Everything you need to know about genomics in crop Plants !
Q. 1. What is genomics?
Ans. The term genomics was first used by Thomas Roderick in 1986. It refers to the study of structure and function of entire genome of a living organism.
Q. 2. Define Genome.
Ans. Genome refers to the basic set of chromosomes. In a genome, each type of chromosome is represented only once. Now genomics is being developed as a sub discipline of genetics which is devoted to the mapping, sequencing and functional analysis of genomes.
Q. 3. Explain main points related to genomics.
Ans. Main points related to genomics are listed below:
(i) It is a computer aided study of structure and function of entire genome of an organism.
(ii) It deals with mapping and sequencing of genes on the chromosomes.
(iii) It is a rapid and accurate method of gene mapping. It is more accurate than recombination mapping and deletion mapping techniques.
(iv) The genomic techniques are highly powerful, efficient and effective in solving complex genetic problems.
(v) Now use of genomic techniques has become indispensible in plant breeding and genetics.
Q. 4. What do you mean by structural genomics?
Ans. The discipline of genomics consists of two parts, viz. structural genomics and functional genomics. Structural Genomics deals with the study of the structure of entire genome of a living organism. In other words, it deals with the study of the genetic structure of each chromosome of the genome. It determines the size of the genome of a species in mega-bases (Mb) and also the genes present in the entire genome of a species.
Q. 5. Define Functional Genomics.
Ans. The study of function of all genes present in the entire genome is known as functional genomics. 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. 6. How would you classify genomics?
Ans. The genomics can be classified as plant genomics, animal genomics, eukaryotic genomics and prokaryotic genomics.
These are defined as follows:
(i) Plant Genomics:
It deals with the study of structure and function of entire genome of plant species.
(ii) Animal Genomics:
It deals with the study of structure and function of entire genome of animal species.
(iii) Eukaryotic Genomics:
It deals with the study of structure and function of entire genome of higher (multi-cellular) organisms.
(iv) Prokaryotic Genomics:
It deals with the study of structure and function of entire genome of unicellular organisms.
Q. 7. Give a brief description of genome mapping.
Ans. The discipline of genomics is of recent origin. The genome mapping was first completed in free living bacteria Haemophillus influenza in 1995. Later on genome sequencing work was intensified both in prokaryotes and eukaryotes. In plants, genome sequencing was first completed in Arabidopsis thaliana a weedy relative of mustard followed by rice (Oriza sativa). Now genome sequencing work has been completed in more than 40 crop plants.
Q. 8. Give genome size in ten crop plants.
Ans. The list of some field crops, fruit crops and other plant species in which genome sequencing work has been completed is presented in Table 47.1.
Q. 9. Name the species with smallest and largest genome size.
Ans. In plants, the smallest genome size has been reported in Arabidopsis thaliana (120Mb) and the largest in corn (2500). Thus, in plants the genome size investigated so far varies from 120Mb to 2500Mb. After gene sequencing, function is assigned to individual gene through various molecular techniques.
Q. 10. What are the genes to be mapped?
Ans. In genome research, both types of genes, viz., major genes (oligogenes) and minor genes (polygenes) can be easily mapped. The mapping of polygenic traits is possible by genome mapping techniques which is not possible by conventional gene mapping techniques such as recombination mapping and deletion mapping.
The genome mapping is done for:
i. Morphological,
ii. Productivity,
iii. Resistance,
iv. Quality,
v. Agronomic and
vi. Some special traits as discussed below.
i. Morphological Characters:
It includes highly heritable traits such as shape, size and color of leaf, flower, calyx, corolla, etc. It also includes surface of leaf and stem (hairiness and smoothness).
ii. Productivity Traits:
Such characters differ from species to species.
iii. Resistance Traits:
Such characters include resistance to diseases, insects, drought, soil salinity, soil alkalinity, soil acidity, heat, frost, water logging, cold, etc.
iv. Quality Traits:
Such traits include nutritional quality, market quality and keeping quality.
v. Agronomic Traits:
Such traits include earliness, plant height, plant type, etc.
vi. Special Characters:
Such characters include genes controlling male sterility, self-incompatibility, photo and thermo insensitivity, toxic substances, apomixis, adaptation, etc.
Q. 11. Give a brief description of genome mapping laboratories.
Ans. The genome mapping work is carried out by collaborative efforts of various International and National Research Laboratories of public domain. The list of some organizations where genome sequencing and mapping work on different crop species is carried out is presented in Table 47.2.
Q. 12. Give a brief account of genome mapping in India.
Ans. In India, the functional genome research projects are looked after by the Depart of Biotechnology (DBT) and ICAR. The DBT has initiated such work on several crops such as rice, wheat, maize, chick pea, banana, tomato, Brassica, etc. The ICAR has created genome mapping facilities for rice at NRCPB, IARI, and New Delhi.
In India, the genome mapping work is carried out at the following centres:
(i) National Research Centre for Plant Biotechnology, IARI, New Delhi.
(ii) International Centre for Genetic Engineering and Biotechnology, New Delhi.
(iii) Jawaharlal Nehru University, New Delhi.
(iv) National Botanical Research Institute, Lucknow.
Q. 13. What are applications of genomics in crop improvement?
Ans. Genomics has several practical applications in crop improvement. Genome mapping is useful in several ways.
It is useful or provides information about:
i. Genome size,
ii. Gene number,
iii. Gene mapping,
iv. Gene sequencing,
v. Evolution of crop plants,
vi. Gene cloning,
vii. Identification of DNA markers,
viii. Marker assisted selection,
ix. Transgenic breeding,
x. Construction of linkage maps and
xi. QTL mapping.
