eChapters

Genetic Transfer and Mapping in Bacteria

Bacteria can transfer genetic material during conjugation

Hfr strains contain an f factor integrated into the bacterial chromosome

Conjugation experiments can be used to map genes along the E. coli chromosome

A detailed genetic map of the E. coli chromosome has been obtained from many conjugation studies

Bacteriophages can also transfer genetic material from one bacterial cell to another in the process of transduction

Cotransduction can be used to map genes that are within 2 minutes of each other

Bacteria can also transfer genetic material by transformation

Horizontal gene transfer is the transfer of genes among different species

Genetic characterization using DNA markers is a cutting edge technology that makes it possible to study animal variability at basic level. A genetic marker can be any stable and inherited variation which is measurable or detectable by a suitable method and can be used subsequently to detect the presence of a specific genotype or phenotype other than itself, which otherwise is non-measurable of very difficult to detect. Such variations exist at morphology, chromosome, biochemistry or DNA levels that can serve as genetic markers. Molecular markers are the markers that reveal variations at the DNA sequence level. The polymorphisms observed at the DNA sequence has many applications which include percentage determination, genetic distance estimation and evolution, determination of individual identity, identification of disease carrier (heterozygous) animals, determination of twin zygosity and freemartinism, gene mapping, marker assisted selection (MAS), sex determination, DNA fingerprinting and transgenic breeding. Gene mapping is a tool to identify the genes responsible for specific traits.  The genetic map is constructed from linkage relationship based on the frequency of meiotic exchange (amount of recombination) among linked traits. Genetic map helps

Genetic purity is the vital determinant in continuing the genetic integrity in seed from generation to generation. This is the basis of variety purity maintenance. The genetic purity depends upon the purity of the seeds planted. The genetic purity of the seeds planted must exceed or equal to the final product purity standards required as the purity generally decreases with subsequent generations of propagation. The improved varieties loose their identity and healthiness unless properly maintained. Maintenance selection can prevent the seed quality deterioration.

Meaning and Importance

Genetic purity denotes the percentage of seeds (by weight) belonging to the variety/hybrid under certification. It is one of the primary criteria of seed quality. The efforts of plant breeders become fruitful only when sufficient quantities of good quality seeds of improved varieties/hybrids reach farmers / growers. This is necessary to take all round care at every step of seed multiplication before the seed is delivered for marketing. Hence, genetic purity testing is of critical importance not only to farmers but also to plant breeders, seed producers as well as quality control enforcing agencies. Increasing emphasis on hybrid cultivars due to their better performance and quality produce, more money and expertise have been put in further research of hybrid development. In this context, protection of parental lines is assuming critical importance and for that purpose, several breeding institutes do adopt various strategies for identification, characterization and protection of their parental lines as to avoid pilferage and misuse of their proprietary lines by other organizations. Use of random amplified polymorphic DNA (RAPD) and other molecular markers for evaluating seed purity of F₁ hybrids and their parental lines are closely related, thus, helps in assessing contamination of F₁ seeds even with the seeds of sib (inbred seed and seed from self-pollination of parental lines). For genetic purity testing of hybrids seeds, it is imperative that parental lines of hybrid be adequately characterized on the basis of maximum number of distinguishable descriptors (morphological, biochemical or molecular markers).

Characterization of Germplasm / Hybrids, Varietal identification, mutants etc.

Accurate identification of plants is desired for patent protection of plant varieties. Accurate characterization is also necessary to trace out the parents of new varieties. Use of present day molecular markers in addition to the classical methods provides more positive identification of new cultivars. RAPD and other molecular techniques have been used in a variety of plant materials for such studies (Sneath and Sokal 1973, Saitou and Nei 1987, Demeke et al., 1992, Selvam and Rajasekaran  1993, 1994, Dubouzet, et al., 1997, 1998, Hallden, et al., 1994, Hu and Quiros 1991, Jain et al., 1994, Matsumoto and Fukui 1996, Williams et al., 1990, Wolff et al., 1995). RAPD technique has been used in the genus Bougainvillea. It is often difficult to distinguish both mutants and hybrids and sports having a common progenitor, or progenitors themselves. Therefore, the industry needs a DNA-based fingerprinting technique to distinguish mutants or cultivars reliably. Reports are available on investigation about the molecular systematics and genetic differences for better understanding of varietal relationships in bougainvillea (Chatterjee et al., 2007, Kumar et al., 2006, Kumar et al., 2014, Hammad 2009, Pavan Kumar et al., 2015). 

