In silico characterisation of novel rice transcripts differentially expressed in phosphorus dificient conditions suggests a role of these transcripts in multiple abiotic stresses

Phosphorus deficiency adversely affects crop productivity. The mechanism of tolerance in plants is not well understood. The current study successfully annotated a set of highly significant (Log2 RPKM ≥3) nine novel sequences up-regulated in P deficient condition identified from a low P tolerant rice genotype. Sequence annotation identified two transcripts (Os01g37260 and Os02g11060) carrying known domains, F-box and WD, respectively. Multiple Expectation maximization for Motif Elicitation (MEME) revealed presence of conserved domains like D[LP][HY][CL]D[CM][DT]C[AP][DQ][IQ]C, [EH][DN]HN[HS] [ER][FY][EP]I[HN]H which might play a role in phosphorus deficiency tolerance. Analysis of the upstream regions indicated presence of stress responsive elements like E Box, ABRE, and MYBCORE suggesting regulation of the novel transcripts by DNA binding. Protein localization prediction tool suggests that these novel proteins might be targeted to nucleus, chloroplast and cell wall. Transcripts Os02g03640 and Os02g10250 revealed potential target sites for microRNA binding suggesting role of novel miRNAs in low phosphorus response. Our analysis suggests that an F-box protein, Os01g37260 (OSFBx14) might be a promising candidate gene playing a role in multiple abiotic stresses including P deficiency

A history of concussions is associated with symptoms of common mental disorders in former male professional athletes across a range of sports

Objective: Recent reports suggest that exposure to repetitive concussions in sports is associated with an increased risk of symptoms of distress, anxiety and depression, sleep disturbance or substance abuse/dependence (typically referred as symptoms of common mental disorders[CMD]) and of later development of neurodegenerative disease, in particular chronic traumatic encephalopathy (CTE). The primary aim of this study was to explore the relationship between sports career-related concussions and the subsequent occurrence of symptoms of CMD among former male professional athletes retired from football (soccer), ice hockey and rugby (union). Methods: Cross-sectional analyses were performed on baseline electronic questionnaires from three prospective cohort studies among former male professional athletes retired from football (soccer), ice hockey and rugby (union). The number of confirmed concussions was examined through a single question, while symptoms of distress, anxiety and depression, sleep disturbance and adverse alcohol use were assessed using validated questionnaires. Results: From 1,957 former professional athletes contacted, a total of 576 (29%) completed the questionnaire. Of these, 23% had not incurred a concussion during their career, 34% had two or three, 18% four or five, and 11% six or more concussions. The number of sports career-related concussions was a predictor for all outcome measures (β = 0.072–0.109; P ≤ 0.040). Specifically, former professional athletes who reported a history of four or five concussions were approximately 1.5 times more likely to report symptoms of CMD, rising to a two- to five-fold increase in those reporting a history of six or more sports career-related concussions. Conclusions: These data demonstrate an association between exposure to sports concussion and subsequent risk of symptoms of CMD in former professional athletes across a range of contact sports. Further work to explore the association between sports concussion and symptoms of CMD is required; in the meanwhile, strategies for effective risk reduction and improved management appear indicated

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers.In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations.Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species

Differential Expression of Iron Deficiency Responsive Rice Genes under Low Phosphorus and Iron Toxicity Conditions and Association of OsIRO3 with Yield in Acidic Soils

