Biochemical Analysis of Rice

Biochemical Analysis of siftRice (Oryza sativa (2n = 24) is a monocot plant and be colossals to the Poaceae family and Oryzoidea subfamily. It occupies almost i-fifth of the f in all land bea under domain cereals. It covers about 148 gazillion hect bes p.a. that is roughly 11 percent of the world- urbane land. It is t whizz for more than half of existence and in past, it shaped the cultures, diets, and economies of billions of people in the world (Farooq et al., 2009). More than 90 percent of the worlds sift is prominent and consumed in Asia where 60 percent of the world state lives. The world major strain consuming countries argon China, India, Egypt, Indonesia, Malaysia, Bangladesh, Vietnam, Thailand, Myanmar, Philippines, Japan, Brazil, South Korea and USA that consume 135, 85, 39, 37, 26, 18, 10, 10, 9.7, 8.7, 8.1, 5.0 and 3.9 million metric ton, respectively (Meng et al., 2005 USDA, 2003-04).Biochemical and nutritional aspects of strainRice is a major character of macro and micronutrients for human being. It feeds more than both billion people world(a) and is the issue one staple food in Asia. It provides over 21 percent of the calorific of necessity of the worlds population and up to 76 percent of the calorific intake of the population of South East (SE) Asia (Fitzgerald et al., 2009). It is loosely consumed as a polished in fluid, which usu all(a) in ally lacks its nutritional components such as minerals and vitamins 41 P. Lucca et al., Genetic technology approaches to enrich sift with iron and vitamin A, Physiol. Plant. 126 (2006), pp. 291-303. Full Text via CrossRef View Record in Scopus Cited By in Scopus (7)( Lucca et al., 2006). Since the advent of molecular techniques, recently transmittedally modified strain verities ingest been developed, which contains more nutritional aspects care minerals and vitamins in endosperm (Vasconcelos et al., 2003 Paine et al., 2005 Fitzgerald et al., 2009). The major value-added nutritional protein constituents of the strain.Rice Position in PakistanIn Pakistan, besides its importance as a food crop, sift is the second historic component of daily diet of bulk of the population after wheat. About 23% of the total unlike alter earnings is shared by rice and thus called as Golden Grain of Pakistan (Shah et al., 1999). Around one third of total production is annually exported and two third is locally consumed to meet food necessarily. Rice is alike utilize in dishes for finical occasions (Sagar et al., 1988). Pakistan is the third largest rice exporting country. In Pakistan, rice occupies about 10% of the total cultivated part, accounts for 6.1% of value added in agriculture and 1.3% in gross domestic product. Production of rice during 2007-08 was estimated at 5,540 gram tones, 10.4% higher(prenominal) than work year with 6.1% adjoin in yield per hectare (Anonymous, 2006).Area, production and yield of rice for the last 5 years are plantn in Fig. 1. Varietie s of basmati rice, sub-species of indica, are economically important due to the high tone of the grain and constitute an important source of revenue for two major rice- ontogenesis countries in Asia (Pakistan and India). The international foodstuff for basmati rice has always been higher than that of the moderate varieties. Pakistans annual rice export stands at about 2.5 million tons, which earn a total of 513.0 million dollars for the country (Anonymous, 1998). During the year 2005-2006 rice export was about one billion US$ (Bashir et al., 2007).Rice growing areas of PakistanDepending upon the irrigation water availability, rice fanny be grown in any part of the country from sea level up to 2500m height. Pakistan has a climate and a capableness in soil that permits the expectations of a most bright future for the productions of rice. Considering temperature deflection, optimum sowing seasons and the varietals performance, rice growing areas shtup be divided in 4 ecological zones (Salim et al., 2003 Table-1.2).Rice is grown in all quaternity provinces of Pakistan. However, the acreage under rice varies greatly from one province to an antithetic. The Punjab and Sindh are the major rice growing provinces with about 59% and 33%, respectively of the total rice in the country. The remaining 5% of the area is planted in Baulochistan and 3% in NWFP (Bhatti and Anwar, 1994). Despite the fact that its cultivated area is far smaller than wheat (more than 7.24 million), it has a great impact on national economy due to two reasons. Firstly, rice is the moreover crop which fag be grown successfully in vast chunks of salt-ridden and water-logged areas where it facilitates non solo the reclamation of land for the cultivation of translucent crops but also provide food.Secondly, superior bore basmati has a consistently increasing demand in the foreign countries. Consequently, there is a great scope for augmenting the foreign exchange earning by exporting it in bigger quantity. In put one across of these facts, it is highly desirable to increase the production and improve the quality of rice the quality is particularly more important from the trade study point, as it is instrument entail in increasing and then sustaining the demand in the foreign market place in competition with other rising exporting countries. There in no denying the fact that faithfulness is the