Cloning and expression analysis of rice genes Essay
Rice is the major basic nutrient of about one half of the universe ‘s population, and contributes over 20 % of the entire thermal consumption of worlds ( Bhattacharjee et al. , 2002 ) . It is the most of import cereal grain nutrient for big portion of human population particularly in East and South Asia, the in-between East, Latin America and the West Indies. Bing the 2nd highest in footings of production after maize worldwide, rice is providing 20 % of the day-to-day Calories of the entire universe population ( World Rice Statistics, hypertext transfer protocol: //www.irri.org ; FAOSTAT, hypertext transfer protocol: //apps.fao.org ) .
Rice is the most of import nutrient harvest of Nepal. It is grown in a diverse environment runing from low fields holding tropical clime to the sub-temperate clime of the mountain part at highest lift ( 3050 masl ) . Nepal has been considered as one of the beginning centre of rice. In Nepal, rice turning country is 1440 1000 hour angle with the productiveness of 2.56 t/ha. It contributes about 20 per cent to the agricultural gross domestic merchandise and provides more than 50 per centum of the entire calorie demand of the Nepali people ( hypertext transfer protocol: //www.narc.org.np/rice_knowledge_bank/index.php ) .
Rice, as many other nutrient harvests, is a monocotyledonous harvest and can be successfully grown in different environmental conditions such as irrigated or rain-fed low land, deep H2O, coastal moisture land and even on highland under dry status. It is the fact that rice is being cultivated in all continents of this universe except in the utmost northern and southern parts which are ever covered by snow. Rice can be cultured in a assorted cropping form which helps to promote biodiversity. Rice in wet land is a good illustration of place of biodiversity as many sorts of tellurian and aquatic beings like fishes, toads, snails, insects and other assorted aquatic animate beings habitat in rice ecosystem which in bend can be a good beginning of protein and fatty acid. Rice byproducts like rice straw, bran have become a major beginning of nutrient for our farm animal which in bend give economic benefits from the farm animal production. Rice is a besides a good shelter for good insects which are termed as natural enemies of several harmful insect plague in our agro-ecosystem, therefore salvaging environment by diminishing the usage of chemical pesticides for harmful pest direction. Even, herbivorous fishes in rice field provender on weeds of the rice harvests, commanding the harmful weeds to some extent in rice eco-system ( http: //www.academon.com/Essay-The-Importance-of-Rice/67607 ) .
As Arabidopsis, a dicotyledonous theoretical account works, recent progresss in molecular surveies in rice includes efficient cistron transmutation, development of extremely saturated molecular map, immense figure analysis of uttered sequence tickets ( ESTs ) . With genome size of 4.3 Mb, rice is a monocot cereal harvest which figure of analyzed complementary DNAs ( complementary DNA ) is about nearing the figure with Arabidopsis. Due to this ground, rice can be considered as Monocotyledonous theoretical account works in the present context ( Izawa and Shimamoto, 1996 ) . To analyze rice genome, around 14,000 molecular markers are already designed ( Kurata, 1994 ) and sequence information of more than 10,000 complementary DNA has been already registered in computerized informations base ( Sasaki, 1994 ) .
Plant diseases and insects ; alimentary lack ; mid and late season H2O emphasis ; H2O direction and weeds for direct seeded rice are considered as the major restraints in rice cultivation ( Kataki et al. 2001 ) . Rice is a good host of several works infective Fungis, bacterium, viruses and roundworms. Production of rice prior to reaping can be lost up to 50 % by insects ( 34 % ) , diseases ( 9.9 ) and weeds ( 10.8 % ) ( Cramer, 1976 ) . Soil borne diseases, particularly diseases caused by works parasitic roundworms ( PPNs ) , are major constrictions to harvest production and productiveness in the intensive cropping systems with high inputs such as the rice and wheat based cropping systems ( Sharma & A ; Rahaman 1998 ) . Sasser and Freckman ( 1987 ) estimated the approximative loss of rice production due to works parasitic nematodes up to 10 % . Among more than 35 genera and 130 species roundworms associated with rice ( Gerber et al. , 1987 ) , rice root roundworm, Hrishmaniella oryzae, has been proved one of the most detrimental works parasitic roundworms in all rice turning zones of the universe. This roundworm has broad scope of major harvests as its host such as rice, cotton, sugar cane and corn and has high harm degree in comparatively lower population densenesss ( Southey, 1972 ) . Hirschmaniella spp. , particularly H. oryzae, is ubiquitous in afloat rice eco-system. They cause important harm in rice and their proper direction during rice cultivation gives important output addition. As irrigated rice covers about 72 % of entire rice production, H. oryzae, being prevailing in afloat status and besides being abundant in rainfed lowland and deep H2O rice eco-system, is proved to be the rice parasitic roundworm holding greatest potency on economic impact ( Prot and Rahaman, 1994 ) . Hirschmanniella spp. do non bring forth specific aboveground symptoms. They can do yellowing of the works, decrease of tillers figure, and cause hold in blooming. Fortuner ( 1974 ) found that H. oryzae can cut down output by 23 % when adequate fertilisers are applied and by 42 % when there is no fertilizer application under experimental secret plan status.
