Putative Functional Genes Research Articles

A random survival forest-based pathomics signature classifies immunotherapy prognosis and profiles TIME and genomics in ES-SCLC patients

BackgroundSmall cell lung cancer (SCLC) is a highly aggressive neuroendocrine tumor with high mortality, and only a limited subset of extensive-stage SCLC (ES-SCLC) patients demonstrate prolonged survival under chemoimmunotherapy, which warrants the exploration of reliable biomarkers. Herein, we built a machine learning-based model using pathomics features extracted from hematoxylin and eosin (H&E)-stained images to classify prognosis and explore its potential association with genomics and TIME.MethodsWe retrospectively recruited ES-SCLC patients receiving first-line chemoimmunotherapy at Nanjing Jinling Hospital between April 2020 and August 2023. Digital H&E-stained whole-slide images were acquired, and targeted next-generation sequencing, programmed death ligand-1 staining, and multiplex immunohistochemical staining for immune cells were performed on a subset of patients. A random survival forest (RSF) model encompassing clinical and pathomics features was established to predict overall survival. The function of putative genes was assessed via single-cell RNA sequencing.Results and conclusionDuring the median follow-up period of 12.12 months, 118 ES-SCLC patients receiving first-line immunotherapy were recruited. The RSF model utilizing three pathomics features and liver metastases, bone metastases, smoking status, and lactate dehydrogenase, could predict the survival of first-line chemoimmunotherapy in patients with ES-SCLC with favorable discrimination and calibration. Underlyingly, the higher RSF-Score potentially indicated more infiltration of CD8+ T cells in the stroma as well as a greater probability of MCL-1 amplification and EP300 mutation. At the single-cell level, MCL-1 was associated with TNFA-NFKB signaling and apoptosis-related processes. Hopefully, this noninvasive model could act as a biomarker for immunotherapy, potentially facilitating precision medicine in the management of ES-SCLC.

Construction and characterization of DNA libraries from cultured phages and environmental viromes.

Despite many efforts to understand and leverage the functional potential of environmental viromes, most bacteriophage genes are largely uncharacterized. To explore novel biology from uncultivated microbes like phages, metagenomics has emerged as a powerful tool to directly mine new genes without the need to culture the diverse microbiota and the viruses within. When a pure computational approach cannot infer gene function, it may be necessary to create a DNA library from environmental genomic DNA, followed by the screening of that library for a particular function. However, these screens are often initiated without a metagenomic analysis of the completed DNA library being reported. Here, we describe the construction and characterization of DNA libraries from a single cultured phage (ΦT4), five cultured Escherichia coli phages, and three metagenomic viral sets built from freshwater, seawater, and wastewater samples. Through next-generation sequencing of five independent samplings of the libraries, we found a consistent number of recovered genes per replicate for each library, with many genes classifiable via the KEGG and Pharokka databases. By characterizing the size of the genes and inserts, we found that our libraries contain a median of one to two genes per contig with a median gene length of 303-381 bp for all libraries, reflective of the small genomes of viruses. The environmental libraries were genetically diverse compared to the single phage and multi-phage libraries. Additionally, we found reduced coverage of individual genomes when five phages were used as opposed to one. Taken together, this work provides a comprehensive analysis of the DNA libraries from phage genomes that can be used for metagenomic exploration and functional screens to infer and identify new biology.IMPORTANCEFunctional metagenomics is an approach that aims to characterize the putative biological function of genes in the microbial world. This includes an examination of the sequencing data collected from a pooled source of diverse microbes and inference of gene function by comparison to annotated and studied genes from public databases. At times, DNA libraries are made from these genes, and the library is screened for a specific function. Hits are validated using a combination of biological, computational, and structural analysis. Left unresolved is a detailed characterization of the library, both its diversity and content, for the purposes of imputing function entirely by computational means, a process that may yield findings that aid in designing useful screens to identify novel gene functions. In this study, we constructed libraries from cultured phages and uncultured viromes from the environment and characterized some important parameters, such as gene number, genes per contig, ratio of hypothetical to known proteins, total genomic coverage and recovery, and the effect of pooling genetic information from multiple sources, to provide a better understanding of the nature of these libraries. This work will aid the design and implementation of future screens of pooled DNA libraries to discover and isolate viral genes with novel biology across various biomes.

