Everything you need to know about bioinformatics in plant breeding and genetics !
Q. 1. Define Bioinformatics.
Ans. The computer aided study of biology particularly genetics and molecular biology is called bioinformatics. Now the science of bioinformatics is gaining increasing importance in life science specially in the field of molecular biology and plant genetic resources.
Q. 2. Explain main points related to bioinformatics.
Ans. Main points related to bioinformatics are listed as under:
(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 large scale data derived from genome sequencing.
(iv) It is used for analysis of data related to genomics, proteomics, metabolomics and other biological aspects.
(v) It has wide applications in handling data related to plant genetic resources.
Q. 3. What are branches of bioinformatics?
Ans. Bioinformatics is broadly divided in to two groups, viz.:
i. Animal bioinformatics and
ii. Plant bioinformatics.
These are defined as follows:
i. Animal Bioinformatics:
It deals with computer aided study of various, animals. It includes gene mapping, gene sequencing, animal breed’ information data base, animal genetic resources data base. It can be further divided as bioinformatics of mammals, reptiles, insects, birds, fishes, etc. It also deals with the study of genomics, proteomics and metabolomics in various animal species.
ii. Plant Bioinformatics:
It deals with computer aided study of plant species. It includes gene mapping, gene sequencing, varietal information data base, plant genetic resources data base. It also deals with the study of genomics, proteomics and metabolomics in various plant species. It can be further divided as agricultural bioinformatics, horticultural bioinformatics, medicinal plants bioinformatics, forest plants bioinformatics, etc.
Q. 4. What are computer programs used in biology?
Ans. Various micro-soft programs which are commonly used in crop improvement (genetics and plant breeding) include:
i. Microsoft Word (M.S. Word),
ii. Microsoft Excel (M.S. Excel),
iii. Microsoft Power Point (M.S. Power Point) and
These are briefly defined as follows:
i. M. S. Word:
It is a very useful program for preparation of annual reports, project reports, writing research papers, varietal information system, plant genetic resources data base, etc.
ii. M.S. Excel:
It is a software program which is useful for various types of statistical and biometrical analyses. It can also be used for graphical and diagrammatic display of experimental results.
iii. M.S. Power Point:
It is a software program which is widely used for preparation of slides and presentation of results in various scientific meetings.
It is very much useful in searching literature, chatting and online transactions.
Q. 5. What are applications of bioinformatics in genetics?
Ans. Bioinformatics or computer aided programs have wide practical applications in genetics and plant breeding.
Some important applications of bioinformatics in plant breeding and genetics include:
(i) Varietal information system,
(ii) Plant genetic resources data base,
(iii) Biometrical analysis,
(iv) Storage and retrieval of data,
(v) Studies on plant modeling,
(vi) Pedigree analysis,
(vii) Preparation of reports,
(viii) Updating of information,
(ix) Diagrammatic representation, and
(x) Planning of breeding programs.
Q. 6. Discuss use of bioinformatics in varietal information system.
Ans. Bioinformatics has useful application in developing varietal information system.
In connection with plant variety protection (PVP) Act, various terms such as:
i. Extant variety,
ii. Candidate variety,
iii. Reference variety,
iv. Example variety and
v. Farmer’s variety are frequently used.
Hence, knowledge of these terms is essential.
These are defined below:
i. Extant Variety:
All released notified and unprotected varieties.
ii. Candidate Variety:
A variety to be registered under Plant Variety Protection Act is referred to as candidate variety.
iii. Reference Variety:
All released and notified extant varieties of common knowledge which are in seed production chain.
iv. Example Variety:
A variety that is used for comparison for a particular character is called example variety.
v. Farmers’ Variety:
A variety that has been developed by a farmer and used for commercial cultivation for several years is called farmers variety.
The detailed information about various types of varieties can be developed using highly heritable characters.
Such information can be used in various ways as given below:
(i) For varietal identification in DUS testing.
(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.
Q. 7. Explain application of bioinformatics in PGR data base?
Ans. The genetic material of plants which is of value 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, yield contributing characters, quality characters, resistance to biotic and abiotic stresses and 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 all over the world. Thus huge data is collected on crop genetic resources for several years. Bioinformatics plays an important role in systematic management of this huge data.
Bioinformatics is useful in handling such data in several ways as follows:
(i) It maintains the data of several locations and several years in systematic way.
(ii) It permits addition, deletion and updating of information.
(iii) It helps in storage and retrieval of huge data.
(iv) It also helps in classification of PGR data based on various criteria.
(v) It helps in retrieval of data belonging specific group such as early maturity, late maturity, dwarf types, tall types, resistant to biotic stresses, resistance to abiotic stresses, superior quality, marker genes, etc.
All such data can be easily managed by computer aided programs and can be manipulated to get meaningful results.
Q. 8. Define proteomics.
Ans. Proteomics refers to the study of structure and function of all proteins found in an individual. 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 programs are available for the study of proteomics.
Q. 9. What are types of proteomics?
Ans. The discipline of proteomics consists of two parts, viz. structural proteomics and functional proteomics.
These are defined as under:
(i) Structural Proteomics:
It refers to the study of the structure of all proteins found in a living organism.
(ii) Functional Genomics:
It deals with the function of all proteins found in a living organism.
Q. 10. Define transcriptome and proteome?
Ans. It deals with transcriptome and proteome. The transcriptome refers to complete set of RNAs transcribed from a genome and proteome refers to complete set of proteins encoded by a genome.