Naturally, workss have elaborate defence mechanisms to protect themselves from many sorts of pathogens, including Fungis, bacteriums, viruses, insects and roundworms. Defense responses following the gene-for-gene hypothesis are triggered in workss when the works opposition ( R ) cistron recognizes, straight or indirectly, a specific pathogen effecter molecule frequently governed by a pathogen avirulence ( avr ) cistron ( Jones and Dangl, 2006 ) . If any of the members of this cistron brace is inactivated and become absent, it consequences in susceptibleness of the host to the pathogen. Till day of the month more than 40 R cistrons have been isolated from several works species, and most of them exhibit extremely conserved constructions, despite differences between the types of pathogens that are recognized ( Takahashi et al. , 2010 ) .
Expression analysis of rice cistrons under Hirschmaneilla oryzae infection has non been done much boulder clay day of the month. Green et Al. ( 2002 ) worked on analysis of look form of Arabidopsis thaliana tubulin-1 and Zea mays ubiqutin-1 boosters in rice workss in association with the infection of highland rice root roundworms Meloidogyne incognita and Pratylenchus zeae and found that UBI-1 booster was active at noticeable degree in most of the root system throughout the growing period of 10 months where 90 % of the root tips showed GUS staining throughout the clip class. Whereas, TUB-1 booster used for this survey showed lower overall activity in the root system giving 11 % decrease in each hebdomad in the proportion of chief root stained. Changes in cistron look correlated with lesion or defence responses have been observed in several plant-nematode interactions particularly with root knot roundworms ( Gheysen and Fenoll, 2002 ) . General ( nonspecific ) works defence cistrons in tomato works are upregulated merely after12 H of vaccination of tomato roots with root-knot roundworms ( Williamson et al. , 1994 ; Williamson and Hussey, 1996 ) . Activated defence cistrons include peroxidase, chitinase, lipoxygenase, extensin, and protease inhibitors.
We have late found some cistrons of rice which are suspected to be up-regulated or down-regulated under infection of Hirschmaneilla oryzae. Therefore the chief aim of this research to
to see the look form ( up-regulation or down-regulation ) of certain rice cistrons under Hirschmaniella oryzae infection
Rice ( Oryza sativa L. )
Rice is a monocotyledonous harvest works falling in the angiosperm division. The genus of rice, Oryza, contains more than 20 species, out of which merely two species are cultivated rice, i.e. Oryza sativa, ( Watanabe, 1997 ) particularly cultivated in South-east Asiatic states and Japan, and Oryza glaberrima cultivated in West Africa. Rice was originally cultivated in tropical Asiatic part, since 5000 old ages BC harmonizing to oldest cultivation record, which afterwards extended to temperate parts besides ( Watanabe, 1997 ) . Rice is the most of import basic nutrient in Asia. More than 90 % of the entire universe ‘s rice is produced and consumed itself in Asiatic part, the part which holds 60 % of the entire universe ‘s population. 35-60 % of the thermal demand of three billion Asians is supplied by rice ( Guyer et al. , 1998 ) . Bouman et Al. ( 2006 ) reported rice ( Oryza sativa ) to be cultivated in approximately 150 million hour angle of land worldwide with the mean output of approximately 3 to 4 dozenss ha-1 ( Padgham et al. , 2004 ) .
2.1.1 Taxonomy and Molecular evolution
The well known rice genus “ Oryza ” consists of 22 wild and 2 cultivated species, one of which is Asiatic rice ( O. sativa ) and the another is African rice ( O. glaberrima ) ( Semagn et al. , 2007 ) .
The genus Oryzae belongs to tribe Oryzeae and household Poaceae ( hypertext transfer protocol: //www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi ) . Hierarchically, Oryza sativa falls in division Angiosperm, category Monocotyledoneae, order Glumiflorae and household Graminae ( Nguyen and Tran, 2000 ) . Terminology of the species which are closely related to O. sativa have created confusion among rice taxonomers, as they are morphologically really similar and it is hard to happen distingushible morphological character ( Vaughan and Morishima, 2003 ) . Time to clip, more than hundred names have been proposed for Oryza species including 19 names for Oryza sativa ( Oka, 1988 ; Lu, 2004 ) . A new terminology has been proposed by Vaugan et Al. ( 2003 ) for cultivated and wild rice in Asia: O. sativa sensu lacto subspp. indica and japonica and O. rufipogan sensu lacto subspp. nivara ( one-year ) and rufipogon ( perennial ) .
Figure 1: ML evolution of Oryzeae inferred from the concatenated 20 chloroplast fragments under the TVM+I+G theoretical account. MP and BI illations generated the same topology. Numbers near subdivisions are bootstrap per centums of ML and MP, severally. The subdivisions without Numberss indicate 100 % bootstrap supports. Stars indicate three consecutive short inside subdivisions in clade II ( beginning: Tang et al. , 2010 )
2.1.2 History: Beginning, domestication and dispersion
The genus Oryza, to which our cultivated rice belongs, is thought to be originated in the super-continent Gondwanaland around 130 million old ages ago as a wild grass. During the geographical impetus the ace continent was broken to organize Asia, Africa, America and Australia and Oryzae species likely spread as wild grass thorough out these drifted continents ( Chang, 1976 ) . Within harvest workss, Asian rice, O. sativa and the African rice O. Glaberrima are thought to be an illustration of parallel development. As shown in figure 2, the Asiatic common wild rice, O. rufipogon is the wild primogenitor of O. sativa and it shows a scope of fluctuation from perennial to one-year types. Annual types such as O. nivara, were domesticated and later became O. sativa. In a parallel evolutionary way, O. glaberrima was domesticated for one-year O. breviligulata which in bend evolved from perennial O. longistaminata ( Khush, 1997 ) .
