferi (Bb) antigens. Serum B. henselae IgG antibodies were detected in 10.1% of healthy dogs and in 27.2% of sick dogs. The difference in seroprevalence between the two groups was statistically significant. The majority of seroreactive dogs (80%) had low titers of 1:64 or 1:128. In healthy dogs, seroprevalence for Rr was 14.1% and for Bvb was 1%. In sick dogs, Rr seroprevalence was 29.7%, Ec 6.5%, Bvb 4.7%, Bb 1.7% and Bc was 0.85%. Of the sick dogs that were seroreactive to B. henselae antigens, 40.6% were also seroreactive to Rr, 15.0% reactive to Bvb antigens, 14.8% reactive to Ec antigens, 1.8% reactive to Bc antigens and 1.75% reactive to Bb antigens. Sera from dogs experimentally infected with B. vinsonii subsp. berkhoffii, E. canis or R. rickettsii did not cross react with B. henselae antigens, by IFA testing. This study indicates that B. henselae IgG antibodies are prevalent in healthy and sick dogs living in the south-eastern USA. Nevertheless, further studies are needed to evaluate the epidemiological, clinical and zoonotic relevance of B. henselae infection in dogs.

Dermatoglyphic analyses were carried out on a sample of children with known sex chromosomal aneuploidies (25 XXY, 10 XXX, 1 XXYY). Digital ridge counts and pattern types were determined for each individual. Palm prints and sole patterns were also examined. The results of our study were compared with data from previous studies of sex chromosomal aneuploidies. Out results for the XXY males agree with the findings from other studies with respect to total ridge counts and plantar dermatoglyphics, but not for digital pattern frequencies. Our one example of an XXYY male showed hypothenar patterns similar to those found for this syndrome by other researchers, but neither the digital pattern types nor the unexpectedly high total ridge count conforms to the findings from other studies. Our sample of XXX females falls within the normal XX female range of variation with respect to hypothenar patterns and total ridge count; plantar features show a higher incidence of patterns than previously reported.