Impact of yeast extract and basal salts medium on 1,4-dioxane biodegradation rates and the microorganisms involved in carbon uptake from 1,4-dioxane

Conventional physical and chemical treatment technologies for 1,4-dioxane can be ineffective and consequently attention has focused on bioremediation. Towards this, the current research investigated the impact of basal salts medium (BSM) and yeast extract on 1,4-dioxane biodegradation rates in microcosms with different soil or sediment (agricultural soil, wetland sediment, sediment from an impacted site). Phylotypes responsible for carbon uptake from 1,4-dioxane were determined using stable isotope probing (SIP), both with and without BSM and yeast extract. Further, putative functional genes were investigated using 1) soluble di-iron monooxygenase (SDIMO) based amplicon sequencing, 2) qPCR targeting propane monooxygenase (large subunit, prmA) and 3) a predictive approach (PICRUSt2). The addition of BSM and yeast extract significantly enhanced 1,4-dioxane removal rates the agricultural soil and impacted site sediment microcosms. The phylotypes associated with carbon uptake varied across treatments and inocula. Gemmatimonas was important in the heavy SIP fractions of the wetland sediment microcosms. Unclassified Solirubacteraceae, Solirubrobacter, Pseudonocardia and RB4 were dominant in the heavy SIP fractions of the agricultural soil microcosms. The heavy SIP fractions of the impacted site microcosms were dominated by only two phylotypes, unclassified Burkholderiaceae and oc3299. SDIMO based amplicon sequencing detected three genes previously associated with 1,4-dioxane. The predicted functional gene analysis suggested the importance of propane monooxygenases associated with Solirubrobacter and Pseudonocardia. Overall, more microorganisms were involved in carbon uptake from 1,4-dioxane in both the wetland and agricultural soil microcosms compared to the impacted site sediment microcosms. Many of these microorganisms have not previously been associated with 1,4-dioxane removal.

Pleiotropically activation of azaphilone biosynthesis by overexpressing a pathway-specific transcription factor in marine-derived Aspergillus terreus RA2905

The genome sequencing of Aspergillus terreus reveals that the vast number of predicted biosynthetic gene clusters have not reflected by the metabolic profile observed under conventional culture conditions. In this study, a silent azaphilone biosynthetic gene cluster was activated by overexpressing a pathway-specific transcription factor gene2642 in marine-derived fungus A. terreus RA2905. Consequently, twenty azaphilone compounds were identified from the OE2642 mutant, including 11 new azaphilones and their precursors, azasperones C−J (1−5, 7−9) and preazasperones A−C (15−17). The structures of those new compounds were unambiguously determined on the basis of NMR and HRESIMS spectra analysis, and the absolute configurations were established depending on ECD calculations. Compounds 1 and 2 were the rarely reported naturally occurring azaphilones with 2-N coupled phenyl-derivative. The bioactivity assay revealed that compounds 18−20 exhibited significant anti-inflammatory activity. Based on the occurrence of diverse intermediates and the putative gene functions, a plausible biosynthetic pathway of these compounds was proposed. The above results demonstrated that overexpression of the pathway-specific transcription factor presents a promising approach for enriching fungal secondary metabolites and accelerating the targeted discovery of novel biosynthetic products.

Short-Term Effects of Cenchrus fungigraminus/Potato or Broad Bean Interplanting on Rhizosphere Soil Fertility, Microbial Diversity, and Greenhouse Gas Sequestration in Southeast China.