All these aspects are briefly discussed as follows:
i. Genome Size:
Genome mapping is a very useful technique for determining the genome size in various plant species. In the plant species studied so far, the largest genome size has been reported in maize (2500Mb) and the smallest in Arabidopsis thaliana (120 Mb).
ii. Gene Number:
Genome mapping provide information about gene number in a species. In crop plants studied so far, the maximum numbers of genes have been reported in rice (56,000).
iii. Gene Mapping:
Genome research is very much useful in mapping/tagging of genes on the different chromosomes of a genome. In other words, it helps in large scale discovery of new gene in a genome.
iv. Gene Sequencing:
Genome mapping helps in determining the order of genes on the chromosomes. The order of genes is determined on each chromosome of a genome.
v. Evolution:
Genome mapping provide information about the evolution of different species. It measures the association between different genomes and thus provides information about the relatedness or evolutionary biology of crop plants.
vi. Gene Cloning:
Genome research is very much useful in making multiple copies of a gene and transfer of the same from one genotype to another. Thus, it aids in specific gene transfer.
vii. Identification of DNA Markers:
The genome mapping techniques are useful in identification of DNA markers which can be used in molecular breeding i.e. marker assisted selection. The mapping populations developed from inter-specific crosses have higher polymorphism for DNA markers than those mapping populations derived from intra-specific crosses.
viii. Marker Assisted Selection:
Marker assisted selection refers to indirect selection for a desired phenotype based on banding pattern of linked DNA markers. The improvement of crop plants using such selection is called molecular breeding. Various DNA markers used for such purpose include RFLP, AFLP, RAPD, SSR, etc. The effect of DNA marker is correlated with morphological markers and then selection is made for particular trait. The selection based on DNA markers is more reliable because DNA markers are not influenced by environmental factors.
ix. Transgenic Breeding:
Genome mapping is useful in gene cloning. The gene of interest can be cloned and used in developing transgenic plants (genetically engineered plants). Transgenic breeding permits direct gene transfer bypassing sexual process.
x. Construction of Linkage Maps:
Genome mapping helps in construction of linkage groups. The linkage groups can be constructed from the information of gene mapping and gene sequencing.
xi. QTL Mapping:
The genome mapping techniques is widely used for mapping of quantitative trait loci (QTL). The mapping of QTL or polygenic traits is not possible by conventional methods, viz., recombination mapping and deletion mapping techniques.
Q. 14. What are practical achievements of genome mapping?
Ans. In crop plants, genome mapping work has been completed in more than 40 field and fruit crops. Important crop plants in which genome sequencing has been completed include Arabidopsis, Brassica rapa, Rice, Corn, Cucumber, Soybean, Pigeon pea, Tomato, Potato, Melon, Flax, Cotton from field crops: and oranges, apple, peaches, papaya, Grapes, Date palm. Banana etc. from fruits crops. The genome sequencing of many more crop plants is in progress.
Q. 15. What are limitations of genome mapping?
Ans. These days, the genome mapping of crop plants is gaining increasing importance.
However, there are some limitations of genome mapping such as:
i. High cost,
ii. High technical skill,
iii. Laborious work,
iv. Availability of limited genes and
v. Lake of proper markers.
These are briefly presented below:
i. Expensive Technique:
The genome research requires well equipped sophisticated laboratory with costly chemicals and glassware. Thus lots of funds are required for carrying genomic research. Lack of adequate funds sometimes becomes limiting factor in the progress of such project.
ii. High Technical Skill:
The genome mapping work requires high technical skill. It requires training of scientists in the specialized field of genomics. It also requires International collaboration with other leading genome research laboratories which sometimes becomes limiting factor. The international collaboration is possible if the crop on which genome research work is to be carried out is of global significance.
iii. Laborious Work:
The genome mapping requires detection of various DNA markers (RFLP, AFLP, RAPD, SSR, etc.) which is a laborious and time consuming work. Huge populations related to F2, RILs, NILs and doubled haploids need to be screened for such purpose. This limits the progress of the work.
iv. Limited Genes Available:
Firstly, limited number of genes and promoters are available for development of transgenics. Secondly, such genes are protected under Intellectual .Property Rights and, therefore, cannot be used for developing transgenic plants.
v. Lack of Proper Markers:
Most of the useful agronomic traits are governed by polygenes and are complex in nature. Tightly linked DNA markers are yet to be identified for such characters.
Q. 16. What points should be taken in to account for rapid progress of genome mapping work?
Ans. Considerable research work on genome sequencing and mapping has been done on various crop plants so far. In future, for rapid progress of genome sequencing work several points need consideration. Important points include funding, training, material sharing, research priorities, important traits, selection of species, etc.
These are briefly discussed as follows:
(i) Funding:
Since genome mapping projects are very expensive, there is need of International collaboration for supporting such prestigious projects.
(ii) Training:
Some laboratories are well equipped for genomic research. Such Laboratories should impart training to scientists from various countries for human resource development in genomic research.
(iii) Material Sharing:
The leading laboratories should develop and distribute frame work DNA markers to other research laboratories for their use and further research.
(iv) Research Priorities:
In order to get International collaboration, areas of common interest or global significance should be identified for genomic research work.
(v) Important Traits:
In genome mapping, the major emphasis needs to be given to characters of economic importance such as productivity, quality and resistance to biotic and abiotic stresses. The experience gained in genome mapping of one species may be helpful in the study of related species.