Poultry has been extensively used for various biological experiments and its contributions to science are impressive. Among poultry species, chickens have made fundamental contributions to our current understanding of many immunological processes and it ranks high in the biological world. It still serves as an animal model to investigate immunogenetic aspects of disease resistance and tumor regression. Among the major contribution from poultry, the first evidence for viral induced tumor came from chicken (Rous, 1911; Nobel prize, 1966), reverse transcriptase enzyme was isolated from Avian Leukosis virus (Tamin and Baltimore, 1963; Nobel Prize, 1975), oncogenes in virus are from host cells (Bishop & Harold Varmus; Nobel Prize, 1989) and major two arms of immune response i.e. the T and B cells were first discovered in chicken.

Introduction

India is a vast country comprised of different agro-ecological regions with diverse climate, natural vegetation resources, topography, possesses almost all domesticated animal species, landraces and crops with different production systems. Domestic animals provide a considerable amount of   food requirements for mankind. India ranks first in milk production with 112.5 million tonnes milk produced in 2010-11. As India is a tropical country, in summer the temperature hikes about 40-48°C in various parts of the country. Such a temperature is certainly not within the comfort range of animals and thus the animals respond to the stress imposed by temperature on them in various ways to combat the stress and to maintain the homeostasis.

Mastitis is a disease of the mammary gland caused by pathogens that find their way into the lumen of the gland through the teat canal. Our efforts have been focused on developing mastitis resistant dairy cattle for a variety of reasons. Firstly, mastitis is a significant detriment to agricultural productivity. Mastitis is on every dairy farm and affects both the production and post harvest segments of the dairy industry. It is clearly a global disease. Secondly, the incidence of mastitis has not declined appreciably since the implementation of the extensive antibiotic therapy and culling of infected animals. Thirdly, considerable effort has been expended in developing vaccines that have not been as efficacious as hoped. Given these past efforts it is far from certain that a truly effective vaccine will ever be realized. Finally, because of the low heritability of mastitis resistance selective breeding has not been a useful tool for combating mastitis. Additionally, there is a strong desire to reduce the on-farm use of those antibiotics that are also used in human medicine, and certainly not least is a desire to improve the welfare of our dairy animals.

International Board for Plant Genetic Resources (IBPGR) now known as International Plant Genetic Resources Institute (IPGRI) uses the following items in genetic resources documentation. 
    i)    Passport (accession identifiers and information recorded by collectors) 
    ii)    Characterization (consists of recording those characters which are highly heritable, can be easily seen by the eye and are expressed in all environments) 
    iii)    Preliminary evaluation (consists of recording a limited number of additional traits thought to be desirable by a consensus) of users of the particular crop
Characterization and preliminary evaluation will be the responsibility of the curators while further characterization and evaluation should be carried out by the plant breeders. The data from further evaluation should be fed to the curators who will maintain a data file.

Introduction

Carrot (Daucus carota L., 2n=2x=18) is a cool-season root vegetable grown all over the world in temperate as well as sub-tropical climates. In India, it is cultivated over an area of 24,000 hectares with an annual production of 3,50,000 metric tones with a productivity much lower (14.58 t/ha) than the world average (22.17 t/ha) as per FAO, 2004. Carrots are used for human consumption as well as for animal feed. Carrot can thus be used for augmenting fresh fodder supply to milch animals during the lean winter in Kashmir (Hussan and Ahmed, 1999). Carrot has a significant place as an ingredient in soups and sauces and in dietary composition and also as a salad. A sweet preparation called Gajar Halwa is very famous dish in North India. Besides canning, it is also used in preparation of pickles. It is also exported in the form of fresh roots to the countries like Kuwait and Sharjah. Carrot is a rich source of á and â- carotene. The total carotenoid content in the edible portion of carrot roots ranges from 6.00 to 54.80 mg/100g. The yellow and orange coloured roots contain relatively more carotenoid. Carrot roots contain protein, fat, carbohydrate, minerals (especially Ca, Mg, Na, K, Cu, S etc.) besides vitamin A, B₁, B₂, nicotinic acid and vitamin C. In carrot roots, sucrose is the most abundant with endogenous sugar contents 10 times than those of glucose and fructose.

Asia minor, Afghanistan, North West India, Iran and Turkey are the centers of origin of carrot. As per Encyclopedia Britannica, carrots have originated from Afghanistan, Punjab and Kashmir with secondary centers in Ethiopia and North America. The European carotene carrot (syn. Western carotene carrot, temperate carrot) has been derived from the Asiatic anthocyanin containing forms of carrot (syn. Eastern anthocyanin carrot, tropical carrot). Afghanistan is the centre of diversity of the purple coloured carrot (anthocyanin carrot) and as such this country is suggested as the primary centre for origin. Integration between the Asiatic and European carrots has given the present day forms which are fleshy, smoother, less forked and better coloured.

Punjab and Kashmir are also considered as primary centre of origin with secondary centers in Ethopia and North America. It is still found in its wild form in Himachal Pradesh and Kashmir valley where wild animals especially brown bear feed on its roots. People still eat the wild carrots in some parts of Kashmir (Yawalkar, 1980). In north India highly coloured types of carrots are found which are not available in Europe. The colour of carrot ranges from absolute colourless to light lemon, light orange, orange and deep orange, light purple, deep purple and almost black. It is also an indication of this region being a primary centre of origin of carrot.

Introduction

Turnip is an important root crop which is very popular particularly in northern India. It is a cool season crop mainly grown as a fall or winter crop in the hills and winter crop in the plains. Turnip (Brassica rapa L. syn. Brassica compestris var. rapa) belong to family Brassicaceae. It has a chromosome number of 2n=2x=20. Two main centers of origin have been indicated. The Mediterranean area is considered to be the primary centre of origin of European type/temperate types. While Eastern Afghanistan with adjoining areas of Pakistan is considered to be another primary centre with Asia Minor, Transcaucasus and Iran as secondary centre. The parents of cultivated turnip are found in the wild form in Russia, Siberia and Scandnavia. It was cultivated by the ancients and ranked next to grapes and cereals in Italy. It was introduced in England probably in 1590 and United States in 1606 (Yawalkar, 1980). Turnips are now cultivated throughout the world.

Turnips are botanically biennial herbs, but are cultivated as annual root crops for both animal and human consumption. The turnip root contains 41.6% moisture, 6.2 g carbohydrates, 0.5 g protein, 0.2 g fat, 0.04 mg thiamin, 0.04 mg riboflavin, 43 mg ascorbic acid, 30 mg Ca, 40 mg P and 0.4 mg Fe per 100 g of edible portion. The turnip green contains 15,669 IU vitamin A per 100 g (Aykroyd, 1963). Turnip is grown for its enlarged root as well as for its foliage. Extra seedlings from thinning are often used as greens. The fresh roots are consumed in salads or cooked as vegetable or used in pickles. The young leaves contain high amount of ascorbic acid and iron, rank second in vitamin A content and are cooked as greens.

The fleshy thickened underground portion of turnip is actually the hypocotyl. The colour and shape of this underground portion vary with the cultivars and the roots are flat globular to top-shaped and long. The colour of under ground portion may be white or yellow, while that of above ground portion may be red, purple, white, yellow or green. A distinct tap root and secondary roots arise from the lower part of the swollen hypocotyl. Thickening begins in the central part of the hypocotyle, followed by the upper and lower parts. Normally, the roots attain edible maturity in 40-80 days depending on cultivar and climatic conditions.

Abstract

The potato research in India was started systematically after the establishment of Central Potato Research Institute (CPRI) in 1949. Forty-one potato varieties having attributes of early, medium and late maturity vis-à-vis resistance to various biotic and abiotic stresses have already been developed indigenously for varied agro-ecoregions in the hills and sub-tropical plains. After the establishment of CPRI, collection of potato germplasm was made mandatory. Presently there are over 2,700 accessions including 133 wild species (related to potato) in the germplasm collection of CPRI. Despite the large collection of potato germplasm at the institute the genetic base of all 41 Indian potato varieties released so far can be traced to only about 50 parents and most of these represent tetraploid potato cultivars while only a few of the exotic diploid wild species have been used in improvement of potato varieties in India. Under utilization of wild species could be mainly due to the pre- and post zygotic crossability barriers inherent in many species of genus solanum. Nevertheless, about seven wild species have been used in potato breeding for introgression of resistance genes for various biotic and abiotic stresses in the improved Indian potato varieties.

Introduction

‘Cole crops’ is a general term used to describe several vegetables in the Brassicaceae family. It is an important and highly diversified group of vegetable crops grown worldwide that belongs to Brassica oleracea (Monteiro and Lunn, 1998) and includes particularly six Brassica crops (cabbage, cauliflower, Brussels sprouts, broccoli, kale and knol kohl). All of these crops can trace their history to a common ancestry of wild cabbage originating in the Mediterranean and Asia Minor regions. Cole crops are one of the oldest cultivated plant groups in the world. They are cultivated in Europe since very ancient time from where they have spread to other parts of the world (Nieuwhof, 1969). All the cole crops (except few cauliflower, broccoli and cabbage types) require chilling temperatures for about two months to transform from vegetative phase into reproductive phase. However, the period of chilling requirement differs according to the kind of crop and varieties. Cole crops are also commonly called as European or biennial vegetables due to their cool temperatures requirements and two season requirement to complete their life cycle.

Major Resources of Cole Crop Germplasm

Germplasm is any form of the hereditary material from an organism. Genetic resources encompass all the various forms of germplasm that are available for collection, storage and use. The genetic diversity of crops, represented by traditional local cultivars and wild relatives has been disappearing rapidly during recent decades. Initial concern was noted by H.V. Harlan in the 1930s (Harlan and Martini, 1936) but by the 1960s, modern plant breeding and land-use changes accelerated loss and stimulated the realization that genetic resources in regions of diversity were being lost at an alarming rate. To conserve the genetic variation within the cole group, a comprehensive base collection of the cultivated forms of Brassica oleracea has been established at the vegetable gene bank of Horticulture Research International (HRI), Wellesbourne, (U.K.). Gene banks have also been established at Instiuut de veredeling van Tuinbouwgewssen, Wageningen, the Netherlands and the Instituto del Germoplasm, Bari, Italy (Van der Meer et al., 1984) for conservation of genetic resources. The International Board for Plant Genetic Resources (IBPGR) has recognized HRI as an international centre for conservation of Brassica oleracea (Innes, 1975). Large number of collections of cole crops is also available with the United States Department of Agriculture, Plant Introduction Service. In India, National Bureau of Plant Genetic Resources (NBPGR), New Delhi has been assigned the duty of conserving the germplasm of all crops, including vegetables. Germplasm of all the cole crops is being maintained at the Indian Agricultural Research Institute, New Delhi (tropical types) and its regional station at Katrain (temperate types). Other major institutes maintaining germplasm of cole crops include Punjab Agriculture University, Ludhiana, G. B. Pant University of Agriculture & Technology, Pantnagar, Indian Institute of Vegetable Research, Varanasi, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan and SKUAS&T, Srinagar.

Introduction

Cowpea, {Vigna unguiculata (L.) Walp.} is an important food legume in the semi-arid tropics covering Asia, Africa, Southern Europe and Central and South America (Henriet et al., 1997; Mortimer et al., 1997; Van Ek et al., 1997). It is a drought tolerant and warm weather crop. Therefore, well adapted to the drier regions of the tropics where other food legumes do not perform as well. It fixes atmospheric nitrogen and grows well even in the poor soils with more than 85% sand and with less than 0.2% organic matter and low levels of phosphorus (Kolawale et al., 2000 and Sanginga et al., 2000). Also, it is shade tolerant and therefore, compatible as an intercrop with maize, millet, sorghum, sugarcane and cotton as well as with several plantation crops (Singh and Emechebe, 1998). Coupled with these attributes, its quick growth and rapid ground cover checks soils erosion and in situ decay of its roots and nitrogen rich residues improves soil fertility and structure which together have made cowpea an important component of cropping system in the dry savannas of the sub-Saharan Africa (Carsky et al., 2001 and Mortimer et al., 1997).

Cowpea is cultivated in about 14 million ha world wide with about 5 million tons annual production. However, a substantial part of the cowpea production comes only from few countries. Nigeria is the largest producer and consumer of cowpea with about 5 million ha area and about 3 million tons production annually. Niger Republic is the next largest producer with 3 million ha and over 1 million ton production. Northeast Brazil grows about 1.5 million ha of cowpea with about 500.000 tons production. In the southern USA about 40,000 ha of cowpea is grown with an estimated 45,000 tons annual production of dry cowpea seed and a large amount of frozen green cowpeas. Even though exact statistics are not available, India is the largest cowpea producer in Asia and together with Sri Lanka, Pakistan, Nepal, Bangladesh, Thailand, Indonesia and other far eastern countries, there may be over 1.5 million hectares under cowpea in Asia.

Introduction

Radish (Raphanus sativus L., 2n=2x=18) is a root cum leafy vegetable suitable for sub tropical and temperate climate. Radish probably originated in Europe and Asia. It has been under extensive cultivation in Egypt since long. It was introduced to England and France in the beginning of 16^th century. In 1806, it was introduced to America. Radish does not exist in wild stack. It is believed to have originated from R. raphanistrum which is widely distributed as weed in Europe. Radish is primarily a winter crop but with the development and release of new varieties, it can be grown all the year round. The new varieties can withstand heat and does not bolt in spring. Radish is a favourite crop because of its quick growth and availability in 4-7 weeks.

Its fleshy roots are modified roots, developed from both the primary root and hypocotyl. The leaves and roots are consumed both as salad and cooked. The radish root is a good appetizer; its different preparations are useful in curing liver and gall bladder problems. Roots are also used in treating urinary complaints and piles. The juice of fresh leaves is useful as diuretic and laxative. Pungency in radish is due to volatile isothiocyanates while pink colour is due to pigment anthocyanin.

Radish is a good source of vitamin C containing 15-40 mg per 100g of edible portion. Roots also contain proteins, fat, minerals, fibre and carbohydrates, besides trace elements like aluminium, barium, lithium, manganese, silicon, titanium, fluorine and iodine. Pink skinned radish is generally richer in vitamin C than the white skinned type. Radish contains glucose as the major sugar and also contains fructose and sucrose in smaller quantities. Pectin and pentosans are also reported to be present. The leaves are good source of extraction of protein on a commercial scale and seeds are potential source for non-drying fatty oil suitable for soap making, illuminating and for the edible purposes.

Introduction

Peas (Pisum sativum L., 2n = 2x =14) are consumed as fresh vegetables or dry seeds throughout the world. In India, peas are grown as winter vegetable in plains and as summer vegetable in the hills. As field pea, it occupies about 0.45 m ha area in India, accounting for only about 2% of the total pulse area. About 90% of its area and production is limited to Uttar Pradesh alone. The area under vegetable peas is on increase. The acreage of vegetable pea in India is 2.72 lakhs ha with a productivity of 9.9 tons/ha. Pea is a rich source of protein (7.2% in green pea & 20 % in dry pea) and minerals (0.8%).

The geographical region comprising of Central Asia, the Near East, Abyssinia and the Mediterranean is considered as centre of origin based on genetic diversity. According to Blixt (1970), the Mediterranean is the primary center of diversity with secondary centers in Ethiopia and the Near East.

Garden pea, seeds have been observed in archeological excavations of Mohan Jodaro and Harappa, there are distinct hot weather tolerant and round-seeded varieties which carry high resistance to fusarium wilt and powdery mildew (Erysiphe polygoni). These varieties have a different use as a pulse crop for meeting protein requirements of common people. These are considered as intermediate stages of domestication of the present day vegetable (garden) pea, which is sweet and wrinkled-seeded. In fact, the quick spread of Arkel variety, an introduction from England in seventies, has displaced some of the native round-seeded varieties like Asauji, Hara Bonia, Hoshiarpuri, Kaparkheda, Kalanagni, Lucknow Bonia etc. there is need to conserve these valuable germplasm, before they are swept away by genetic erosion.

Introduction

Potato is a wonder crop that can be grown under diverse range of agro-climatic conditions. Short duration; high yield per unit area and time and wide flexibility in planting and harvesting time are important virtues of potato that enable its inclusion in intensive cropping systems.