very sole of quality. The impurities not only restrict the export trade, but also inflict losings to the growers, millers and the consumers alike. Therefore, these should mayhap be minimized (Saleem et al., 2003).Major rice varieties in PakistanMore than 20 rice varieties have been released for general cultivation in Pakistan (Bashir et al., 2007). A general description of agronomical and physiochemical characteristics of these varieties.Importance of Basmati Rice in PakistanThere are thousands of rice varieties and landraces, which differ with respect to plant and grain characteristics. Of these, tonetic (Basmati) rice constitutes a small but special group that is regarded as best in grain quality, superior aroma and usually subroutined for special dish preparation (Khush and dela Cruz, 2001). Quality of rice may be considered from the view point of size, shape and appearance of grain, milling quality and cooking properties (Dela Cruz and Khush, 2000). Pakistan is famous for the production and export of Basmati rice. The cable of the word Basmati can be trade to the word Basmati meaning earth recognized by its fragrance. The Hindu word Bas was derived from the Pakrit word BAS and has a Sanskrit root Vassy (Aroma), while Mati originated from Mayup (ingrained from the origin). In common usage Vas is marked as Bas and while combining Bas and Mayup, the later changed to Mati thus the word Basmati (Ahuja et al., 1995 Gupta, 1995).The fragrance of basmati rice is most nearly associated with the presence of 2-acetyl-1-pyrro distinction (Buttery et al ., 1983 Lorieux et al., 1996 Widjaja et al., 1996 Yoshihashi et al., 2002). Although many other compounds are also found in the headspace of fragrant rice varieties (Widjaja et al., 1996) possibly due to secondary effects related to the heritable background of the rice admixture, 2-acetyl-1-pyrroline is widely known to be the main cause of the distinctive basmati and jasmine fragrance. The desirability of fragrance has resulted in strong human preference and extract for this trait. Non-fragrant rice varieties contain very low levels of 2-acetyl-1-pyrroline, while the levels in fragrant geno graphic symbols are much higher (Widjaja et al., 1996).Basmati rice occupies a prime position in the Indian subcontinent and is becoming increasingly popular in Middle East, Europe, USA and even in non- traditionalistic rice growing countries such as Australia (Bhasin, 2000). High-quality, traditional Basmati rice varieties command premium sets, more than ternion times that of non-Bamati ric es in the world market due to its dainty aroma, superfine grain characteristics and excellent cooking (extra e gigantication, soft and flaky metric grain) qualities (Bhasin, 2000 Singh et al., 2000a Khush and dela Cruz, 2002). Basmati rice traditionally grown in the Himalayan foothills regions of Pakistan and India, and the name is traditionally associated with this region. Basmati rice is the result of centuries of rention and cultivation by matureers (Khush, 2000).Cultivation of basmati rice in mainly confined to the Kallar tract (Gujranwala, Sheikhupura and Sialkot districts) of Punjab province. Basmati rice always fetch a higher price in the domestic as well as in the international market due to their crotchety quality features such as pleasant aroma, fine grain, extreme grain elongation (7.6mm long) and soft texture on cooking. In spite of hard competition from India, Thailand and the United States, Pakistan enjoys a good position in the global trade of aromatic rice and e very year earns a lot of foreign exchange (Akram and Sagar, 1997).Genetic Diversity in RiceDiversity among organisms is a result of funs in deoxyribonucleic acid terms and of environmental effects. The variety in crop varieties is essential for agricultural development for increasing food production, poverty stand-in and promoting economic growth. The available diversity in the germplasm also serves as an insurance against unknown future learns and conditions, thereby contributing to the stability of farming systems at local, national and global levels (Singh et al, 2000). In crop approach program, hereditary variability for agronomic traits as well as quality traits in almost all the crops is important, since this component is transmitted to the next generation (Singh, 1996). Study of transmitted divergence among the plant materials is a full of life peckerwood to the plant breeders for an efficient choice of parents for plant improvement. Genetically various parents are likely to precede desirable segregants and/or to produce high heterotic crosses. Parents set on the infrastructure of divergence for any life program would be more promising (Arunachalam, 1981). In early 1970s, public authorities felt the study that familial resources should be collected, upholded and conserved, especial focus was on important food crops e.g wheat, rice, barley etc (Hawkes 1983 Bellon et al., 1998 Barry et al., 2007). This was the scratch line official attempt to preserve contagious diversity. Currently different genetic diversity assessment methods including morphological, biochemical and molecular prints are available.Morphological Markers used to study genetic diversityMorphological evaluation is the oldest and considered as the first hand tool for detection of genetic variation in germplasm (Smith and Smith, 1989). It is cheap and convenient. It requires not any in depth knowledge at genomic or proteomic level. However, morphological markers are relat ively less trenchant for genetic diversity analysis due to sensitivity to environmental influences and developmental stage of the plant (Werlemark et al., 1999). It takes long time, requires seasonal changes and quite laborious. The genetic variability for some of the traits needed for high yield performance and show tolerance is limited in cultivated germplasm. This is because a small content of adapted progenitors has been used repeatedly in rice breeding programs such that the genetic base of rice has become narrow (Moncada et al. 2001 Hargrove et al. 1980 Dilday 1990). Introgression of genes from other rice species can provide genetic variation to improve rice and meet the challenges affecting rice production. Morphological traits including both qualitative and valued ones are used to evaluate genetic relationship among genotypes (Goodman 1972 Bajracharya et al., 2006). Fida et al. (1995) report the evaluation of elite rice genotypes for agronomic traits during 1992 at NARC, Islamabad. All the genotypes possessed similar grain quality. agronomic evaluation was used for screening of lines with desired performance by Akram et al. (1995), in field leading to the realisation of varieties possessing longer and fine grains as donors for utilization in breeding programmes aimed for the improvement of grain duration in Basmati rice. Iqbal et al. (2001) morphologically evaluated selected landraces for paddy yield and other important agronomic traits as a propose to select parents for hybridization program. All the landraces possessed some desirable agronomic traits so these proved effective in rice breeding programmes. Koutroubas et al. (2004) described variation in grain quality traits among some European rice lines. They concluded that these lines could be used as parents for introgression of desired traits into different rice cultivars grown in Europe. They also suggested that the interrelations among grain quality traits found in these lines could be usef ul to study the relationship among their grain quality components and for improving selection criteria. Nabeela et al. (2004) evaluated fifteen agronomical important traits in landrace genotypes of rice collected from various separate of Pakistan. A significant amount of genetic variation was displayed for most of the traits examined. The coefficient of variation was more than 10% for all the characters with exception of grain length. Seven accessions with best performance for individual character were identified, by exploiting their genetic potential. These genotypes can have a beneficial use in the breeding programs. Nepali rice landrace diversity was evaluated by Bajracharya et al. (2005) by using morphological traits as one of the parameter for selection. The genotypes varied only for few quantitative traits controlled by major genes husk color, semen coat and panicle traits. Agronomic characterization also helped to decide which traits need to be ameliorate for kick upstairs crop improvements. Zaman et al. (2005) studied fifteen different rice varieties which showed that the different morphological characteristics such as the yield, tiller number per hill and filled grains per panicle did not contribute towards the total divergence. This suggested that the breeding improvement of these morphological characteristics have the little possibility. Little phenotypic variation at farm level was observed in Vietnamese rice by Fukuoka et al. 2006, which was considered to be the result of genetic social movement and selection by the farmers, on farm conservation of the landraces of rice is considered to be under a repel to decrease phenotypic diversity. Different phenotypic profiles contribute to the conservation of regional genetic diversity of the landraces of rice. Veasey and colleagues (2008) investigated the genetic variability among different rice species from South in a greenhouse experiment. They showed a significant difference (pKeeping in view thes e benefits, morphological variation is a selection criterion for plant scientists among landrace genotypes. though the environmental factors also play an important role in morphological variation but the knowledge of agro-morphological diversity and the dispersal pattern of variation among crop species could be an invaluable aid in germplasm circumspection and crop improvement strategies. Zeng et al. (2003) studied ecogeographic and genetic diversity based on morphological characters of rice landraces (Oryza sativa L.) in Yunnan, China. A great difference in ecological diversity baron of rice resources amid prefectures or counties in Yunnan province exists. Kayode et al. (2008) studied the relationship in geographic pattern and morphological variation of 880 rice landrace in Cte dIvoire for 13 agro-morphological characters. Result of the phenotypic frequency showed differential distribution of landraces with height, heading and maturity period which reflected the distribution pa ttern of different Oryza sativa landraces in Cte dIvoire that proved useful in germplasm management and breeding programs. The altitudinal distributions of grain length, grain width, grain length to width ratio and grain weight were