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Finding candidate genes underlying early flowering barley mat-e mutants

Saha, Chayan Kumar (2017) BINP30 20171
Degree Projects in Bioinformatics
Abstract
Barley, Hordeum vulgare, is a commercially important crop plant mostly used as animal feed but also as human food where it serves as an important source of _-glucan and other nutrients. As populations are growing worldwide, early flowering cultivars can play a vital role to increase the production of barley to meet the increasing demand of this crop. We analyzed five early flowering mat-e mutants from barley cultivar Bonus using different bioinformatics programs and identified fourteen gene candidates that contain variants in all mat-e mutants which could help explain the phenotype. Among these candidates, MLOC 2368 gene having length of 1369 bases, might be the potential candidate to affect flowering time. The gene product showed homology... (More)
Barley, Hordeum vulgare, is a commercially important crop plant mostly used as animal feed but also as human food where it serves as an important source of _-glucan and other nutrients. As populations are growing worldwide, early flowering cultivars can play a vital role to increase the production of barley to meet the increasing demand of this crop. We analyzed five early flowering mat-e mutants from barley cultivar Bonus using different bioinformatics programs and identified fourteen gene candidates that contain variants in all mat-e mutants which could help explain the phenotype. Among these candidates, MLOC 2368 gene having length of 1369 bases, might be the potential candidate to affect flowering time. The gene product showed homology with the protein PER27 (Peroxidase) found in Arabidopsis thaliana which is a member of the peroxidase subfamily that affect flowering time in Arabidopsis thaliana by regulating the endogenous ascorbic acid content. In this analysis, we identified five different positions inside the MLOC 2368 gene that contained non-synonymous substitutions which might change the regulation of the ascorbic acid content thus affecting the flowering time. Experimental validation is essential to verify these results. (Less)
Popular Abstract
Finding candidate genes underlying early flowering barley mat-e mutants


Barley is mostly used as animal feed but also as human food where it serves as an important source of β-glucan and other nutrients. It has been an important food source in many parts of the world, including the Middle East, North Africa and Northern and Eastern Europe and in Asia. The demand for early crop by farmers is in part a necessity for an effective crop rotation. As early as 1928, experiments were started where mutations were induced in barley to identify early flowering plants. As populations are growing worldwide and global weather is changing, these early flowering mutants can play a vital role to increase the production of barley to meet the demand of... (More)
Finding candidate genes underlying early flowering barley mat-e mutants


Barley is mostly used as animal feed but also as human food where it serves as an important source of β-glucan and other nutrients. It has been an important food source in many parts of the world, including the Middle East, North Africa and Northern and Eastern Europe and in Asia. The demand for early crop by farmers is in part a necessity for an effective crop rotation. As early as 1928, experiments were started where mutations were induced in barley to identify early flowering plants. As populations are growing worldwide and global weather is changing, these early flowering mutants can play a vital role to increase the production of barley to meet the demand of this crop.

The project

For this Master’s Degree Thesis my aim was to develop a pipeline that consists of a chain of processing elements used by computers to find the underlying gene for the early flowering mutants from barley having same parental cultivar. The pipeline uses several computational tools and programs to analyze biological data, specifically the DNA-sequencing data which were processed by applying recent techniques from the samples of interest. The purpose of this thesis is to develop an efficient pipeline that could possibly be able to find candidate gene(s) explaining the early-flowering characteristics after mutations took place, which can then be evaluated by lab-experiments. The developed pipeline has proved to be successful in identifying 14 gene candidates. Among these candidates, MLOC_2368 gene is the most promising candidate, as the gene product showed similarity with the protein PER27 (Peroxidase) found in model plant organism named as ‘Thale cress’ (Arabidopsis thaliana). It has been reported that mutation in this gene can change the regulation of the ascorbic acid content which affects the flowering time of the thale cress. However, the pipeline is not fully automated due to some technical challenges.


Master’s Degree Project in Bioinformatics 30 credits 2017
Department of Biology, Lund University

Advisor: Björn Canbäck
Advisors Unit/Department : Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Saha, Chayan Kumar
supervisor
organization
course
BINP30 20171
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8925099
date added to LUP
2017-09-08 14:40:00
date last changed
2017-09-08 14:40:00
@misc{8925099,
  abstract     = {Barley, Hordeum vulgare, is a commercially important crop plant mostly used as animal feed but also as human food where it serves as an important source of _-glucan and other nutrients. As populations are growing worldwide, early flowering cultivars can play a vital role to increase the production of barley to meet the increasing demand of this crop. We analyzed five early flowering mat-e mutants from barley cultivar Bonus using different bioinformatics programs and identified fourteen gene candidates that contain variants in all mat-e mutants which could help explain the phenotype. Among these candidates, MLOC 2368 gene having length of 1369 bases, might be the potential candidate to affect flowering time. The gene product showed homology with the protein PER27 (Peroxidase) found in Arabidopsis thaliana which is a member of the peroxidase subfamily that affect flowering time in Arabidopsis thaliana by regulating the endogenous ascorbic acid content. In this analysis, we identified five different positions inside the MLOC 2368 gene that contained non-synonymous substitutions which might change the regulation of the ascorbic acid content thus affecting the flowering time. Experimental validation is essential to verify these results.},
  author       = {Saha, Chayan Kumar},
  language     = {eng},
  note         = {Student Paper},
  title        = {Finding candidate genes underlying early flowering barley mat-e mutants},
  year         = {2017},
}