Cenchrus fungigraminus is a new species and is largely used as forage and mushroom substrate. However, it can usually not be planted on farmland on account of local agricultural land policy. Interplanting Cenchrus fungigraminus with other crops annually (short-term) is an innovative strategy to promote the sustainable development of the grass industry in southern China. To further investigate this, C. fungigraminus mono-planting (MC), C. fungigraminus-potato interplanting (CIP) and C. fungigraminus-broad bean interplanting (CIB) were performed. Compared to MC, soil microbial biomass carbon (SMBC), soil organic matter (SOM), ammoniacal nitrogen (AMN), pH and soil amino sugars had a positive effect on the rhizosphere soil of CIP and CIB, as well as enhancing soil nitrogenase, nitrite reductase, and peroxidase activities (p < 0.05). Moreover, CIP improved the root vitality (2.08 times) and crude protein (1.11 times). In addition, CIB enhanced the crude fiber of C. fungigraminus seedlings. These two interplanting models also improved the microbial composition and diversity (Actinobacteria, Firmicutes, and Bacteroidota, etc.) in the rhizosphere soil of C. fungigraminus seedlings. Among all the samples, 189 and 59 genes were involved in methane cycling and nitrogen cycling, respectively, which improved the presence of the serine cycle, ribulose monophosphate, assimilatory nitrate reduction, methane absorption, and glutamate synthesis and inhibited denitrification. Through correlation analysis and the Mantel test, the putative functional genes, encoding functions in both nitrogen and methane cycling, were shown to have a significant positive effect on pH, moisture, AMN, SOM, SMBC, and soil peroxidase activity, while not displaying a significant effect on soil nitrogenase activity and total amino sugar (p < 0.05). The short-term influence of the interplanting model was shown to improve land use efficiency and economic profitability per unit land area, and the models could provide sustainable agricultural production for rural revitalization.

Heterologous activation and metabolites identification of the pks7 gene cluster from Saccharopolyspora erythraea

The microbial genome remains a huge treasure trove for the discovery of diverse natural products. Saccharopolyspora erythraea NRRL23338, the industry producer of erythromycin, has a dozen of biosynthetic gene clusters whose encoding products are unidentified. Heterologous expression of one of the polyketide clusters pks7 in Streptomyces albus B4 chassis resulted in the characterization of its function responsible for synthesizing both 6-methylsalicyclic acid and 6-ethylsalicyclic acid. Meanwhile, two new 6-ethylsalicyclic acid ester derivatives were isolated as shunt metabolites. Their structures were identified by comprehensive analysis of MS and NMR experiments. Putative functions of genes within the pks7 BGC were also discussed.

An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress.

Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.

A chromosome-level genome assembly of the soybean pod borer: insights into larval transcriptional response to transgenic soybean expressing the pesticidal Cry1Ac protein

BackgroundGenetically modified (GM) crop plants with transgenic expression of Bacillus thuringiensis (Bt) pesticidal proteins are used to manage feeding damage by pest insects. The durability of this technology is threatened by the selection for resistance in pest populations. The molecular mechanism(s) involved in insect physiological response or evolution of resistance to Bt is not fully understood.ResultsTo investigate the response of a susceptible target insect to Bt, the soybean pod borer, Leguminivora glycinivorella (Lepidoptera: Tortricidae), was exposed to soybean, Glycine max, expressing Cry1Ac pesticidal protein or the non-transgenic parental cultivar. Assessment of larval changes in gene expression was facilitated by a third-generation sequenced and scaffolded chromosome-level assembly of the L. glycinivorella genome (657.4 Mb; 27 autosomes + Z chromosome), and subsequent structural annotation of 18,197 RefSeq gene models encoding 23,735 putative mRNA transcripts. Exposure of L. glycinivorella larvae to transgenic Cry1Ac G. max resulted in prediction of significant differential gene expression for 204 gene models (64 up- and 140 down-regulated) and differential splicing among isoforms for 10 genes compared to unexposed cohorts. Differentially expressed genes (DEGs) included putative peritrophic membrane constituents, orthologs of Bt receptor-encoding genes previously linked or associated with Bt resistance, and those involved in stress responses. Putative functional Gene Ontology (GO) annotations assigned to DEGs were significantly enriched for 36 categories at GO level 2, respectively. Most significantly enriched cellular component (CC), biological process (BP), and molecular function (MF) categories corresponded to vacuolar and microbody, transport and metabolic processes, and binding and reductase activities. The DEGs in enriched GO categories were biased for those that were down-regulated (≥ 0.783), with only MF categories GTPase and iron binding activities were bias for up-regulation genes.ConclusionsThis study provides insights into pathways and processes involved larval response to Bt intoxication, which may inform future unbiased investigations into mechanisms of resistance that show no evidence of alteration in midgut receptors.