Figure 2: Evolutionary tract of 2 cultivated rice species ( beginning: Khush, 1997 )
Harmonizing to Porteres ( 1956 ) , the African cultivar, O. glaberrima, was originated in Niger river delta. The boggy basin of the upper Niger river is considered as the primary centre of diverseness for O. glaberrima and there are two secondary centres for the same species to the sou’-west near the Guinean Coast. The primary centre was thought to be formed around 1500 BC, while the secondary centres were formed 500 old ages subsequently.
Probably, the domestication of wild rices has been started since 9000 old ages ago. during Neothermal age about 10 000-15 000 old ages ago, natural development of one-year rice species at different lifts in East India, Northern Southeast Asia and West China occurred due to mutable climatic factors like jumping periods of drouth and fluctuations in temperature ( Whyte, 1972 ) . Domestication in Asia could hold occurred independently and at the same time widening from the fields below the eastern foothills of the Himalayas in India towards upper Myanmar, Northern Thailand, Laos and Vietnam, to South China ( Chang, 1976 ; Ramiah, 1937 ; Roschevitz, 1931 ) . In this Asiatic discharge, rice was grown as a signifier of switching cultivation by uncluttering the forest countries. The harvest was likely grown by direct seeding and without standing H2O. China was the first state which started the procedure of dirt puddling and transplantation seedlings, the system which made rice go genuinely domesticated. In Southeast Asia, in the early period, rice used to be produced under dryland conditions in the highlands and it is recent record that the people started cultivating in lowland, therefore, covering huge river deltas. Linguistic grounds besides provide sensible cogent evidence that the early beginning of cultivated rice in this Asiatic discharge. In several regional linguistic communications, the general footings for rice and nutrient or for rice and agribusiness are synonymous which shows that the construct of agribusiness originated as the domestication of rice started. At the really beginning, Welhelm G. Solheim II in 1966 discovered the most convincing archaeological grounds for domestication of rice in Southeast Asia ( Solheim, 1972 ) . 14C and thermoluminescence trial of the imprints of grain and chaff discovered in clayware shards grain and chaffs of O. sativa at Non Nok Tha in the Korat country of Thailand gave the dating to at least 4000 B.C older prints. Ancient India is one of the oldest parts for the cultivation of O. sativa. The oldest grain samples of rice excavated at Mohenjodaro now in Pakistan ( before in India ) day of the month back to about 2500 B.C. ( Andrus and Mohammed, 1958 ) . Sharma and Manda ( 1980 ) reported that the oldest carbonized grains found in India day of the month back to about 6750 B.C. Harmonizing to Chang ( 1976 ) , the oldest remains of cultivated rice day of the month back to 500 BC whereas carbonized rice grains found in Tongxieng County of Zhejiang state were identified as 7040 old ages old. Similarly, the 2nd oldest of 6960 old ages old was obtained from Hemdu relic in Yuyao county of the same state.
The dispersion of rice from the Himalayan pes hills of ancient India began towards Western and Northern plain part of India, Afghanistan, Iran and Sri Lanka. It has been known that the rice was major nutrient harvest in Srilanka every bit long as 1000 BC. In Greece and adjacent states of the Mediterranean, rice was introduced by members of Alexander the Great when they were returning to India in 324 BC. However, in Europe rice was established much later than the 15th or 16th century. From India rice besides spread to Madagascar and East Africa and so to states of West Africa ( Khush, 1997 ) . Evidence shows that O. rufipogon was dispersed from Pakistan to China and Indonesia ( Oka, 1988 ) .
Japonica rice, which is domesticated as tropical Japonica in the northern portion of Southeast Asia and South China besides being cultivated as temperate japonica as it, subsequently, moved towards Korea from China and from Korea to Japan at the beginning of the first century. Both indica and japonica were transferred to Malaysia, Indonesia and Philippines from mainland Southeast Asia. Afterwards they were distributed from the Philippines to Taiwan. Tropical japonica was introduced by migrating Malayans to Madagascar from Indonesia during the 5th or sixth century. At the same clip, it besides migrated to West African states from Indonesia through the Lusitanian priests. Due to this ground, all of the highland assortments in West African states are tropical japonica. The Portuguese besides brought the tropical japonica and indica to Brazil while Spanish people were the one to transport them to the other Latin American states. That ‘s why, in Latin American states, all of the cultivated highland assortments are tropical japonica and lowland assortments are indica rice. In USA, the first record of rice is from 1685, and it was likely introduced from Madagascar while slaves were imported by USA from that country. ( Khush, 1997 ) .
2.1.3 Importance of rice
22.214.171.124 Dietary supply
Figure 3: Share of rice of entire Calories consumed ( beginnings: FAO and World Bank, 2010 )
Rice is said to be staple nutrient of universe ‘s hapless. Rice is the most of import nutrient harvest of the underdeveloped universe and a staple nutrient of the half of the universe ‘s population. More than 3.5 billion people throughout the universe depend on rice for more than 20 % of their day-to-day Calorie demand. In many Asian states, per capita ingestion of rice can be higher than 100 kilograms per annum. For about 520 million Asian people, most of which are really hapless, rice provides more than 50 % of their Calorie demand. In sub-Saharan Africa, the people, before a decennary, seldom ate rice, but these yearss, they have started devouring rice daily and per capita ingestion has doubled since 1970 to 27 % . Average per capita ingestion of rice in South America is 45 kilogram and more than 70 kilogram has been reached in Caribbean ( hypertext transfer protocol: //www.cgiarfund.org/cgiarfund/sites/cgiarfund.org/files/Documents/PDF/fc3_GRiSP % 20proposal_rev3 % 20Sept % 2016.pdf ) .