evaluated by Siddiqui and coworkers in 2007. It was noticed that grain length decreased with the increase in elevation, while the grain width increased with the increase in altitude, resulting into a decrease in length to width ratio with the increase in altitude. Considering the change in altitude as a difference in habitat and environment, it can be assumed that Pakistan rice cultivars show a wide variation amongst and within locations. It may be concluded that the Pakistan rice genetic resources comprise of great diversity for grain morphological characteristics. The prevailing diversity for grain type (shape and size) and seed vessel color has distinct correlation to its geographical distribution in terms of altitude. Morpho-physiological traits a re an important tool in hands of plant breeders for denomination and purity testing of rice varieties. Sharief et al. (2005) investigated the genetic purity of four different rice varieties on the basis of morphological characteristics at their different growth stages. All of the varieties were identified by different morphological characteristics in terms of flag leaf area, grain color, seed width, number of tillers, time of heading, absent awing, slemma, palea pubescence, plant height, and culm diameter.Biochemical markers for analysis of diversitySeed proteins are very facilitatory in genetic diversity evaluation in cereal crops because the seeds of these crops have nutritional value. Glutelin, globulin and prolamin are important seed proteins in rice. Variation in these proteins at subunit level changes the quality of rice. mingled tools were used to assess variability at peptide level. Biochemical markers have some disadvantages being tissue specific and affect by environme ntal and developmental changes. These disadvantages could be eliminated by the use of seed storage protein as they are conservative in nature and least effected by environmental changes. (Thanh et al., 2006) Sodium Dodecyl Sulphate-Polyacrylamide Gel electrophoresis (SDS-PAGE) is useful method not only for revealing variations but also for identification of a variety in seed storage proteins. Four protein fractions (albumin, globulin, gliadin and glutenin) separated by SDS-PAGE as biochemical marker for evaluating pleomorphism in three spelt wheat varieties. Very significant difference was observed at protein profile level in old cultivars and new breeding lines (Dvoracek and Curn 2003). Sengupta and Chattopadhyay (2000) identified twelve rice varieties on the basis of banding pattern obtained by SDS-PAGE. Aung et al. (2003) investigated 350 local rice cultivars from different regions of Myanmar. These were analyzed by using SDS-PAGE and IEF. Various cultivars differed in their SDS- PAGE profiles. Padmavathi et al. (2002) evaluated seven aromatic and five non-aromatic rice cultivars using SDS-PAGE. Two bands of 60.3 and 51.3KDa were polymorphic for their presence in both aromatic and non-aromatic genotypes and suggested that these polymorphic bands can be used as markers for verification of hybridity in pass over programme. Rehana et al. (2004) investigated twenty accessions of Pakistani rice germplasm for total seed protein by using SDS-PAGE, to determine the magnitude of genetic variation with respect to geographical distribution. Variation in protein banding pattern with respect to various geographical regions was evaluated and it was suggested that the inter-specific variations were more pronounced as compared to intra-specific variations. Variation in banding profile of globulin and glutelin was used as identification tool for differentiating coarse, fine and super fine rice cultivars by Thind and Sogi (2005). Jahan et al. (2005) studied protein diversity in 576 rice cultivars from Bangladesh and SDS-PAGE was used for separation. Thanh et al., 2006 used seed storage protein profiles of different varieties including rice for evaluation of genetic purity and variability.molecular(a) markers for diversity analysisVariation in a DNA sequence is known as DNA pleomorphism. This quality of DNA can be used as a marker to assess diversity in the genome of any organism. An ideal DNA marker must have any of the following qualities super polymorphic in nature, co-dominant inheritance, frequent occurrence in genome, selective neutral behaviour, user-friendly access/availability, easy and fast assay, high duplicability and easy exchange of data between laboratories (Joshi et al., 1999). DNA-based molecular markers/DNA reproduce can increase screening efficiency in breeding programs in a number of other ways. For example, they provide the ability to screen in the seedling stage for traits that are expressed late in the life of a plant (i.e. gra in or fruit quality, male sterility, photoperiod sensitivity), the ability to screen for traits that are highly difficult, expensive, or time consuming to score phenotypically (i.e. root morphology, resistance to quarantined pests or to specific races or biotypes of diseases or insects, tolerance for certain abiotic stresses such as drought, salt, or mineral deficiencies or toxicities), the ability to stigmatize the homozygous versus heterozygous condition of many loci in a unity generation without the need for payoff testing (since molecular markers are co-dominant), and the ability to perform simultaneous marker-aided