With the hypothesis that iron (Fe) deficiency responsive genes may play a role in Fe toxicity conditions, we studied five such genes OsNAS1, OsNAS3, OsIRO2, OsIRO3 and OsYSL16 across six contrasting rice genotypes for expression under high Fe and low phosphorus (P) conditions, and sequence polymorphism. Genotypes Sahbhagi Dhan, Chakhao Poirieton and Shasharang were high yielders with no bronzing symptom visible under Fe toxic field conditions, and BAM350 and BAM811 were low yielders but did not show bronzing symptoms. Hydroponic screening revealed that the number of crown roots and root length can be traits for consideration for identifying Fe toxicity tolerance in rice genotypes. Fe contents in rice roots and shoots of a high-yielding genotype KMR3 showing leaf bronzing were significantly high. In response to 24 h high Fe stress, the expression levels of OsNAS3 were up-regulated in all genotypes except KMR3. In response to 48 h high Fe stress, the expression levels of OsNAS1 were 3-fold higher in tolerant Shasharang, whereas in KMR3, it was significantly down-regulated. Even in response to 7 d excess Fe stress, the transcript abundances of OsIRO2 and OsNAS3 were contrasting in genotypes Shasharang and KMR3. This suggested that the reported Fe deficiency genes had a role in Fe toxicity and that in genotype KMR3 under excess Fe stress, there was disruption of metal homeostasis. Under the 48 h low P conditions, OsIRO2 and OsYSL16 were significantly up-regulated in Fe tolerant genotype Shasharang and in low P tolerant genotype Chakhao Poirieton, respectively. In silico sequence analysis across 3 024 rice genotypes revealed polymorphism for 4 genes. Sequencing across OsIRO3 and OsNAS3 revealed nucleotide polymorphism between tolerant and susceptible genotypes for Fe toxicity. Non-synonymous single nucleotide polymorphisms and insertion/deletions (InDels) differing in tolerant and susceptible genotypes were identified. A marker targeting 25-bp InDel in OsIRO3, when run on a diverse panel of 43 rice genotypes and a biparental population, was associated with superior performance for yield under acidic lowland field conditions. This study highlights the potential of one of the vital genes involved in Fe homeostasis as a genic target for improving rice yield in acidic soils

Cloning and regulation of a stress-regulated Pennisetum glaucum vacuolar ATPase c gene and characterization of its promoter that is expressed in shoot hairs and floral organs

We have cloned and characterized the cDNA, genomic clone and upstream promoter region of a vacuolar ATPase (V-ATPase) c subunit (PgVHA-c1) from Pennisetum glaucum. The deduced amino acid sequence shows 98-71% sequence identity with V-ATPase from rice and Arabidopsis, and is a highly hydrophobic protein with four transmembrane regions. PgVHA-c1-GFP fusion protein is expressed in BY2 cells on the endo-membranes surrounding vacuoles; however, PgVHA-c1 could not functionally complement V-ATPase-c deletion mutants of yeast. The sequence analysis of the genomic clone revealed the presence of two introns in the coding region, and the splice junctions followed the typical canonical GU-AG consensus sequence. The transcript analysis showed that the expression of PgVHA-c1 was stimulated more in response to salinity stress and very marginally in response to drought and low temperature stress. Exogenous application of abscisic acid, salicylic acid and calcium stimulated the transcript level in the absence of stress. We have cloned the 5'-flanking regions of PgVHA-c1 and mapped its transcript start site at 78 bp upstream of ATG. Transgenic tobacco with promoter::GUS constructs showed that the region −288/+78 was sufficient for GUS expression. The expression of the reporter gene even with the full-length promoter was limited to shoot hairs and to male and female reproductive organs. The dehydration-responsive element (DRE) and ABA-responsive element (ABRE) in the promoter did not show consensus flanking regions; however, gel mobility shift assays showed that Pennisetum has specific transacting factors that showed binding to the core DRE, ABRE and TCA elements

A Ca<SUP>2+</SUP>/CaM-dependent kinase from pea is stress regulated and in vitro phosphorylates a protein that binds to AtCaM5 promoter

An immuno-homologue of maize Ca2+/calmodulin (CaM)-dependent protein kinase with a molecular mass of 72 kDa was identified in pea. The pea kinase (PsCCaMK) was upregulated in roots in response to low temperature and increased salinity. Exogenous Ca2+ application increased the kinase level and the response was faster than that obtained following stress application. Low temperature-mediated, but not salinity-mediated stress kinase increase was inhibited by the application of EGTA and W7, a CaM inhibitor. The purification of PsCCaMK using immuno-affinity chromatography resulted in coelution of the kinase with another polypeptide of molecular mass 40 kDa (p40). Western blot revealed the presence of PsCCaMK in nuclear protein extracts and was found to phosphorylate p40 in vitro. Gel mobility shift and South-Western analysis showed that p40 is a DNA-binding protein and it interacted specifically with one of the cis acting elements of the Arabidopsis CaM5 gene (AtCaM5) promoter. The binding of p40 to the specific elements in the AtCaM5 promoter was dependent of its dephosphorylated state. Our results suggest that p40 could be an upstream signal component of the stress responses