126.96.36.199 Production and economic importance
China was the highest rice manufacturer in 2007 with the production of 186454,000 dozenss which was 29.29 % of the entire universe rice production and India was in the 2nd place with the production of 143534,000 dozenss. Indonesia and Bangladesh were 3rd and the 4th highest manufacturers, bring forthing 55039,000 and 42904,000 dozenss severally followed by Vietnam, Thailand, Myanmar and Philippines, ( WRS, 2009 ) . Harmonizing to USDA ( 2009 ) study, China, India, Indonesia and Bangladesh produce two-third of the planetary rice production. Rice is besides produced in North & A ; South America and Africa but in really less measure compared to Asiatic states.
In planetary market, merely 4 % of the entire rice produced is traded worldwide. Thailand is the top most exporter of rice trading 6 to 7 million ton yearly followed by US which export about 40 % of its entire rice production yearly. Major importers of rice are Iran, Iraq and Saudi Arabia followed by Bangladesh, Cote D ‘ Ivoire, North and South Korea, Mexico, Nigeria and Senegal. In Africa, the demand of rice each twelvemonth is increasing by 2 % and the people here consume 25 % of the sum imported rice globally ( Khush, 1997 ) .
188.8.131.52 Importance in molecular surveies
Rice can be a good theoretical account among monocot workss as its complete genome sequence is already known ( IRGSP, 2005 ) . Now, the obtained complete genome sequences of both japonica and indica rice ( Phillips et al. , 2007 ) facilitates the survey sing cistron look, cistron fundamental law and genomic construction. This high-quality map-based sequence is now available worldwide in several public databases, such as GenBank, DDBJ and EMBL ( Vij et al. , 2006 ) . The genome size of rice is comparatively little ( 420 Mb ) compared to other known species, such as wheat ( 1500 Mb ) which favors rice to be more preferable in the works research community as it is much easier to do faster progresss with relatively little genome ( Paterson et al. , 2005 ) .
Besides genome sequences, a batch of ESTs have been sequenced and presently more than 250 1000s rice ESTs are available in REDB ( Rice EST DataBase ) ( hypertext transfer protocol: //redb.ncpgr.cn ) . Harmonizing to Kikuchi et Al. ( 2003 ) , over 28000 full length complementary DNA ringers from japonica rice are available in Gene Bank. Harmonizing to Hiei & A ; Komari ( 2006 ) , Agrobacterium-mediated transmutation can be performed expeditiously in rice which besides adds more importance in rice as a liliopsid theoretical account works for the field of molecular biotechnology.
2.1.4 Rice ecology
Rice has adapted itself in broad scope of climatic status, which is being cultivated from the hot comeuppances of Australia and Egypt, to the cool Himalayan foothills of Nepal ( Bhagat, 2003 ) .
Harmonizing to Rutger ( 1981 ) , for the rice works to turn optimally, it requires pH of 5.0-7.5, although it can digest a pH of 4.3-8.7 ( Duke 1973 ) . Coronel ( 1980 ) did non happen any inauspicious consequence of acidic dirt with pH of 3.5-5.0 on rice root growing in a alimentary civilization survey in the Philippines. As most of the rice workss are rainfed type, and they are cultivated during the moisture season so that the necessity of H2O is fulfilled of course. If cultivated during dry season, this rice need patronize irrigation, otherwise. In the Torrid Zones, monsoon dependent rice cultivation in predominating due to the scarceness of irrigation H2O ( Datta, 1981 ) . Harmonizing to Quayyum and Vergara ( 1993 ) , comparative humidness of 80 % is best for rice during seedling phase. Temperature has important consequence on the growing and development of the rice works. The mean temperature for the rice works ranges between 21A°C to 37A°C ( AIC, 1996 ) .
2.1.5 Rice by H2O direction
Rice can be successfully grown in diverse H2O environments from aerophilic highland rice to deep H2O rice. Types of rice harmonizing to H2O direction can be grouped as irrigated rice, highland rice, rain Federals lowland rice, deepwater rice, tidal wetland rice, and aerophilic rice. Water tabular array in lowland irrigated rice is by and large maintained at 5-10 centimeter of deepness while in rain fed Lowlandss and uplands status, the rice field is flooded by rain at least for a portion of the cropping season to H2O deepnesss that exceed even 100 centimeter for some yearss. For both irrigated and rain Federal lowland, rice seedlings are prepared in baby’s room bed and so the seedlings are transplanted in puddled field. Deepwater rice assortments can defy the submersed status of more than 50 centimeter of H2O tabular array for at least a month ( Catling, 1992 ) . Rice can be grown in submersed conditions as it contains aerenchymatous cells ( internal air channels ) which can stretch quickly when partly covered by floodwater. This biological character of rice enables them to turn above the inundation Waterss avoiding drowning ( Kende et al. , 1998 ) . Aerobic rice cultivation refers to the new system of rice cultivation done in the nonflooded and unsaturated aerophilic dirt environment similar as the wheat and maize cultivation ( Bouman et al. 2006 ) . Under this system, potentially high giving up assortments are dry seeded in the Fieldss and limited auxiliary irrigation is provided when harmonizing to the necessity.
2.1.6 Progresss in rice thru genteelness and molecular biotechnology
Vitamin A lack is one of the major results of malnutrition. Worldwide, about 100 to 140 million kids are vitamin A-deficient and an estimated 250 to 500 thousand vitamin A-deficient kids become blind every twelvemonth. Though rice is an of import beginning of nutrient energy and Calories for 50 % of the entire universe population preponderantly in developing states, polished rice is lacking in many indispensable micronutrients like Fe, Zn, vitamin E and vitamin A ( Vasconcelos et al. , 2003 and Tan et al. , 2005 ) . This could be one of the chief grounds for high prevalence of vitamin A lack ( VAD ) in developing states. Though rice workss possess carotenoids in photosynthetic tissues, carotenoids deficiencies in the comestible portion of rice, endosperm. Genes responsible for two cardinal enzymes in b-carotene ( provitamin A ) biogenesis tract, phytoene synthase ( psy ) and phytoene desaturase ( crtI ) were isolated and characterized from Narcissus pseudonarcissus ( Narcissus pseudonarcissus ) and the works infective bacteriums ( Erwinia uredovora ) severally ( Misawa et al. , 1990 ; Misawa et al. , 1993 ) . Ye et Al. in 2000 successfully demontrated familial technology of the metabolic tract for biogenesis of b-carotene ( 1.6 mg/g entire carotenoids ) in the endosperm of japonica-type rice cultivar. Subsequently, the success was made in indica-type cultivated rice cultivars excessively ( Datta et al. , 2003 ; Hoa et al. , 2003 ) . After this accomplishment, the construct of familial engineering-based nutritionary sweetening of rice began with the high outlook to lend to a sustained decrease of vitamin A lack ( VAD ) in developing states. Recently scientists are farther seeking to increase the entire carotenoids content and besides to add other lacking micro-nutrients like Fe and Zn.
After the development of transgenic workss, consumers and conservationists have arose issue over the usage of antibiotic selectable marker cistron for development of transgenic workss, although strong grounds against the antibiotic markers have non been found yet. Sing the populace concern, Datta et Al. ( 2006 ) have developed transgenic rice utilizing a nonantibiotic positechTM choice system with phosphomannose isomerase ( pmi ) as an option to antibiotic opposition or weedkiller tolerance marker system for choice. They have introduced two cardinal cistrons, psy and crtI, of carotenogenic tract in two indica-type rice cultivars, BR29 ( a popular high-yielding assortment of Bangladesh ) and IR64 ( of import IRRI-bred line popularly grown in Asia ) , efficaciously to synthesise b-carotene in the mark endosperm tissue.
Lucca et Al. ( 2006 ) reported that successes in increasing Fe root soaking up by transgenic attacks improved the workss ‘ ability to get by with iron-deficient conditions but there are no grounds reported till now for increased micronutrient content in the comestible portion. Therefore, uniting high Fe traits or rice with aureate rice could take to a extremely effectual, inexpensive and simple part to the alleviation of major wellness jobs. Researches for uniting high Fe and Zinc rice with Golden rice is in advancement which can be a great accomplishment in battling the malnutrition jobs at greater degrees ( Khalekuzzaman et al. , 2006 ) .
Aromatic rice has been of great economic value these yearss. The biochemical footing of olfactory property was identified as 2-acetyl-l-pyrroline. The compound is found to be present in natural grain every bit good as in works. In add-on to 2-acetyl-l-pyrroline, there are about 100 other volatile compounds which include 13 hydrocarbons, 14 acids, 13 intoxicants, 16 aldehydes, 14 ketones, 8 esters, 5 phenols and some other compounds, which are associated with the olfactory property development in rice ( Singh et al. , 2000 ) . Several assortments of Basmati lines have been developed as aromatic rice by utilizing assorted biotechnological tools. In Basmati rices, familial transmutation was obtained utilizing Agrobacterium, electroporation and protoplast transmutation systems ( Chowdhury et al. , 1997 ) . Burikam and Attathom ( 1997 ) used atom barrage mediated transmutation system to reassign I”1pyrroline-karboxylate synthetase ( P5CS ) cistron in rice curriculum vitae. KDML-105. Inez et Al. ( 1997 ) used Agrobacterium tumifaciens incorporating a various binary vector ( pCAMBIA 1301 ) to develop aromatic rice curriculum vitae. Rajalele. Some selectable marker and newsman cistrons used were bur, npt II/hpt II and GUS. Several of import cistrons like chitinase, Bt, bacterial blight opposition ( Xa-21 ) , rice tungro opposition ( RTBV CP cistron, RTSV polymerase in sense and antisense orientation ) , drought tolerance ( P5CS ) and submerged tolerance ( adh and pdc ) have been introduced into non-aromatic and aromatic rices ( Abrigo and Datta 1996 ; Burikam and Attathom, 1997 ; Datta et al. , 1997 ; Fauquet et al. , 1997 ; Gill et al. , 1997 ; Li et al. , 1997 ) .
Africa Rice Center ( WARDA ) has developed a new rice assortment particularly for African continent naming NERICA which is an acronym for New Rice for Africa. The scope of NERICA assortments were developed from a cross between an highland O. sativa tropical japonica assortment, WAB 56-104, as the receiver parent, and an O. glaberrima assortment, CG14, as the giver parent ( ) .The most popular NERICA assortments have obtained the best traits of both parents: high output, which could be derived from the O. sativa parent and the ability to turn good in rough environments from the O. glaberrima parent ( Jones et al. , 1997 ; www.warda.org ) . The NERICA assortments are hoped for high part in bettering the productiveness, profitableness, and sustainability of rice farming in sub-Sahara Africa.
The job of H2O scarceness in the productiveness of Asia ‘s irrigated rice systems is increasing twelvemonth by twelvemonth. It has been estimated that 2 million hour angle of Asia ‘s irrigated dry-season rice and 13 million hour angle of its irrigated wet-season rice may see ”physical H2O scarceness ” by 2025, and most of the irrigated dry-season rice bring forthing land out of 22 million hour angle in South and Southeast Asia may endure ”economic H2O scarceness ” ( Tuong and Bouman, 2003 ) . To extenuate this job, scientists are developing aerophilic rice cultivars with high output capacity which can be cultivated like an irrigated highland harvest, such as wheat or corn. It is possible to accomplish high outputs under irrigated but aerophilic dirt conditions by bring forthing new assortments of ”aerobic rice ” that combine the drought-resistant features of highland assortments with the high-yielding features of lowland assortments ( Lafitte et al. , 2002 ) . Some successes have been achieved in China, where breeders have produced aerophilic rice assortments with the productiveness of 6-7 T ha-1 which are now being intensively cultivated by husbandmans on some 190,000 hour angles, in irrigated Lowlandss where H2O is scarce and in favourable rainfed highlands ( Wang Huaqi et al. , 2002 ) .
2.1.7 Biotic restraints in rice
The major biotic factors impacting rice outputs are insect plagues, diseases, and roundworms. Rice root bore bit is one of the major plagues of rice and found to be more destructive in tropical parts of Asia, the Mediterranean parts and the Middle East. Brown works hopper ( BPH ) , which is besides virus sender, leaf roller, army worms, rice ear cutting caterpillar and rice bug are other destructive insect plagues of rice works. Rats, as a gnawer, are besides major jobs in rice production ( IRRI, 2009 ) . Rice has been attacked by more than 70 diseases caused by Fungis, bacteriums, virus and roundworms ( Ou, 1985 ) . Each twelvemonth, immense sum of rice production is being destroyed fungal diseases which would otherwise be sufficient to feed 60 million people ( Barman and Chattoo, 2005 ) . ) . Rice blast caused by Magnaporthe grisea, sheath blight caused by Rhizoctonia solani and brown topographic point caused by Bipolaris oryzae are the three major fungous diseases of rice. Rice sheath blight disease ( Rhizoctonia solani ) occurs throughout the rice-growing countries in semitropical, tropical and temperate states due to its wider host scope and adaptative capableness. Normally, this disease causes 20-25 % output decrease but can do 50 % output loss in instance of susceptible cultivars. Output losingss of 50 to 85 % , in rice, due to blare pathogen Magnaporthe grisea has been recorded in the Philippines which can do even upto 100 % output losingss under favourable environment ( IRRI, 2009 ) . Bipolaris oryzae, the causal microorganism of Brown topographic point disease in rice is cosmopolition and is found in all rice-growing states worldwide including Asia, Africa and America. This disease can do a loss of 50 % to 90 % of rice production. Bakanae ( Gibberella fujikuroi ) is another widely distributed fungous disease in all rice turning countries and affects both highland and lowland rice doing up to 20 % output loss ( IRRI, 2009 ) . Among bacterial diseases associated with rice, bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae, and bacterial foliage run caused by Xanthomonas oryzae pv. oryzicola, are the most of import 1s ( Datta, 1981 ) . Ou ( 1985 ) reported the output loss of 20-50 % by bacterial blight while Wang et Al. ( 2007 ) reported that bacterial foliage run may do 30 % of output loss in rice. Tungro, grassy stunt and xanthous midget are the most of import viral diseases ( Datta, 1981 ) . More than 35 genera and 130 species roundworms associated with rice ( Gerber et al. , 1987 ) .
2.1.8 Nematode jobs in different rice eco-system
Plant parasitic roundworms are microscopic concealed worms assailing many economically of import harvest workss which can be a major restraint to obtain high outputs of rice. They are frequently unnoticed as most of them are root parasitic. Except a foliar roundworm Aphelenchoides besseyi, the “ white tip ” roundworm that occurs in most rice environments ( Bridge et al. , 1990 ) , the rice works parasitic roundworms are non homogenous across all rice ecosystems. Output losingss due to A. besseyi scope from 0 to 70 % and vary with assortment, twelvemonth, and state ( Port and Rahaman, 1994 ) . Meloidogyne spp. and Pratylenchus spp. are the major rice parasitic roundworms in highland. M. incognita, M. javanica, and M. arenaria occur in most of the highland rice-growing countries in Africa ( Luc and de Guiran,1960 ; Babatola, 1980 ; Fortuner, 1981 ) and South America ( Bridge et al. , 1990 ) . Output losingss of 16-32 % were reported with M. graininicola in India ( Biswas and Rao 1971, Rao and Biswas 1973 ) . Pratylenchus indicus and P. zeae are two major root lesion roundworms found in highland rice ecosystem ( Bridge et al. , 1990 ) . In an experiment, important output losingss ( 34 % ) have been observed with P. indicus under low initial figure ( 30 per seedling ) of roundworms ( Prasad and Rao, 1978 ) . 7 species of genus Hirschmaniella viz. H. belli, H. gracilis, H. imamuri, H. mexicana, H. mucronata, H. oryzae, and H. spinicaudata ( Bridge et al. , 1990 ) harm rice works among which H. oryzae is the most prevalent one in afloat rice ecosystem ( Prot et al. , 1994 ; CUC and Prot, 1992 ) . Beside, A. besseyi, few roundworms like Meloidogyne graminicola and Ditylenchus angustus can do harm to rice works in deep H2O rice ecosystem. D. angustus, is the causal agent of ufra disease in Bangladesh, India, Myanmar, and Vietnam ( Ou, 1985 ) which can do few to 100 % output loss in rice.