selection for several(prenominal) characters at one time.Random Amplified Polymorphic DNAs (RAPDs)Randomly-amplified polymorphic DNA markers (RAPD) are imperative sequence markers developed by chisel and McClelland in 1991. This procedure detects nucleotide sequence polymorphisms in DNA by using a single primer of arbitrary nucleotide sequence. In this reaction, a single species of primer anneals to the genomic DNA at two different sites on complementary strands of DNA template. If these priming sites are within an amplifiable range of for each one other, a discrete DNA product is formed through thermocyclic amplification. On an average, each primer directs amplification of several discrete loci in the genome, making the assay useful for efficient screening of nucleotide sequence polymorphism between individuals. However, due to the stoichastic nature of DNA amplification with random sequence primers, it is important to optimize and maintain consistent reaction conditions for reproducible DNA amplification. They are dominant markers and hence have limitations in their use as markers for mapping, which can be overcome to some extent by selecting those markers that are linked in coupling. RAPD assay has been used by several groups as efficient tools for identification of markers linked to agronomically important traits, which are introgresse d during the development of near isogenic lines. though it is less popular due to problems such as poor reproducibility faint or fuzzy products, and difficulty in scoring bands, which lead to inappropriate inferences but it is still applied as markers in variability analysis and individual-specific genotyping has largely been carried out,. Raghunathachari et al. (2000) differentiated a set of 18 accessions from Indian scented rice by random amplified polymorphic DNA (RAPD) analysis. The RAPD analysis offered a rapid and reliable method for the love of variability between different accessions, which could be utilized by the breeders for further improvement of the scented rice genotypes. Porreca et al. (2001) reported confirmation of genetic diversity among 28 rice cultivars, different for biometric traits, biological cycle and suitability to water limitation, using RAPD markers. High level of polymorphism was found between maules quince and indica subspecies, whereas japonica cul tivars with long grains (tropical) resulted to be genetically different from the short grains genotypes (temperate). Genetic relationships among indica and japonica cultivars and between tropical and temperate japonica was estimated. Variability among the varieties could lead to good heterotic combinations between japonica genotypes. Neeraja et al. (2002) determined genetic diversity in a set of landraces in comparison to a representative sample of improved rice varieties, using random amplified polymorphic DNA (RAPD). Analysis of 36 accessions using 10 arbitrary decamer random primers, revealed 97.16% polymorphism. Similarity values among the landraces ranged from 0.58 to 0.89 indicating wide diversity. The landraces and improved varieties formed separate clusters at 0.65 similarities suggesting that genetically distant landraces could be potentially valuable sources for enlarging and enriching the gene pool of improved varieties. Kwon et al. (2002) evaluated genetic divergence amo ng 13 Tongil type rice cultivars and the relationship between genetic distance and hybrid performance in all mathematical nonreciprocal crosses between them assessed. These results indicate that GDs based on the microsatellite and random amplified polymorphic DNA (RAPD) markers may not be useful for predicting heterotic combinations in Tongil type rice and support the idea that the level of correlation between hybrid performance and genetic divergence is dependent on the germplasm used. Rabbani et al. (2008) evaluated the genetic polymorphism and identities of several Asian rice cultivars by using random amplified polymorphic DNA technique. On the basis of analysis performed on similarity matrix by using UPGMA, they grouped 40 cultivars into three main clusters correspondent to aromatic, non-aromatic and japonica group, and a few independent cultivars. The cluster analysis placed most of the aromatic cultivars close to each other showing a high level of genetic relatedness. But the clusters produced by the aromatic cultivars were distinct from those of non-aromatic and japonica types. In this study, several improved and obsolete cultivars originating from diverse sources did not produce well be distinct groups and indicated no association between the RAPD patterns and the geographic origin of the cultivars used. Amita et al. (2005) performed molecular and hybridization studies to investigate variation patterns in O. meridionalis by producing 119 polymorphic RAPD markers from 12, 10-mer operon primers. In addition, they find 67 alleles by using 11 SSR primers. They showed speciation in O. meridionalis a with respect to its geographic distribution in northern Australia and Irian Jaya. Santhy et al. (2003) tested application of RAPD markers for the identification of three rice (Oryza sativa L.) hybrids and their parental lines i.e. CMS female parent (A line), maintainer (B line) and pollen parent (R line), using 17 random oligonucleotides. It was affirmable t o distinguish each of these