eChapters

Jack bearing the largest edible fruit in the world, is a tropical evergreen tree belonging to the family Moraceae. Previously, it was known as Artocarpus integrifolia.It is an indigenous fruit crop, probably originated in Western Ghats of India (Santapau, 1966) and is widely cultivated in South Asia, East Indies and other warm areas of both the hemispheres. Jack tree is commonly grown in Burma, Malaysia and Brazil. It is hardly recognized as a commercial fruit crop in India even though it is widely distributed in Southern states viz,. Kerala, Tamil Nadu, Karnataka and Andra Pradesh. It is also cultivated in other states like Assam, Bihar, Orissa, Maharashtra and West Bengal. It is an invariable component of Kerala’s homesteads and also grown as a shade crop in coffee, arecanut and cardamom plantations. It is also grown as a standard crop in pepper plantations. The crop has got a rare distinction of being used as the staple food of Kerala tribals and also in some African countries like Uganda.

The mango is one of the choicest fruit crops of tropical and sub-tropical regions of the world. Its popularity and importance can easily be realized by the fact that it is referred as ‘King of fruits’ in the tropical world. India ranks first, both in area (2.51 million hectares) and production (15.02 million tonnes) of mango and it contributes to 42.1 per cent of world’s mango production. Presently, India is home to more than 1000 mango cultivars differing in taste, aroma, size, fibre content and pulp characteristics.

Though more than 1000 mango cultivars are reported, only 25-30 are of commercial importance. Most of the important cultivars are not amendable to hi-tech cultivation practices and do not meet the requirements of modern horticultural production systems like precocity in bearing, dwarfing, regularity in bearing with high yield, resistant to diseases, pests, physiological disorders and good keeping quality. Hence, breeding attempts to develop an ideal mango variety would be dwarf, regular bearer with medium size fruits (250-300g). Additionally, it should be highly tolerant to various fungal and bacterial diseases. A variety suitable for pickling is also gaining the attention of the breeders. An ideal pickling type should have high acidity, high fibre, good texture and characteristic raw mango flavour.

The first and foremost step in developing an ideotype is to explore the vast diversity and systematic characterization for utilization in the breeding programme.

Considering the importance of conserving the available gene pool, systematic exploration works are being carried out by National Institute like Indian Institutes of Horticultural Research (IIHR, Bangalore), National Bureau of Plant Genetic Resources (NBPGR, New Delhi) and others to collect and conserve the germplasm in Field Gene Banks. Recently, in addition to the traditional germplasm conservation methods, cryopreservation is also gaining importance especially in the conservation of nuclear gene (pollen parent) diversity for future breeding.

Utilizing the conserved germplasm in the breeding programme requires precise information on the genetic relationships within such germplasm. Information on the genetic distance among the germplasm accessions will also help to avoid the duplicates, widen the genetic base of the core collections and ultimately help in preserving the valuable diversity.

Pomegranate is one of the popular fruit crops of tropical and sub tropical in India and enjoys high reputation for its dietetic and medicinal properties. The fruit is native of Iran and is extensively cultivated in Mediterranean countries like Spain, Morocco, Egypt, Iran, Afghanistan. It is also grown to a lesser extent in Myanmar, China, Japan, India and U.S.A.

The area under pomegranate cultivation has increased several folds in the recent past after the introduction of soft seeded varieties. Out of 30,000 hectares under this crop in India, Maharashtra state alone grows over eighty per cent of area with an average production of 8000 kg ha^-1 (Mote et al.,1992). The export of pomegranate fruits was 1790.3 tonnes in 1991-92 valued at rupees 215.3 lakhs which was more than two fold over the previous year’s export earnings (Chadha, 1994). The utility of the crop is gaining importance and at present new orchards of pomegranate are being planted on large acreage. Because of its versatile adaptability, hard nature, low maintenance cost, steady and high yields, fine table and therapeutic values, better keeping quality and very good export potential, there is greater scope for extending its area and increasing the production especially in the hot and semi arid regions of India.

In pomegranate, market preference is for the attractiveness of the fruit which are exhibited through better size, colour with bold and deep coloured arils besides possessing high juice-content. However consumers prefers the softness of the arils with low acidity. While, there are number of cultivated types available with these desirable characters, there are hardly cultivar having a combination of all or atleast a majority of them. Pomegranate improvement work, therefore has to be oriented towards the production of soft seeded type with other desirable characters (Phadnis, 1974).

The Coconut palm is a monotypic species of the family Arecaceae, under the tribe Cocoideae. It is considered as an important commercial crop in more than 18 countries in the world. The palm provides food, drink, shelter and also supplies raw materials for a large number of industries. Every part of the palm is utilized for some economic purpose or another. Hence, it is referred to as ‘Tree of Wealth” or the “Tree of Life” (Satyabalan, 1993). It is native of South East Asia. Genetic diversity has become one of the keywords of scientists who are concerned about the sustainable management of different tree crops. Genetic diversity plays an important role in tree breeding, because hybrids between populations of diverse origin, generally display a greater heterosis than between closely related parents (Zobel and Talbert, 1986). The present study was formulated to identify divergent parents for future breeding programme.

Two hundred and fifty genotypes of coconut cultivar Chawghat green dwarf, distributed in the two districts of Kerala viz., Kottayam and Pathanamthitta were evaluated for nut yield per plant during June-July, 2000. Seventy five genotypes, which had single tree nut yield of more than population mean ± 2 SE were selected as per the method outlined by Ledig (1974). These 75 genotypes were observed for 10 nut and endosperm characters in two seasons (years), during June-July 2000 and 2001.

Each tree was considered as a single genotype. Thirty nuts from a single tree were collected and divided into three replications (Chauhan and Kanwar, 2001; Thirugnanakumar, 2006a, b). Observations were recorded on 10 nut and endosperm characters viz.,1) oil content (%), cold percolation method; (Kartha and Sethi, 1957), 2) weight of unhusked nut (g), 3) weight of husked nut (g), 4) diameter (polar) of the husked nut (cm), 5) diameter (equatorial) of the husked nut (cm), 6) thickness of husk (cm), 7) husk: nut ratio, 8) thickness of meat (mm), 9) weight of kernel (g) and 10) weight of copra (g). The mean values so obtained were subjected to statistical analyses, in Randomized Block Design, as suggested by Chauhan and Kanwar (2001) and Thirugnanakumar et al.(2006a, b). The D² estimates were made following Mahalanobis (1936), as described by Rao (1952). Clusters were prepared following Tocher (Rao, 1952).

In recent years, we are just experiencing a surplus production in cereals and oil seeds leading to self-sufficiency through green revolution and yellow revolution. However, shortage in the production of vegetables has drawn the attention for increasing the cultivation of vegetables to provide food and nutrition security.

Vegetables are being cultivated over an area of 49 million hectares with the production potential of 487 million tonnes in the world. This accounts for 2.85 per cent of total cropped area in the world. India is the second largest producer of vegetables next to China, sharing nearly 12 per cent of the total world output (Joshi and Shukla, 1997). Vegetables occupy nearly 8.02 million hectares with the production potential of 133.10 million tonnes in the year 2009 in India (Anonymous, 2009).

Bhendi (Abelmoschus esculentus (L.) Moench) is an important member of family malvaceae and commonly known as okra or ladyfinger in India. It is one of the most ancient and traditional vegetable crops grown in tropical and subtropical regions of the world (Martin and Ruberte, 1978). Bhendi is originated from tropical Africa with 2n = 8x = 72 or 130 or 144 chromosomes and is an allopolyploidy in nature (Joshi and Hardas, 1956; Suresh Babu, 1987). Martin (1982) reported that it behaves as a diploid. Under the genus Abelmoschus, there are 30 species in the old world and four in the new world (Joshi et al., 1974). Out of them, Abelmoschus esculentus, is the only species known to be cultivated. Bhendi is being raised in India in an area of 0.44 million hectares with an average production of 4.52 mt with the productivity of 10.27 t/ha (Anonymous, 2009).

Introduction

The nature and magnitude of genetic variability present in the genetic stock afford the plant breeder, information to formulate a purposeful breeding programme for crop improvement. The association and the influence of yield components with yield, their heritability and genetic advance would characterise the various steps in the breeding programme in achieving the aim of the breeder. Studies on these lines in various crops have hastened the realization of crop improvement in general.

India grows a variety of pulse crop which probably no other country in the world grows. These are multiple utility, energy high crops as they provide protein for human consumption, green nutritious fodder and enrich soil fertility through biological nitrogen fixation. Vigna radiata (L.) Wilczek, commonly known as greengram or mungbean, is the most widely distributed of the six cultivated Asiatic Vigna species.

The current breeding approaches to yield improvement in greengram are based on the recognition that this crop have lost a large part of their genetic variability in the process of adaptation to stress environment. This variability must now be regenerated.

The foremost need for this purpose is the collection of germplasm from different parts of the world and the organisation of a very intensive hybridization programme, using diverse genetic stocks as parental lines. Selection of parents for hybridization based merely on geographic diversity can no more be a suitable criterion. The importance of genetic diversity has long been appreciated by crop specialists. Such an analysis will eventually help to choose desirable parents for hybridization and evolve superior genotypes.

Introduction

India is the largest producer of pulses in the world, both in quantity and variety. But, presently, India is one of the largest importer of pulses. India imported pulse grains upto a tune of approximately 4000 crore rupees during 2006-07. It accounts for about 20 per cent of the total import bill during 2006-07. This is because of the green revolution (quantum jump in cereal production) accompanied with changes in the infrastructures and incentives including input supplies and price support systems in favour of major cereals. It altered the traditional cropping pattern against pulses with decades of emphasis on research as well as production in superior cereals coupled with a near total neglect of the rainfed areas, pulses were driven out of not only the irrigated areas, but also the rainfed farming and were relegated to the marginal lands. Further more, the weak infrastructural support for input supply, credit and marketing in the rainfed areas, the traditional home of pulses, also adversely affected the prospects for pulses. A vicious circle of low input use and low output thus got built in. Lack of processing and marketing facilities in pulses also contributed its share to the woes of pulse growers. The increasing shortage of pulses, resulted in the need for more and more import which, in turn has dampened the speed of rejuvenation of pulses sub-sector of agriculture sector.

The net per capita availability of pulses has fallen from 60.7 (1950-51) to 33.4 g (1991-92). On the contrary, the daily per capita availability of cereals has registered an increase from 334.2 (1950-51) to 443 g (1991-92). It leads to increase in the pulses/cereal ratio from 0.18 to 0.08 g i.e., by 55 per cent. This is despite the increases of 24.36 per cent in area; 61.71 per cent in production and 29.93 per cent in production. It is significant to note that almost all these increases had taken place during 1950-51 to 1960-61. The area, production and yield of pulses have either stagnated or declined since then. This stagnation of pulse production and productivity should be viewed seriously not only from the point of security and quality of food for our people, especially the poor and the rural population, but also from the soaring import bill, imbalance and distribution in the cropping pattern and resource allocation among various sub-sectors of agriculture.

In recent years, we are just experiencing marginal surplus production in cereals leading to self-sufficiency through green revolution. However, the shortage of production in edible oils has drawn the attention for the increased cultivation of oil seeds, and increased productivity per unit area to provide sustainable food and nutrition security (Swaminathan, 1989).

The importance of oil seeds cannot be over emphasized in the Indian economy. Oilseed occupied nearly 19 million hectares, next only to food grains, in 1986-1987. Yet, the domestic production in the country has lagged far behind the increasing demand for edible oils, necessitating a massive import of edible oils which lead to the drain of the valuable foreign exchange. The total import bill on edible oil has increased from 1.41 per cent in 1970-71 to 3.05 per cent in 1986-87. Even then, the annual per capita availability of edible oils registered only a nominal increased from 3.5 kg to 5.9 kg during the same period, against the nutritional norm of 14 kg (Suresh Pal, 1989). Due to the concerted efforts made through the ‘Technology Mission on Oilseeds’, oil seeds production reached a peak of 178.9 lakh tonnes during 1988-’89 in India (GOI, 1990a). This is an impressive achievement in Indian Agriculture, to reduce the bill on the import of edible oils from 4.11 per cent (1987-’88) to 2.58 per cent (1988-’89) (Gill, 1990). Further efforts in increasing oilseeds production definitely will go a long way in drastically reducing the present import bill.

Among the oilseed crop, sesame (Sesamum indicum L.), “The Queen of Oil Seeds”, is one of the important ancient and traditional crops occupying third position in terms of acreage on the oilseeds map of the country. It is commonly known as Gingelly, Til, Benniseed and Simsim. It is an important source of edible oil for the nutritional refugees of most part of the world, especially for India. The oil is rich in oleic and linoleic acid. In addition, it serves as a good source of proteins, vitamins and minerals (Nagaraj, 1990). Its high keeping quality deserves special mention.

Rice (2n = 24) is an annual grass (family: Graminae) with terminal panicles bearing the grains. It originated in Asia between the fourth and fifth millennia B.C. A substantial portion of the people in south and Southeast Asia and the southern part of China are depending on rice as staple food (Chang, 1976). Rice is planted in the most diverse environmental conditions of any major food crop, from sea level to around 3000 m altitude and from 30°S to 49°N. Temperature and day lengths are therefore quite diverse in the rice growing areas. Rice is also grown under water regimes ranging from dry land to deepwater fields where water may reach 5 m depth. The wide geographical distribution of rice and its early history of cultivation have resulted in the development of a great diversity of varietal types (Vergara, 1985).

Rice has been used as food by man for over 10,000 years and has fed a great number of people for a longer period than has any other crop. “Rice is life” for almost four billion people of the world contributing over 20 per cent of the total caloric intake of human population (Chaudhary and Tran, 2001). Rice is cultivated in 113 countries and on all continents except Antarctica and it is the staple food for 17 countries in Asia and the pacific, eight countries in Africa, seven countries, in Latin America and the Caribbean and one in the near east (IRC, 2003).

Globally rice is grown in around 155 million ha occupying one tenth of arable land, with an annual production of 579 million tonnes of rough rice (Iiyas Ahmed, 2003). The average productivity of 3.89 t ha^-1 of rice provides a per capita. Consumption of 100 to 240 kg per year across the globe. Over 90 per cent of the world’s rice is produced and consumed in Asia and more than half of it from India and China exploiting maximum arable land. More than two billion people obtain their 80 per cent calorie from rice and its derived products from 90 per cent of world’s rice area (FAO, 1999). Rice based on production systems and their associated post harvest operations employ nearly a billion people in rural areas in developing countries (IRC, 2003).

Genetic architecture of a population is the result of prolonged natural selection. The populations which exist in diverse environments might have been strongly diversified genetically. So, it is necessary to understand the extent and rates of genetic divergence existing between the diversified forms or types. Genetic diversity must be sufficient enough to justify breeding effort. Genetic diversity may be available in improved germplasm or it may exist only in genetically inferior stocks. The availability of statistical tools to quantitatively measure the genetic divergence between two or more populations and the relative contribution of individual characters to the total divergence have permitted to trace the evolutionary patterns in some crops such as rice and tobacco and in choosing the parents for hybridization in crop plants (Rao, 1958; Blackith, 1960; Morishima and Oka, 1960; Murthy et al.,1962). Among the several statistical methods developed for measuring the divergence between population, multivariate analysis (D² statistic) developed by Mahalanobis in 1936, has been found to be potent tool.

Mahalanobis D² analysis is an effective tool in quantifying the degree of divergence at genetic level and provides a quantitative measures of the association between geographic and genetic diversity based on generalized distance.

Words like rDNA (recombinant DNA) technology, cloning, genetically modified organism (GMO), living modified organism (LMO) and transgenics are of today’s common knowledge. However rather than scientific interest, debates on biosafety issues have made these terms more agnized among general people. Global, sectorial and individual protests against transgenic plants and animals are enunciated allover the world raising issues and concerns over risks and health hazards of using these organisms. Despite these protests and concerns, commercial use of transgenic organism as food, feed or other purposes are increasing at an exponential rate. Although there is not much scientific evidence where transgenics have caused havocs on ecological balance or human health, the biosafety issues need to be solved to provide a safer environment rather than be sorry and lament in the future for today’s mistakes. One of the major problems in supporting use of GMOs lies in the incapability of biosafety science to draw reliable and widely acceptable conclusions for labeling a safe tag on these organisms and their derivatives.

Food is the basic requirement for maintaining the life process. Plants supply the bulk of foods required for human and animal. With limited cultivable area and ever increasing pressure of human population, the demand for food is constantly rising which can not be alone met by conventional plant breeding technologies. Novel techniques like plant genetic engineering are gaining momentum for production of superior plants or yield enhancement of a species.  It has been observed that the most commercially successful application of recombinant DNA technology is in genetic engineering of plants, which led development of multinational seed companies deriving monetary benefit from genetically modified crop and food products. From production of herbicide resistant or insect pest tolerant plants to alter the inherent quality composition of human food, plant genetic engineering has established firmly the commercial viability of recombinant DNA technology.

Preternatural development of recombinant DNA technology has established genetic engineering in animals the most important field in application of biology for human benefit, from production of genetically modified animals to providing crucial technologies to medical science sector. On the basis of the nature of the target tissues, genetic engineering may target single cell line, particular tissue sectors or the organism as a whole. The purpose of transformation may be basic research involving elucidation of gene function, study effect of directed mutations, examination of physiological and developmental processes in animals or may be target oriented, such as production of proteins or metabolites in large quantities in a cell line, incorporating rDNA in the germline cells, gene therapy, use of rDNA in disease diagnostics, or production of transgenic animals for specific purposes.