2.2 Rice root roundworm: Hirschmaniella oryzae
About half, out of 24 known species of Hrishmaniella, are parasitic to rice and worldwide, worldwide and H. oryzae is the most normally found plant-parasitic roundworm on irrigated rice particularly in countries where rice has been cultivated, for a long, with uninterrupted irrigation installation and when the workss are grown under invariably flooded status ( Bridge et al. , 2005 ) . H. oryzae can accommodate really expeditiously to the changeless afloat conditions in which irrigated rice is frequently being grown in the Lowlandss ( Fortuner & A ; Merny, 1979 ) . It is one of the few plant-parasitic roundworm species that can easy last under anaerobiotic conditions ( Babatola, 1981 ) .
2.2.1 Systematic place of Hirschmaniella oryzae
Speciess: Hirschmanniella oryzae
( Beginning: Duncan & A ; Moens, 2006 )
2.2.3 Morphology of H. oryzae
The species was described by de Man ( 1880 ) from a moist hayfield at Wassenaar near Den Haag, The Netherlands. More elaborate informations on morphological characters of this species were peculiarly given by Hirschmann ( 1955a, B ) , who based her observations on specimens collected in southern Germany. Sher ( 1968 ) provided a brief description from his surveies of specimens from the type vicinity, from a 2nd vicinity in The Netherlands, and from Texas, USA, and Brzeski ( 1998 ) added informations supplementing old descriptions.
Fig. 4 Hirschmanniella oryzae. ( A ) Whole female. ( B ) Female tail. ( C ) Female terminus.b ( D, E ) Variation in gubernaculum form. ( F ) Male anterior terminal. ( G ) Male tail ( after Sher, 1968 ) . ( Beginning: OEPP/EPPO Bulletin, 2009 )
Harmonizing to Bridge & A ; Starr ( 2007 ) , the size of this nematode varies from 1.1-4 millimeter and is slender in form with annulated, anteriorly flattened or hemispherical labial part which is uninterrupted with the organic structure contour. The stylet is strong with good developed basal boss and its length varies from 15-46 I?m. The oesophageal secretory organs are elongated and are ventrally overlapped with the bowel. Ebsary & A ; Anderson ( 1982 ) gave the description of venereal variety meats of both male and female of this species. Harmonizing to him, female genital system is didelphic with two equal good developed subdivisions and the vulva is present at mid-body. Tail of this roundworm is conoid or pointed with mucron. There is no sexual diamorphism in grownups. The male Bursa does non cover the whole length of the tail.
2.2.3 Life rhythm of H. oryzae
It is migratory endo-parasite of root, the larva and grownup of which ever enter roots from root tip, moves freely in the air channel between radial gill of the parenchyma and in older roots, may be found anyplace between the part of base and tip and sometimes even found in coleoptiles but non in the lower portion of the leaf sheath ( Buangsuwon et al. , 1971 ) . After few yearss of entry, female starts puting eggs which hatch within 4-5 yearss after being laid inside the root. Under favourable environmental status this roundworm can finish life rhythm in about 30 yearss ( Mathur and Prasad, 1974 ) . Karakas ( 2004 ) reported that the roundworm completes its life rhythm from L2 phase to following L2 phase in 33 yearss at 28a-¦C. Each phase of juveniles changed after sheding and sheding phases M2, M3 and M4 lasted for 2, 3 and 6 yearss severally to develop grownup male or female. Mode of reproduction for this roundworm is sexual ( Southey, 1972 ; Karakas, 2004 ) .
2.2.4 Symptoms in rice works on H. oryzae infection
Hirschmanniella spp. do non bring forth specific aboveground symptoms. Their infection in root may ensue in yellowing of the works, decrease of tiller figure, and hold in blooming. H. oryzae does non do specific symptoms in infested workss ( Kawashima and Fujinuma, 1965 )
Vander Vecht and Bergman ( Verma and Singh, 1989 ) observed the roundworm perforating into the roots of healthy rice workss, feeding on parenchymatous tissues and multiply in there which leads eventually to the stain of cerebral mantle. Decrease in entire sugar, lessening in aminoacids and release of phenols are some metabolic alterations that have been recorded in the rice workss infected by Hrishmaniella oryzae ( Rao et al. , 1986 ) . The figure of panicles ( Yamsonrat, 1967 ) and grain weight ( Venkitesan et al. , 1979 ) were affected in rice due to H. oryzae infection. In Japan, lessening in stooling induced by H. oryzae is more of import in dirts with low rhesus factor, ensuing in a disease called “ Akiochi ” and give losingss are more important in these dirts. ( Kawashima, 1964 ) . Infested seedlings undergo growing deceleration, tallness and weight of the works are decreased and, at the same clip, the Browning of the roots is higher at high initial densenesss ( Kawashima & A ; Fujinuma, 1965 ) . The same writers reported that, roundworms interfere with the physiology of the roots, diminishing their oxidizing capacity and bring oning their colour by Fe oxide. H. oryzae affected rice works by doing decreased tillering and root weight in India ( Mathur & A ; Prasad, 1972 ) . In the U.S.A. , this root parasitic roundworm caused decay of the tip of primary roots in the bed of the dirt with a high rhesus factor ( Hollis, 1967 ) . Hirschmanniella spp. stunted rice in Thailand ( Buangsuwon et al. , 1971 ) .
