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Title: Secale cereale : Analysis of mutations disrupting the formation of the wax layer in rye, and assessment of their impact on morphological, biochemical and physiological traits      
keywords:
raw sequence reads
ID:
PRJNA371298
description:
The main aim of the grant is to analyze four mutations disrupting the formation of a correct wax layer on the green parts of rye plants. Basic research material consists of four pairs of near-isogenic lines (NIL). Three pairs are different in terms of another recessive mutation. It is planned to detect studied genes, identify their sequences, compare expression levels and determine the location in the genome. In addition, an attempt will be made to determine whether the studied genes show pleiotropic effects by analyzing the differences of various morphological and physiological traits. The extent to which the wax cover provides protection against water loss in optimum conditions and reduced soil moisture will be assessed.Four pairs of NIL will be characterized using molecular, biochemical and physiological methods. Molecular studies will include the analysis of mRNA performed using RNA-Seq method and q-PCR. Three different mapping populations will be characterized using GBS technique and different markers based on PCR (STS, SCAR, RAPD, ISSR, SSR). Mapping procedure will be carried out using JoinMap package. The sequence analysis of selected markers is planned by a capillary sequencer (Sanger method) and based on NGS methods.Some physiological characteristics will be evaluated, such as gas exchange, water balance, assimilation pigments content (chlorophyll and carotenoids) and photochemical activity of PSII. Gas exchange parameters will be measured with the use of gas analyzer and porometer. Pigments content will be determined by a spectrophotometric method and chlorophyll a fluorescence kinetics will be assessed by a fluorymetric method. Water balance will be evaluated on the basis of the ratio of the relative water content (RWC) and water saturation deficit ratio (WSD). The water impairment test and the weight of cut-off leaves test will be carried out (RWL).The chemical composition and amount of wax will be determined using capillary gas chromatography (GC) and ultra-high performance liquid chromatography (UHPLC).Comparing to other crops, i.e. barley (Hordeum vulgare) and wheat (Triticum aestivum), rye (Secale cereale) is not well known in terms of its nucleotide sequences. The resulting data will supply the complete set of mRNA sequences of four pairs of inbred lines, expanding the knowledge about rye transcriptome and providing information about the new SNP and SSR markers.By characterizing the three genes involved in the control of wax biosynthesis, our research will contribute to a better understanding of the molecular mechanism of this complex substance biosynthesis in plants. The mapping results will complement the knowledge on the genetic base of a waxy coat formation on the leaves, stems and spikes.
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA371298
authentication:
none
authorization:
none
name:
Secale cereale
ncbiID:
ncbitax:4550
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject