In this article we will discuss about:- 1. Meaning of Bioinformatics 2. Branches of Bioinformatics 3. Applications of Bioinformatics in Crop Improvement 4. Advantages 5. Limitations.
Meaning of Bioinformatics:
Bioinformatics is the computer aided study of biology and genetics. In other words, it refers to computer based study of genetics and other biological information. Now the science of bioinformatics is gaining increasing importance in life science especially in the field of molecular biology and plant genetic resources.
Main points related to bioinformatics are given below:
(i) It is the interface between computer and biology. In other words, it is the application of information technology in the study of biology.
(ii) It utilizes information science for the study of biology.
(iii) It is used for computer based analysis of bio-molecular data especially large scale data set derived from genome sequencing.
(iv) It is used for analysis of data related to genomics, proteornics, metabolomics and other biological aspects.
(v) It has wide applications in handling data related to plant genetic resources.
Branches of Bioinformatics:
The science of bioinformatics can be divided into several branches based on the experimental material used for the study. Bioinformatics is broadly divided into two groups, viz., animal bioinformatics and plant bioinformatics.
Various branches of bioinformatics are defined below:
1. Animal Bioinformatics:
It deals with computer added study of genomics, proteomics and metabolomics in various animal species. It includes study of gene mapping, gene sequencing, animal breeds, animal genetic resources etc. It can be further divided as bioinformatics of mammals reptiles, insects, birds, fishes etc.
2. Plant Bioinformatics:
It deals with computer aided study of plant species. It includes gene mapping, gene sequencing, plant genetic resources, data base etc.
It can be further divided into following branches:
(i) Agricultural Bioinformatics:
It deals with computer based study of various agricultural crop species. It is also referred to as crop bioinformatics.
(ii) Horticultural Bioinformatics:
It refers to computer aided study of horticultural crops, viz. fruit crops, vegetable crops and flower crops.
(iii) Medicinal Plants Bioinformatics:
It deals with computer based study of various medicinal plant species.
(iv) Forest Plant Bioinformatics:
It deals with computer based study of forest plant species.
Computer Programmes used in Biology:
Computers refer to electronic devices which can input, store and manipulate data and output information in a desired form. Now various types of computers such as micro-computer, minicomputer, mainframe computer, super computer, laptop computer and palmtop computers are available which can be used for multiple purposes.
Various computer programmes are used for the study of biological problems. Such programmes include Microsoft word (MS Word), Microsoft excel (MS excel) and Microsoft power point (MS Power Point).
A brief description of these programmes is presented below:
(i) MS Word:
It is a very useful programme for preparation of project reports, annual reports, writing research papers, varietal information system, plant genetic resources data base, etc.
(ii) MS Excel:
It is useful Computer programme for various types of statistical and biometrical analyses. It can also be used for graphical and diagrammatic display of experimental results.
(iii) MS Power Point:
It is widely used for preparation of slides and presentation of results in various scientific meetings.
Applications of Bioinformatics in Crop Improvement:
Bioinformatics has wide practical applications in genetics and plant breeding.
Some important applications of bioinformatics in plant breeding and genetics are tested below:
1. Varietal Information system
2. Plant Genetic Resources Data Base
3. Studies on Genomics
4. Studies on Proteomics
5. Studies on Metabolomics
6. Studies on Plant Modelling
7. Pedigree Analysis
8. Biometrical Analysis
9. Forecasting Models
1. Varietal Information System:
Bioinformatics has useful applications in developing varietal information system. Variety refers to a genotype which has been released for commercial cultivation (b) State Variety Release Committee or Central Variety Release Committee and notified by the Government of India. Various types of varieties are used in plant breeding.
All such terms are defined below:
The detailed information about various type of varieties can be developed using highly heritable characters.
Such information can be used in various ways as given below:
(i) In DUS testing for varietal identification
(ii) In grouping of varieties on the basis of various highly heritable characters.
(iii) In sorting out of cultivars for use in Pre-breeding and traditional breeding.
The information can be stored in the computer memory and be retrieved as and when– required.
2. PGB Data Base:
Genetic material of plant which of value as resource for present and future generations of people is referred to as plant genetic resources. It is also known as gene pool, genetic stock and germplasm.
The germplasm is evaluated for several characters such as highly heritable morphological and other characters as given below:
(i) Highly heritable morphological traits
(ii) Yield contributing traits
(iii) Quality characters
(iv) Resistance to biotic and abiotic stresses
(v) Characters of agronomic value.