2.3 Rice transmutation system
Initially, protoplast transmutation with electroporation or PEG was the method of rice transmutation. Toriyama et Al. ( 1988 ) and Zhang and Wu ( 1988 ) recovered transgenic rice utilizing PEG. In the same twelvemonth, Zhang et Al. ( 1988 ) reported recovery of transgenic rice utilizing electroporation. Shimamoto et Al. ( 1989 ) and Datta et Al. ( 1990 ) were the first to retrieve fertile transgenic workss utilizing electroporation and PEG in japonica and indica rice, severally. Later this technique became less popular as it is clip devouring, arduous and extremely genotype-dependent. Somaclonal fluctuations, multi-copy integrating and regeneration of albino workss are other jobs related to this technique ( Tyagi and Mohanty, 2000 ) .
2.3.1 Particle gun mediated cistron bringing
Microprojectile barrage technique utilizing atom gun or biolistics was used successfully for transmutation in immature embryos of rice ( Christou et al. , 1991 ) . After Cao et Al. ( 1992 ) and Li et Al. ( 1993 ) farther improved this engineering ; this method has been widely used for transmutation of japonica rice. Further, many scientist used this method in transmutation of indica and javanica rice ( Tyagi and Mohanty, 2000 ) . Chen et Al. ( 1998 ) reported transmutation of japonica rice with multiple cistrons utilizing biolistics. The group bombarded rice tissue with 14 different pUC-based plasmids and out of entire transformed workss, 17 % of had more than nine mark cistrons and 85 % contained more than two mark cistrons. The growing behavior and morphology of these workss were normal. During this work, integrating of multiple transgenes, interestingly, occurred at individual or two venue which have derived hope for technology of fresh biosynthetic tracts in rice. Tang et Al. ( 1999 ) reported transmutation of rice with four cistrons by co-transformation utilizing biolistics. Two out of the four cistrons used were economically of import, viz. , Xa 21 and GNA, responsible for supplying opposition against bacterial blight and sap-sucking insects, severally. Molecular analysis confirmed that over 70 % of the transgenic workss recovered contained all four cistrons. The bulk of the transgenic workss showed look of these cistrons. By the biolistics method more than 70 rice assortments already transformed and this method is claimed to be genotype-independent and transmutation frequence every bit high as in magnoliopsid has been reported in some instances ( Tyagi and Mohanty, 2000 ) . It should, nevertheless, be noted that different workers have reported variable frequence of transmutation. This method has been successfully used to reassign a figure of economically of import cistrons in rice ( Oard et al. , 1996 )
2.3.2 Agrobacterium mediated rice transmutation
The first dependable Agrobacterium mediated transmutation in rice was achieved in 1994 ( Hiei et al. , 1994 ) who produced big figure of fertile and morphologically normal transgenic workss from japonica rice. This group demonstrated successful integrating of foreign DNA in rice chromosome through A. tumefaciens though there was contention earlier in the ability of Agrobacterium in transmutation of monocotyledonous workss as they are non natural host of this bacteria. Hiei et al. , 1994 reported that add-on of acetosyringine to the media and temperature of 22a-¦C – 28a-¦C was mandatory during co-cultivation stage. GUS look in the tissue instantly after infection gave good choice of preferable tissues for co-cultivation. Among the 2 strains and 2 vectors used, they found strain LBA4404 with vector pTOK233 was more effectual in transmutation. This method took 3 to 4 months to bring forth transgenic rice workss from the beginning of tissue civilization. Similarly, Rashid et Al. ( 1996 ) described the production technique of transgenic indica rice. Toki ( 1997 ) besides followed the same work and methodological analysis of Rashid et Al. ( 1996 ) on japonica rice expect with some alteration by adding casamino acids and proline in the medium for callus initiation and in the medium used for choosing transgenic callosity and all civilizations were stored under 30a-¦C except during co-culture period. This improved civilization method shortened the period of tissue civilization, ie. , distinction period, minimising the somaclonal fluctuation and transgenic workss were regenerated from callosity within 2 months. The writer besides developed new binary vector “ pSMABuba ” for rice transmutation. Agrobacterim tumefaciens strain EHA101 with vector pSMABuba has been found more effectual in rice transmutation.
Figure 5: Conventional representation of Agrobacterium mediated transmutation in rice ( beginning: Toki, 1997 )
Hoque et Al. ( 2005 ) developed an efficient Agrobacterium mediated transmutation method in Bangladeshi indica rice. Among mature and immature embryos used, immature embryos gave higher frequence in transgenic works production though callosities derived from3-week old matured embryo was first-class as get downing stuff. For fractious Bangladeshi genotypes such as BR22, super-binary vector ( pTOK233 ) was by and large more effectual than the binary vector ( pC1301-Xa21mSS ) . The writers besides found acetosyringone ( 200 AµM ) necessity for co-cultivation period.
Toki et Al. ( 2006 ) reported the scutellum tissue from twenty-four hours 1 pre-cultured seed in the media incorporating 2 mg l-1 of 2,4-dichlorophenoxyacetic acid ( 2,4-D ) were competent for Agrobacterium-mediated rice transmutation. This early infection of rice with Agrobacterium besides enhanced the efficient choice of transformed callosities due to which the transmutation process was instead speedy and transgenic plantlets were produced within a month. Earlier, it has been reported that 2 to 3 hebdomads old rice callosity derived from scutellum tissue of full-blown seeds is competent for Agrobacterium-mediated rice transmutation ( Hiei et al. , 1994 ) .