genotypes, following a combination of selected primers. The results are discussed in view of its application for the answer of Plant Variety Protection and for testing the genetic purity of A line and hybrid seed lots.Simple Sequence Repeats AnalysisMicrosatellites or simple sequence repeats (SSRs) are simple tandemly repeated di- to penta-nucleotide sequence motifs. Microsatellite data are also commonly used to assess genetic relationships between populations and individuals through the estimation of genetic distances (e.g. Beja-Pereira et al., 2003 Ibeagha-Awemu et al., 2004 Joshi et al., 2004 Sodhi et al., 2005 Tapio et al., 2005). The most commonly used measure of genetic distances is Neis standard genetic distance (DS) (Nei, 1972). Because of microsatellite copiousness and even distribution in nuclear genomes of eukaryotes and some prokaryotic genomes, they offer valuable good source of polymorphism, which make them a promising class of genetic mar kers. The high levels of polymorphism performed by these markers they are more often than not referred as SSLP (simple sequence length polymorphism). Li et al. (2004) examined genetic diversity within and differentiation between the indica and japonica subspecies, including 22 accessions of indica and 35 of japonica rice by using five microsatellite loci from each chromosome having total 60 loci. Evaluating on chromosome-based comparisons it is concluded that nine chromosomes (1, 2, 3, 4, 5, 8, 9, 10 and 11) harboured higher levels of genetic diversity within the indica rice than the japonica rice. By applying chromosome-based comparisons they suggested that the extent of the indica-japonica differentiation varied substantially, ranging from 7.62% in chromosome 3 to 28.72% in chromosome 1. At 15 of the SSR loci, traditional and crossbred Basmati rice varieties amplified different alleles than those in the indica and/or japonica rice varieties. During this study the identified SSR m arkers, which can be used to differentiate among the traditional Basmati varieties and between traditional Basmati and other crossbred Basmati or long grain, non-Basmati rice varieties. Genetic relationships among rice genotypes as determined by UPGMA cluster analysis and three-dimensional scoring based on principal component analysis showed that the three traditional Basmati rice varieties are virtually related and have varying degree of similarity with other crossbred Basmati rice varieties Priyanka et al. (2004). Amanda et al. (2004) classified 234 accessions of rice into five distinct groups corresponding to indica, aus, aromatic, temperate japonica, and tropical japonica rices using 169 microsatellite markers. Yunbi et al. (2004) evaluated diversity in 236 rice accessions by applying 113 restriction fragment length polymorphism (RFLP) and 60 simple sequence repeat (SSR) loci at DNA level. Higher value of polymorphism information contents (0.66) was recorded for SSR markers as compared to RFLP (0.36). A diverse subset of 31 rice cultivars was identified that embodied 95% of RFLP and 74% of SSR alleles. This subset was useful in developing core collections and an efficient source of genetic diversity for future crop improvement. Zhang et al. (2005) evaluated the potential of discriminate analysis (DA) to key candidate markers linked with agronomic traits among inbred lines of rice (Oryza sativa L.). A sum of 218 lines originating from the US and Asia were planted in field plots of Texas. Data were collected for 12 economically important traits, and DNA profiles of each inbred line were produced using 60 SSR and 114 RFLP markers. Model-based methods revealed population structure among the lines. Associated marker alleles pointed to the same and different regions on the rice genetic map when compared to previous QTL mapping experiments. Results of the study suggested that candidate markers associated with agronomic traits can be readily detected among inbre d lines of rice. Bajracharya et al. (2005) estimated genetic diversity of rice landraces collected from different locations of Nepal based on agro-morphological variability and microsatellite marker polymorphism. They 39 microsatellite (simple sequence repeats, SSR) markers among these collected accessions by using 10 different names. After studying all these qualitative and quantitative traits they concluded that these accessions showed low morphological diversity having an average Shannon Weaver diversity index of 0.23. Among the studied traits only 16 morphological traits showed significant variation among the accessions. Discriminant function analysis showed that only 36% of accessions could be clustered according to name by morphological traits. Only one SSR locus was polymorphic, distinguishing only one accession. Genetic differences among new rice lines (NERICA), developed by cross breeding of African rice (Oryza glaberrima) with high yielding Asian rice (Oryza sativa subsp. japonica), were explored by using simple sequence repeat markers (Semagn et al. 2006). Michael et al. (2006) characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, by studying 30 fluorescently-labeled microsatellite markers. By using genetic diversity analysis they characterized the Indonesian landraces as 68% indica and 32% tropical japonica, having an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56