The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut

BackgroundThe ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome.ResultsThe genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors.ConclusionsThis study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen’s life cycle and a solid foundation for studying EFB.

Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits.

The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein-protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Comprehensive genotyping analysis of single nucleotide polymorphisms responsible for beef marbling in Japanese Black cattle.

Beef marbling is considered a desirable trait in the meat industry. Therefore, understanding the genetic factors that cause marbling is important. Previously, we performed a genome-wide association study to examine genetic factors associated with beef marbling in Japanese Black cattle and identified a candidate region between 10-30 Mbp on chromosome 7. We verified the effect of the SNPs in this region on beef marbling using linkage disequilibrium block analysis. We narrowed down the candidate region to a range of 15.8-16.1 Mbp. In this study, we comprehensively detected all of the SNPs in this region and verified their effects on beef marbling. Genome resequencing using four animals exhibiting high beef marbling standard (BMS) and four with low BMS revealed a total of 1,846 polymorphisms within the candidate region. Based on the annotation, we selected 13 SNPs exhibiting a moderate impact, as no high-impact SNPs were detected. All of the SNPs represented missense polymorphisms and were located in the following seven genes: RDH8, ANGPTL6, DNMT1, MRPL4, ICAM1, ICAM3, and ICAM5. Finally, we determined the effects of these SNPs on the BMS of a Japanese Black cattle population (n = 529). Analysis of variance revealed that the five SNPs were located in genes encoding the intercellular adhesion molecules (ICAM1, ICAM3, and ICAM5), and showed a highly significant association compared with the remainder (p < 0.01). The lowest p-value was observed for ICAM3_c.739G > A (p = 1.18E-04). Previous studies have suggested that intercellular adhesion molecules (ICAM) may be an upstream factor that regulates adipocyte differentiation. Therefore, considering the polymorphism and putative gene function, we suggest that ICAM1 is potentially responsible for beef marbling. c.470C > G and/or c.994G > A on ICAM1 may be responsible for this quantitative trait locus. Promising SNP candidates responsible for beef marbling were identified using extensive polymorphism verification in a previously reported QTL region. We aim to elucidate the mechanism of beef marbling in future studies by investigating how these polymorphisms alter protein structure and function.

Transformation to small cell lung cancer is irrespective of EGFR and accelerated by SMAD4-mediated ASCL1 transcription independently of RB1 in non-small cell lung cancer

ObjectivesHistological transformation to small cell lung cancer (SCLC) has been identified as a mechanism of TKIs resistance in EGFR-mutant non-small cell lung cancer (NSCLC). We aim to explore the prevalence of transformation in EGFR-wildtype NSCLC and the mechanism of SCLC transformation, which are rarely understood.MethodsWe reviewed 1474 NSCLC patients to investigate the NSCLC-to-SCLC transformed cases and the basic clinical characteristics, driver gene status and disease course of them. To explore the potential functional genes in SCLC transformation, we obtained pre- and post-transformation specimens and subjected them to a multigene NGS panel involving 416 cancer-related genes. To validate the putative gene function, we established knocked-out models by CRISPR-Cas 9 in HCC827 and A549-TP53-/- cells and investigated the effects on tumor growth, drug sensitivity and neuroendocrine phenotype in vitro and in vivo. We also detected the expression level of protein and mRNA to explore the molecular mechanism involved.ResultsWe firstly reported an incidence rate of 9.73% (11/113) of SCLC transformation in EGFR-wildtype NSCLC and demonstrated that SCLC transformation is irrespective of EGFR mutation status (P = 0.16). We sequenced 8 paired tumors and identified a series of mutant genes specially in transformed SCLC such as SMAD4, RICTOR and RET. We firstly demonstrated that SMAD4 deficiency can accelerate SCLC transition by inducing neuroendocrine phenotype regardless of RB1 status in TP53-deficient NSCLC cells. Further mechanical experiments identified the SMAD4 can regulate ASCL1 transcription competitively with Myc in NSCLC cells and Myc inhibitor acts as a potential subsequent treatment agent.ConclusionsTransformation to SCLC is irrespective of EFGR status and can be accelerated by SMAD4 in non-small cell lung cancer. Myc inhibitor acts as a potential therapeutic drug for SMAD4-mediated resistant lung cancer.9vNWjpNbo9djtsBQF6k7BHVideo

Genome-wide analysis of transmembrane 9 superfamily genes in wheat (Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions.