Potato is not an Indian crop but is a native of high Andean region of South America. It was introduced in India perhaps in 16^th or early 17^th century by either the Portuguese traders or the British missionaries. The present day cultivated potatoes (tetraploid, 2n=4x=48) in most of the world represent Solanum tuberosum spp. tuberosum and S. tuberosum spp. andigena, although it’s numerous diploid (2n=2x=24) relatives are still under cultivation in and around its primary and secondary centers of origin in South America (Pandey and Sarkar, 2005). The great Irish famine in the 19^th century, caused by late blight disease, nearly wiped out all the earliest potato introductions in the Europe and dramatically changed the potato cultivation and production scenario in rest of the world.

Unlike in European Countries 80% of the potato is grown in India under short day conditions as a short duration crop i.e. 70-90 days. The tubers are exposed to high temperatures during planting (September-October) and harvesting (February-May). The crop is irrigated and suffers mid day water stress. The potato varieties introduced from Europe were unsuitable for growing under the above conditions. Systematic potato research in India spanned over the last half-a-century of the 20^th century in the past millennium. The Central Potato Research Institute (CPRI), which was established in 1949, has bean mainly responsible for tremendous growth of potato production in the country. The indigenous technological advances made it possible to extend potato cultivation in almost all part of the country. Now in India, compared to the production, area and yield of potato in 1949-50, the increase over the same period was 1513%, 559% and 270% respectively (Naik and Thakur, 2007). According to the FAO, potato production worldwide stands at 329 million tones and covers more then 19 million ha.

The Cucurbitaceae family is characterized by long training viny stems. There is variation for flower size and colour among the species but all of them have similar general morphology. The species are open pollinated and self compatible. Most of them are either monoecious (eg. Cucurbita spp.) Or andromonoecious (e.g. common in melon). Other species show gynomonoecy, androgynomonoecy, androecy, gynoecy, hermaphrodite or dioecy. Chow-chow is the only member of the Cucurbitaceae that is viviparous, contains single seed and propagated by planting whole fruit. The Indian gene centre has rich diversity in genetic resources of ridgegourd (Luffa acutangula), bottlegourd (Lagenaria siceraria), bittergourd (Momordica charantia), ashgourd (Benincasa hispida), snakegourd (Trichosanthes anguina), pointed gourd- parval (Trichosanthes dioica), pumpkin (Cucurbita spp.) and roundgourd (Praecitrullus vulgaris). Cucurbits are of tremendous economic importance and are cultivated throughout the world from tropical to sub-temperate zones. China, Turkey, India and Iran are important cucurbit growing countries. In India, this diversity is concentrated in Indo-Gangatic plains, north eastern region, north western Himalayas, the Western and Eastern Ghats and sporadically in the tribal dominant belts of central India.  More diversity occurs in Cucurbita spp. in the north east as also for ashgourd, bottlegourd while for Luffa, it is more concentrated in the eastern peninsular tract.

Plant genetic resource (PGR) is fundamental to crop improvement programme and key to establish future food and nutritional security. In recent times there is a worldwide awakening about the conservation of natural resources viz., land, water and plant genetic resources for the sustainable development of mankind. With the increasing risk from the events like climatic change, natural resource degradation,habitat destruction and environmental pollution etc, now there is an worldwide  debate asking many questions - where the humanity is heading in the this 21st century? Whether the present form of indiscriminate growth pattern is sustainable over a long run?

INTRODUCTION

Potato belongs to a genetically diverse genus Solanum having nearly 235 tuber bearing species. These speciesform a polyploid series ranging from diploids (2n=2x=24)tohexaploids (2n=2x=72), with12 asthebasic chromosome number. There is also arichdiversity within the cultivatedspecies of potato and they were initially grouped under six different species. Later studies, however, recognized those species as land race populations of S. tuberosum, with the eight groups: Ajanhuiri, Andigenum, Chaucha, Chilotanum, Curtilobum, Juzepczukii,Phurejaand Stenotomum(Spooner & Salas, 2006). Thisrich genetic diversity of the species is available in the Andean mountain where potato originated. In India,however, it was quite natural that genetic variability within the locally available material will be meager since, it was introduced here only about 400 years ago. On the contrary, more than 500 differentvarieties existed in India by 1940. This paradoxical situation was primarily due to assigning different local names toasingle variety in different parts ofthe country. The available local varieties in India consisted of both early introductions belonging to either pure Solanum tuberosum ssp. andigenum or their hybrids with S. tuberosumssp.tuberosumas well as later European introductions belonging to S. tuberosum ssp. tuberosum.