Q. 11. Give a brief description of metabolomics.
Ans. Metabolomics refers to the study of all metabolic pathways in a living organism. In other words, it is U5e computer aided information of all metabolic pathways of a living organism.
Q. 12. Explain main points related to metabolomics.
Ans. Main points related to metabolomics are listed below:
(i) It deals with study of all metabolic pathways in a living organism.
(ii) It is the computer aided information of all metabolic pathways of a living organism.
(iii) It helps in detection and correction of metabolic disorders in an organism.
(iv) It helps in selection of individuals with normal metabolic pathways.
(v) It helps in early detection of genetic disorders associated with metabolic pathways.
Q. 13. Describe applications of bioinformatics in biometrical analysis.
Ans. In crop improvement, various biometrical analyses are performed.
Important biometrical analyses that are performed in plant breeding and genetics are given below:
(1) Simple measures of variability such as mean, standard deviation, standard error, coefficient of variation, etc.
(2) Correlations: It includes genotypic, phenotypic and environmental correlations. It also includes simple, partial and multiple correlations.
(3) Path Coefficients: It includes analysis of genotypic, phenotypic and environmental paths.
(4) Discriminant function analysis.
(5) Metro-glyph analysis and D2 statistics
(6) Stability analysis
(7) Diallel, partial diallel, line x tester triallel, quadriallel, biparental and triple test cross analysis.
(8) Generation mean analysis, etc.
All these analyses can be easily performed through computer aided programs.
Q. 14. Explain applications of bioinformatics related to storage and retrieval of data.
Ans. In crop improvement, huge data is collected on the following aspects:
(i) Segregating Populations:
Single plant selections are made in segregating populations and data are recorded on various characters such as yield components, quality characters, resistance to biotic and abiotic stresses, etc.
(ii) Multi-Location Experiments:
Such experiments are conducted mainly for identification and release of new varieties and hybrids and also for assessment of varietal stability.
(iii) Multi-Seasonal Experiments:
Such experiments are conducted for several years (3-5 years) for identification of new varieties and hybrids.
The above data remain in active use generally for two decades. Handling of such a huge data is a difficult task. However, such data can be easily stored in various storage devices such as hard disks, compact disks, pen drive, data cards, etc. Storage of data in computers require less space and is very safe as compared to storage of data in paper registers and files.
Q. 15. Discuss use of computers in plant modeling.
Ans. Computers are useful tools for undertaking studies on modeling of plants. First the theoretical model can be prepared with the help of computer keeping in view various plant characters. Then such model plants can be developed through hybridization and directional selection. This types of studies are useful in developing crop ideotypes or ideal plant types in different field crops.
First the conceptual model is prepared and then efforts are made to achieve such model by combining desirable genes from different sources into a single genotype through appropriate breeding procedures. Such studies have been made in field pea.
Q. 16. Explain use of computers in pedigree analysis.
Ans. 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 which 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 programs especially in the selection of parents for use in hybridization programs. The study of proteomics also helps in pedigree analysis.
Q. 17. Explain use of computers in preparation of reports.
Ans. After biometrical analysis of data, results are interpreted and various types of reports or documents are prepared.
In crop improvements following types of reports are prepared:
(i) Research Project Report: The annual progress report of each project is prepared and salient findings are documented.
(ii) Monthly, quarterly, half yearly and annual progress reports of all the research projects are also prepared.
(iii) Sometimes, bulletin and booklets are prepared to document specific information for adoption and benefit of farmers.
(iv) Research papers and popular articles are prepared based on research findings.
(v) Germplasm catalogues are prepared for various characters.
Such reports can be easily being prepared with the help of computers using MS Word program. This information can be stored in computer memory and reused as and when required. The editing and updating of reports can be done any time without much extra efforts.
Q. 18. Discuss use of computers in updating of information.
Ans. In plant breeding and genetics, results of multi-seasonal and long term experiments require continuous updating. Computers have made this task very simple. The information related to any experiment which is already stored in the computer memory, can be updated any time by editing the concerned file. Any portion of information can be deleted or revised easily.
Q. 19. Explain use of computers in diagrammatic representation.
Ans. Inclusion of diagrams makes the reports, research papers, articles, bulletins, etc. more attractive, informative and easily understandable.
The following types of diagrams are made in plant breeding:
(i) Line diagrams, bar diagrams, histograms and pie diagrams.
(ii) Cluster diagram: It is prepared when data is subjected to D2 analysis.
(iii) Path diagram: It is prepared when data is subjected to path coefficient analysis.
(iv) Vr-Wr Graph: It is prepared when data is subjected to Hayman’s graphical approach of diallel cross analysis.
(v) Metro-glyph Chart: It is prepared when data is subjected to Metro-glyph analysis.
All these diagrams can be easily prepared with the help of computer using specific program.
Q. 20. Describe use of computers in planning of breeding programs.
Ans. Plant breeders have to plan various breeding programs every year. Computers are useful tools in such planning.
The following activities can be easily planned with the help of computers:
(i) Sowing plans of various breeding experiments.
(ii) Selfing and crossing plans.
(iii) Breeder seed production plan.
(iv) Hybrid seed production plan.
(v) Germplasm collection, conservation, evaluation, distribution, utilization and documentation plan.
(vi) Screening plan of breeding material against biotic and abiotic stresses.
(vii) Selection quality evaluation and multi-location testing plans.
All the above plans can be easily prepared with the help of computer well in advance. This is very important for proper implementation of various breeding programs. Computers are also useful in printing out labels and list of observations to be recorded in various breeding experiments.