Transmembrane 9 superfamily (TM9SF) proteins play significant roles in plant physiology. However, these proteins are poorly characterized in wheat (Triticum aestivum). The present study aimed at the genome-wide analysis of putative wheat TM9SF (TraesTM9SF) proteins and their potential involvement in response to nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatments. TraesTM9SF genes were retrieved from the wheat genome, and their physiochemical properties, alignment, phylogenetic, motif structure, cis-regulatory element, synteny, protein-protein interaction (PPI), and transcription factor (TF) prediction analyses were performed. Transcriptome sequencing and quantitative real-time polymerase reaction (qRT-PCR) were performed to detect gene expression in roots under single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1. Forty-seven TraesTM9SF genes were identified in the wheat genome, highlighting the significance of these genes in wheat. TraesTM9SF genes were absent on some wheat chromosomes and were unevenly distributed on the other chromosomes, indicating that potential regulatory functions and evolutionary events may have shaped the TraesTM9SF gene family. Fifty-four cis-regulatory elements, including light-response, hormone response, biotic/abiotic stress, and development cis-regulatory elements, were present in the TraesTM9SF promoter regions. No duplication of TraesTM9SF genes in the wheat genome was recorded, and 177 TFs were predicted to target the 47 TraesTM9SF genes in a complex regulatory network. These findings offer valued data for predicting the putative functions of uncharacterized TM9SF genes. Moreover, transcriptome analysis and validation by qRT-PCR indicated that the TraesTM9SF genes are expressed in the root system of wheat and are potentially involved in the response of this plant to single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1, suggesting their functional roles in plant growth, development, and stress responses. These findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.

Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach

Rice germination and seedlings’ growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.

Genome wide association study of growth and feed efficiency traits in rabbits

Feed efficiency is a major production trait in animal genetic breeding schemes. To further investigate the genetic control of feed efficiency in rabbits, we performed a genome-wide association study (GWAS) for growth and feed efficiency on 679 rabbits genotyped with the Affimetrix Axiom Rabbit 200K Genotyping Array. After quality control, 127 847 single-nucleotide polymorphisms (SNP) were retained for association analyses. The GWAS were performed using GEMMA software, applying a mixed univariate animal model with a linear regression on each SNP allele. The traits analysed were weight at weaning and at 63 days of age, average daily gain, total individual feed intake, feed conversion ratio and residual feed intake. No significant SNP was found for growth traits or feed intake. Fifteen genome-wide significant SNPs were detected for feed conversion ratio on OCU7, spanning from 124.8 Mbp to 126.3 Mbp, plus two isolated SNP on OCU2 (77.3 Mbp) and OCU8 (16.5 Mbp). For residual feed intake, a region on OCU18 (46.1-53.0 Mbp) was detected, which contained a putative functional candidate gene, GOT1.

Amelioration of a saline‐alkaline soil using biochar and compost: Impacts on plant growth, soil biological and chemical characteristics

AbstractLand degradation reduces productivity and biodiversity, and requires restoration of both soil condition and vegetation to re‐establish ecosystem services. Organic amendments can improve soil biological and chemical properties, thereby enhancing revegetation success in severely degraded soil. This study investigated the use of compost and biochar to support revegetation and soil restoration. Soil was collected from a severely degraded creek bed in an agricultural farm in south‐western Australia (UWA Farm Ridgefield) and amended with compost (2.5% and 5%) and biochar (5% and 10%), both alone and in all pairwise combinations. Saltbush (Atriplex nummularia) seedlings were grown for 10 weeks in glasshouse conditions. Following harvest, plant growth and soil chemical properties were analysed. DNA was extracted from rhizosphere soil for bacterial diversity profiling with subsequent putative functional genes relating to carbon, nitrogen and phosphorus cycling using an in‐silico approach. Compost improved growth of root and shoot biomass. Both compost and biochar improved the alkaline soil by reducing pH and increasing nitrate, phosphorus and potassium levels. Compost addition also had a significant effect on rhizosphere bacterial community structure, decreasing alpha diversity and altering beta diversity indices. Amendment of soil also changed the relative abundance of putative nutrient cycling genes, with an increase in the potential for denitrification, carbon and phosphorus cycling and a decrease in ammonification potential. Application of this compost‐biochar combination improved plant growth and soil condition by altering both chemical and biological characteristics of the soil, and therefore may provide an effective management strategy for supporting restoration in a degraded landscape.