Molecular markers or DNA markers are considered to be one of the most successfully applied component of molecular biology techniques that have relevance in almost every sphere of biology, from paleobotany to transgenic technology. In true sense, a marker is a characteristic of an individual that differentiates the individual from others. Morphological descriptions like cotyledon colour of Pea, eye colour of Drosophila, shape and size of fruits in summer squash etc. are examples of typical morphological markers. However, a single morphological marker is not sufficient for describing the uniqueness of an individual, for many pea plants will have green cotyledon or many Drosophila may have red eye. To define the uniqueness of an individual, we have to find a number of marker traits characteristic of that individual. Unfortunately, morphological variations are not sufficient to differentiate between a large number of individuals, or between groups or sub groups within a species, simply because the level of polymorphism is low. Besides, morphological characters or phenotypic expressions are affected by environmental changes, so stability of expression is low and sometimes uncertain.

While structural genomics aims to describe the protein structures coded by the genes present in the genome, functional genomics deciphers meaning of the coded information at transcriptome, proteome and interactome level. In the previous chapter we have seen how a gene can be identified by creation of mutants, genetic and physical mapping, and by sequencing the gene. Another source of possible gene structures come from genome sequence information, which by using computational algorithms identifies a number of ORFs that have the structural configuration of a gene. A third option of identifying a gene is identification of differences between wild type and mutant at RNA level, by analyzing the transcriptome. If we are able to identify differences in RNA expression pattern between these two, the information can be used to search back the gene sequences responsible for the differences. From proteome analysis inferences on expression of proteins and their interaction in the functional network of the cell with other proteins, DNA, RNA and cellular 

The primary target of genomics is identification and characterization of genes and gene products. Starting point of genomics may be a whole genome sequence, from which gene and protein structures can be predicted by computational and bioinformatics approaches (in silico genomics), or genes can be identified step by step starting from identification of a phenotype by induction and detection of mutation, construction of a genetic map demarkating the position of the character, physical location, identification of the gene, cloning and characterization of the gene or genome sequence by sequencing followed by expression analysis to correlate the phenotypic expression (in vivo genomics). Alternatively, genes can be identified by developing knockout mutants by random or site directed disruption of a reading frame and then determining the protein product as well as phenotypic expression.

One of the primary targets of genome analysis is to manipulate it at the level of genes, the units of inheritance. Genes, as explained earlier have distinct positions and sequence configurations in the genome which are expressed in the form of RNA or proteins controlling the functionality and identity of an organism. To understand the function of a gene several methodologies may be adopted. As genes have conserved sequences like promoters preceding the reading frame, initiation sequences, exon-intron junctions and end sequences, these features can be used to screen genome sequence to identify the regions containing genes. An open reading frame (ORF) is the sequence of a gene for which functions have been assigned, i.e., the sequence codes for a protein or RNA. On the other hand, an unassigned reading frame (URF) is a sequence which has structural features of a gene, but no function has yet been assigned to it.

The information that drives the process of life is encoded in the genome of the organism. Structurally defined, a genome is an organization of genetic information consisting of nucleic acids (deoxyribonucleic acid or ribonucleic acid). Arrangement of nitrogenous bases in the nucleic acid codes the information for execution of cellular processes. Four types of bases (Adenine, Guanine, Cytosine and Thymine) are present in deoxyribonucleic acid (DNA) while in RNA Uracil replaces thymine group of any three bases on transcribed RNA represent a codon. With four types of bases, sixty four types of codons can be formed. Genetic information encrypted in these codons is released in the form of arrangement of polypeptides consisting proteins via mRNA intermediate. This universal process of flow of genetic information from DNA to RNA to protein is known as the central dogma of life. The whole set of information coded in 64 codons, out of which 61 codes for one or more amino acids (building block of polypeptides/proteins) and three indicating where to stop is called the book of life or genetic code.

Process of life of an organism is defined, driven and depicted by its genetic constitution, or the genome. A genome is a collection of genetic material present in the cell as nuclear or organelle DNA. To be precise, it is the sum of all single copy genetic materials present in the cellular subcompartments. Thus a diploid organism having two copies of each chromosome contains genetic material constituting two copies of the genome, while a gamete of the same organism contains single copy of the same. Organelle genome is shared by chloroplast and mitochondria. In these two organelle genetic material is present in single copy per organelle, although many copies of organelle ensures that a cell harbours many copies of mitochondrial or plastid genome. Unraveling the structure and function of the genome is, therefore, the central objective of biological science. Technologies that would help to understand the basis of genetic, biochemical and physiological processes are pivotal to execute the knowledge for the betterment of mankind and environment.

Tissue culture consists of growing plants cells as relatively on organized masses of cells on an agar medium (callus culture) or as a suspension of free cells and small cell masses in a liquid medium (suspension culture). In other words, In plant cell culture, plant tissues and organs are developed in vitro on artificial media, under aseptic and controlled environment. The procedure depends mainly on the concept of totipotentiality of plant cells (Haberlandt, 1902) which refers to the ability of a single cell to express the full genome by cell division.