International Plant Genetic Resources Institute (IPGRI), Rome, Italy has developed descriptors and descriptor states for various crop plants. Such descriptors help in uniform recording of observations on germplasm of crop plants throughout the world. Thus huge data is collected on crop germplasm for several years. Bioinformatics plays an important role in systematic management of this huge data.
Bioinformatics is useful in handling of such data in several ways as follows:
(i) It maintains the data of several locations and several years in a systematic way.
(ii) It permits addition, deletion and updating of information.
(iii) It helps in storage and retrieval of data.
(iv) It also helps in classification of PGR based on various criteria.
(v) It helps m retrieval of data belonging to specific group such as early maturity, late maturity, dwarf types, tall types, resistant to biotic stresses, resistant to abiotic stresses, genotypes with superior quality, genotypes with marker genes, etc.
All such data can be easily managed by computer aided programmes and can be manipulated to get meaningful results.
3. Studies on Genome:
Genome refers to the basic set of chromosome. In a genome each type of chromosome is represented only once. The study of structure and function of entire genome of an organism is referred to as genomics. It is being developed as a sub discipline of genetics which is devoted to the mapping sequencing and functional analysis of genome. The word genomics was coined by Thomas Roderick in 1986.
The discipline of genomics consists of two groups, viz:
(i) Structural genomics and
(ii) Functional genomics.
These are defined below:
(i) Structural Genomics:
It deals with the study of the structure of entire genome of an organism. In other words, it deals with the study of the genetic structure of each chromosome of the basic set of chromosome i.e. genome.
(ii) Functional Genomics:
It deals with the study of genome function. It deals with transcriptome and proteome. Transcriptome refers to complete set of RNAs transcribed from a genome and proteome refers to complete set of proteins encoded by a genome
There are three methods of gene mapping, viz:
(i) Recombination mapping,
(ii) Deletion mapping and
(iii) Molecular mapping.
The last method is widely being used for gene mapping these days. It is computer aided method which is useful in genome mapping. It has been used for genome mapping in various crop plants such as Arabidopsis, rice and maize.
It is a rapid and accurate method of gene mapping. Now computer aided genomic mapping, sequencing and functional analysis studies are being carried out with almost all important field crops. Computer aided programmes have made such studies very simple.
4. Studies on Proteomics:
Proteomics refers to the study of structures and functions of all proteins in an individual. In other words, it deals with the study of entire protein expression in an organism.
Proteomics is of two types, viz:
(i) Structural proteomics and
(ii) Functional proteomics.
These are defined below:
(i) Structural Proteomics:
It refers to the study of the structures of all proteins found in a living organism.
(ii) Functional Proteomics:
It deals with functions of all proteins found in a living organism. In fact, proteomics is a new sub-discipline of functional genomics. It is the study of proteomes which refer to complete set of proteins encoded by a genome. A variety of techniques are used for the study of proteomics. Now computer aided programmes are available for the study of proteomics.
5. Studies on Metabolomics:
Metabolomics refers to the study of all metabolic pathways in a living organism. In other words, it is the computer aided information of all metabolic pathways of a living organism.
Main points related to metabolomics are listed below:
(i) It deals with the study of all metabolic pathways in a living organism.
(ii) It is computer based information about metabolic pathways in a living organism.
(iii) It helps in identification and correction of metabolic disorders in an organism.
(iv) It helps in selection of individuals with normal metabolic pathways.
(v) It helps early detection of genetic disorders associated with metabolic pathways.
6. Modelling of Plants:
Bioinformatics plays an important role in modelling of crop plants. Such computer aided studies have already been made in field pea and several other field crops. First the plant model is conceptualized using various plant traits and then efforts are made to develop such model by using appropriate breeding procedures.
For example, in cotton following characters can be used for developing conceptual plant model:
(i) Maturity duration 160 days
(ii) Plant height 150 cm
(iii) Number of monopodia 2
(iv) Length of sympodia 50 cm
(v) Number of sympodia 20
(vi) Boll weight 4g
(vii) Ginning per cent 38
(viii) Fibre length 28 mm
(ix) Leaf : small and thick
(x) Plant surface—hairy
First donor sources for these traits are identified from the available germplasm. Then efforts are made to combine these traits in one genotype particularly in a popular variety. Such computer based studies help in developing plant ideotype suitable for machine picking and used in multiple cropping system.