Genome-Wide Identification and Expression Analysis of RLCK-VII Subfamily Genes Reveal Their Roles in Stress Responses of Upland Cotton.

Receptor-like cytoplasmic kinase VII (RLCK-VII) subfamily members are vital players in plant innate immunity and are also involved in plant development and abiotic stress tolerance. As a widely cultivated textile crop, upland cotton (Gossypium hirsutum) attaches great importance to the cotton industry worldwide. To obtain details of the composition, phylogeny, and putative function of RLCK-VII genes in upland cotton, genome-wide identification, evolutionary event analysis, and expression pattern examination of RLCK-VII subfamily genes in G. hirsutum were performed. There are 129 RLCK-VII members in upland cotton (GhRLCKs) and they were divided into nine groups based on their phylogenetic relationships. The gene structure and sequence features are relatively conserved within each group, which were divided based on their phylogenetic relationships, and consistent with those in Arabidopsis. The phylogenetic analysis results showed that RLCK-VII subfamily genes evolved in plants before the speciation of Arabidopsis and cotton, and segmental duplication was the major factor that caused the expansion of GhRLCKs. The diverse expression patterns of GhRLCKs in response to abiotic stresses (temperature, salt, and drought) and V. dahliae infection were observed. The candidates that may be involved in cotton's response to these stresses are highlighted. GhRLCK7 (GhRLCK7A and D), which is notably induced by V. dahliae infection, was demonstrated to positively regulate cotton defense against V. dahliae by the loss-of-function assay in cotton. These findings shed light on the details of the RLCK-VII subfamily in cotton and provide a scaffold for the further function elucidation and application of GhRLCKs for the germplasm innovation of cotton.

Genome-wide association study using specific-locus amplified fragment sequencing identifies new genes influencing nitrogen use efficiency in rice landraces.

Nitrogen is essential for crop production. It is a critical macronutrient for plant growth and development. However, excessive application of nitrogen fertilizer is not only a waste of resources but also pollutes the environment. An effective approach to solving this problem is to breed rice varieties with high nitrogen use efficiency (NUE). In this study, we performed a genome-wide association study (GWAS) on 419 rice landraces using 208,993 single nucleotide polymorphisms (SNPs). With the mixed linear model (MLM) in the Tassel software, we identified 834 SNPs associated with root surface area (RSA), root length (RL), root branch number (RBN), root number (RN), plant dry weight (PDW), plant height (PH), root volume (RL), plant fresh weight (PFW), root fractal dimension (RFD), number of root nodes (NRN), and average root diameter (ARD), with a significant level of p < 2.39×10-7. In addition, we found 49 SNPs that were correlated with RL, RBN, RN, PDW, PH, PFW, RFD, and NRN using genome-wide efficient mixed-model association (GEMMA), with a significant level of p < 1×10-6. Additionally, the final results for eight traits associated with 193 significant SNPs by using multi-locus random-SNP-effect mixed linear model (mrMLM) model and 272 significant SNPs associated with 11 traits by using IIIVmrMLM. Within the linkage intervals of significantly associated SNP, we identified eight known related genes to NUE in rice, namely, OsAMT2;3, OsGS1, OsNR2, OsNPF7.4, OsPTR9, OsNRT1.1B, OsNRT2.3, and OsNRT2.2. According to the linkage disequilibrium (LD) decay value of this population, there were 75 candidate genes within the 150-kb regions upstream and downstream of the most significantly associated SNP (Chr5_29804690, Chr5_29956584, and Chr10_17540654). These candidate genes included 22 transposon genes, 25 expressed genes, and 28 putative functional genes. The expression levels of these candidate genes were measured by real-time quantitative PCR (RT-qPCR), and the expression levels of LOC_Os05g51700 and LOC_Os05g51710 in C347 were significantly lower than that in C117; the expression levels of LOC_Os05g51740, LOC_Os05g51780, LOC_Os05g51960, LOC_Os05g51970, and LOC_Os10g33210 were significantly higher in C347 than C117. Among them, LOC_Os10g33210 encodes a peptide transporter, and LOC_Os05g51690 encodes a CCT domain protein and responds to NUE in rice. This study identified new loci related to NUE in rice, providing new genetic resources for the molecular breeding of rice landraces with high NUE.

