Biology subjects

Sharpe, R.

Publications and source records attributed to Sharpe, R..

3 recordsLinked to original sources

bioRxiv2023

Chloroplast Genome Data of Tecticornia indica, a Hygrohalophytic C4 Plant Species

Tecticornia indica is a hygrohalophytic, NAD-malic enzyme-type C4 plant species with near-aphyllous photosynthetic shoots. Total cellular DNA was extracted from the aphyllous shoots and branches of Tecticornia indica for subsequent High Throughput Sequencing (HTS). Illumina HiSeq 2000 technology produced a total of 91,825,666 reads. Reads were trimmed and filtered to retain base calls corresponding to a 99.9% base call accuracy. A de novo assembly produced 413,729 contigs and 45,238 scaffolds with a maximum length of 120,548 nucleotides, an N50 of 881, and an average depth of coverage of 16.29 nucleotides. A subset of 2,196,299 reads were used for assembling the chloroplast genome at an average depth of coverage of 1,094 nucleotides. Sanger sequencing was performed to validate the LSC-IR-SSC junctions and to complete the missing regions of the chloroplast genome. The assembled chloroplast genome map and T. indica genomic sequence is expected to facilitate genetics and genomic research focused on understanding function of genes involved in halophytic and drought tolerant traits. SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@c070bborg.highwire.dtl.DTLVardef@293fd8org.highwire.dtl.DTLVardef@1e9ab6org.highwire.dtl.DTLVardef@13f3126org.highwire.dtl.DTLVardef@1b3c4ca_HPS_FORMAT_FIGEXP M_TBL C_TBL VALUE OF THE DATAO_LIGenomic sequence information of Tecticornia indica and its chloroplast map will be useful for genomics research. C_LIO_LIGenomics and genetics scientists, bioinformatics and biotechnologists in the fields of photosynthesis, taxonomy and drought tolerance will benefit from these data. C_LIO_LIThese data can be used in developing molecular markers and quantitative trait loci in identification and selection of halophyte and drought tolerance, taxonomic resolution, and variables in photosynthetic genes. C_LI

genomics↗

bioRxiv2020

Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes

Pisum sativum (pea) yields have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome V explained 14.76 % of the variance with a confidence interval of 10.36 cM. The other four QTLs located on chromosomes II, III, and V, explained 5.26-8.05 % of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

plant biology↗

bioRxiv2019

Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer

Enhanced levels of antioxidants, phenolic compounds, carotenoids and vitamin C have been reported for several crops grown under organic fertilizer, albeit with yield penalties. As organic agricultural practices continue to grow and find favor it is critical to gain an understanding of the molecular underpinnings of the factors that limit the yields in organically farmed crops. Concomitant phytochemical and transcriptomic analysis was performed on mature fruit and leaf tissues derived from Solanum lycopersicum L. Oregon Spring grown under organic and conventional fertilizer conditions to evaluate the following hypotheses. 1. Organic soil fertilizer management results in greater allocation of photosynthetically derived resources to the synthesis of secondary metabolites than to plant growth, and 2. Genes involved in changes in the accumulation of phytonutrients under organic fertilizer regime will exhibit differential expression, and that the growth under different fertilizer treatments will elicit a differential response from the tomato genome. Both these hypotheses were supported, suggesting an adjustment of the metabolic and genomic activity of the plant in response to different fertilizers. Organic fertilizer treatment showed an activation of photoinhibitory processes through differential activation of nitrogen transport and assimilation genes resulting in higher accumulation of phytonutrients. This information can be used to identify alleles for breeding crops that allow for efficient utilization of organic inputs.\n\nSignificance statementOrganic fertilizer changes the expression of the tomato genome, induces photosynthetic stress which elicits higher production of secondary metabolites.

plant biology↗