7. Pedigree Analysis:
Computer aided studies are useful in pedigree analysis of various cultivars and hybrids. Information about the parentage of cultivars and hybrids is entered into the computer memory which can be retrieved any time. The list of parents that are common in the pedigree of various cultivars and hybrids can be sorted out easily.
It helps in the pedigree analysis which in turn can be used in planning plant breeding programmes especially in the selection of parents for use in hybridization programmes. Through study of protein structures, it helps in pedigree analysis.
8. Biometrical Analysis:
In plant breeding and genetics, various types of biometrical analyses such as correlation, path coefficient, discriminant function, diallel, partial diallel, triallel, quadriallel, generation means, line x tester, triple test cross, stability parameters, D2 statistics, metroglypth etc. are carried out.
Computer aided programmes are very much useful in carrying out such biometrical analyses. The information obtained from such biometrical analysis is used in better planning of plant breeding programmes for achieving specific goal.
9. Forecasting Models:
Computer aided programmes have wide applications in developing various types of forecasting models especially useful for predicting crop production and productivity and in forecasting incidence of insects and diseases in crop plants. Weather parameters are used in making such predictions. Computer aided remote sensing techniques are used for such predictions.
10. Other Applications:
Besides agricultural applications, bioinformatics have several other useful applications.
Such applications include use of bioinformatics in:
(i) Medical science,
(ii) Forensic science,
(iii) Pharmaceutical and biotech industry.
In medical science computer aided studies are useful in detection of genetic diseases at an early stage of life. It can help in cure of genetic diseases in some cases. The pedigree analysis helps in advising future parents to prevent certain genetic diseases.
In forensic science, bioinformatics is useful in settling disputed cases of children and detecting criminal cases. In pharmaceutical industry, computer aided programmes help in detecting various metabolic pathways involved in the production of a medicine. Thus it can help in mass production of such chemicals.
Advantages of Bioinformatics:
Bioinformatics has several practical applications in genetics and plant breeding as discussed above.
Its main advantages in crop improvement are given below:
1. It provides systematic information about genomics, proteomics and metabolomics of living organisms. This information is useful in planning various breeding and genetical programmes.
2. It helps in finding evolutionary relationship between two species. Studies of nucleotide and protein sequences help in such matter. The closely related organisms have similar sequences and distantly related organisms have dissimilar sequence.
The time of divergence between two species can also be estimated from such studies. Thus bioinformatics helps in the study of evolutionary biology. It helps in drawing phylogenic trees (trees of relatedness).
3. Rapid Method. Is a rapid method of gene mapping and sequencing. Earlier methods of gene mapping were time consuming and pains taking. Bioinformatics has made this task very simple. Now gene hunting has become faster, cheaper and systematic.
4. Identification of similar genes. Computer aided studies help in identification of similar genes in two species. For example, genes similar for biotic and abiotic stresses in two species can be easily detected.
5. High Accuracy. The computer based information has very high level of accuracy and is highly reliable.
6. Bioinformatics has led to advances in understanding basic biological processes which in turn have helped in diagnosis, treatment and prevention of many genetic diseases:
7. It has become possible to reconstruct genes from Expressed Sequence Tags (EST). The EST is nothing but short pieces of genes which can express.
8. Computer aided programmes have made it possible to group proteins into families based on their relatedness.
9. Computer aided programmes are useful in designing primers for PCR. Such primers can be designed with little efforts. Such primers are used to sequence unknown genes or genes of interest.
10. In life science, computer aided programmes are useful in storing, organizing and indexing huge databases.
Limitations of Bioinformatics:
Computer based programmes have helped in better understanding of various processes of life science.
However, there are some limitations of bioinformatics which are listed below:
1. Bioinformatics requires sophisticated laboratory of molecular biology for in-depth study of biomolecules. Establishment of such laboratories requires lot of funds.
2. Computer based study of life science requires some training about various computer programmes applicable for the study of different processes of life science. Thus special training is required for handling of computer based biological data.
3. There should be uninterrupted electricity (power) supply for computer aided biological investigations. Interruption of power may sometimes lead to loss of huge data from the computer memory.
4. There should be regular checking of computer viruses because viruses may pose several problems such as deletion of data and corruption of the programmes.
5. The maintenance and up keeping of molecular laboratories involves lot of expenditure which sometimes becomes a limiting factor for computer based molecular studies.