Identification of Candidate QTLs and Genes for Ear Diameter by Multi-Parent Population in Maize.

Ear diameter (ED) is a critical component of grain yield (GY) in maize (Zea mays L.). Studying the genetic basis of ED in maize is of great significance in enhancing maize GY. Against this backdrop, this study was framed to (1) map the ED-related quantitative trait locus (QTL) and SNPs associated with ED; and (2) identify putative functional genes that may affect ED in maize. To accomplish this, an elite maize inbred line, Ye107, which belongs to the Reid heterotic group, was used as a common parent and crossed with seven elite inbred lines from three different heterotic groups (Suwan1, Reid, and nonReid) that exhibited abundant genetic variation in ED. This led to the construction of a multi-parent population consisting of 1215 F7 recombinant inbred lines (F7RILs). A genome-wide association study (GWAS) and linkage analysis were then conducted for the multi-parent population using 264,694 high-quality SNPs generated via the genotyping-by-sequencing method. Our study identified a total of 11 SNPs that were significantly associated with ED through the GWAS, and three QTLs were revealed by the linkage analysis for ED. The major QTL on chromosome 1 was co-identified in the region by the GWAS at SNP_143985532. SNP_143985532, located upstream of the Zm00001d030559 gene, encodes a callose synthase that is expressed in various tissues, with the highest expression level in the maize ear primordium. Haplotype analysis indicated that the haplotype B (allele AA) of Zm00001d030559 was positively correlated with ED. The candidate genes and SNPs identified in this study provide crucial insights for future studies on the genetic mechanism of maize ED formation, cloning of ED-related genes, and genetic improvement of ED. These results may help develop important genetic resources for enhancing maize yield through marker-assisted breeding.

A shared genetic contribution to osteoarthritis and COVID-19 outcomes: a large-scale genome-wide cross-trait analysis.

Patients with osteoarthritis (OA) are exposed to an increased risk of adverse outcomes of COVID-19, and they tend to experience disruption in access to healthcare services and exercise facilities. However, a deep understanding of this comorbidity phenomenon and the underlying genetic architecture of the two diseases is still unclear. In this study, we aimed to untangle the relationship between OA and COVID-19 outcomes by conducting a large-scale genome-wide cross-trait analysis. Genetic correlation and causal relationships between OA and COVID-19 outcomes (critical COVID-19, COVID-19 hospitalization, and COVID-19 infection) were estimated by linkage disequilibrium score regression and Mendelian Randomization approaches. We further applied Multi-Trait Analysis of GWAS and colocalization analysis to identify putative functional genes associated with both OA and COVID-19 outcomes. Significant positive genetic correlations between OA susceptibility and both critical COVID-19 (rg=0.266, P=0.0097) and COVID-19 hospitalization (rg=0.361, P=0.0006) were detected. However, there was no evidence to support causal genetic relationships between OA and critical COVID-19 (OR=1.17[1.00-1.36], P=0.049) or OA and COVID-19 hospitalization OR=1.08[0.97-1.20], P=0.143). These results were robustly consistent after the removal of obesity-related single nucleotide polymorphisms (SNPs). Moreover, we identified a strong association signal located near the FYCO1 gene (lead SNPs: rs71325101 for critical COVID-19, Pmeta=1.02×10-34; rs13079478 for COVID-19 hospitalization, Pmeta=1.09×10-25). Our findings further confirmed the comorbidity of OA and COVID-19 severity, but indicate a non-causal impact of OA on COVID-19 outcomes. The study offers an instructive perspective that OA patients did not generate negative COVID-19 outcomes during the pandemic in a causal way. Further clinical guidance can be formulated to enhance the quality of self-management in vulnerable OA patients.