Some interesting rice facts

K.K.Vinod

Rice is a semiaquatic annual grass belonging to the genus Oryza and has two cultivated and 22 wild species. The cultivated species are Oryza sativa and O. glaberrima. O. sativa is grown all over the world while Oryza glaberrima has been cultivated in West Africa for about 3500 years. There are more than 120,000 varieties of cultivated rice. Cultivated rice is diploid (2n=24) and belong to AA genome. O. sativa has two subspecies O. sativa ssp. indica and O. sativa ssp. japonica. A less prominent intermediate O. sativa ssp. javonica is also available.

Rice was domesticated more than 10,000 years ago is possibly one of the oldest domesticated species. Huke and Huke (1990) observes that the domestication of rice ranks as one of the most important developments in history, for this grain has fed more people over a longer period of time than has any other crop. Rice is the staple cereal for more than 50% people (~3.25 billion) around the world, cultivated in about 9% of the earth's arable land, which is the largest single use of land for producing food. Rice provides 25 to 85 percent of the calories in the daily diet and 15% of per capita protein. In Asia, where rice is the major energy providing food, it accounts for 50-80% of daily caloric intake, especially among the poor. Unlike other major cultivated grains like wheat and corn which are also used for feeding livestock, rice is exclusively used for human consumption.

With China, India and Indonesia producing the most of the world’s rice, Asia accounts for over 90% of the world's production of rice. Only 6-7% of the world's rice crop is traded in the world market. Production of rice in The United States accounts to 1.5% of the world's production, with Arkansas, California and Louisiana producing 80% of the U.S. rice. Thailand, Vietnam, China and the United States are the world's largest exporters.

Rice is the only cereal that can be grown for long period in standing water. Even though predominantly semi-aquatic, rice is grown under many different conditions and production systems, including upland and dry conditions. 57% of the world’s rice is grown on irrigated land, 25% on rainfed lowland, 10% on the uplands, 6% in deepwater, and 2% in tidal wetlands. The flooded rice paddy sustains rich aquatic biodiversity, providing a home for fish, plants, amphibians, reptiles, mollusks, and crustaceans.

Rice has many characteristics, making it useful in various ways to be included in cereals, snack foods, brewed beverages, flour, oil, syrup, flakes and religious ceremonies. Rice grains can be short, medium and long or waxy (sticky) or non-waxy. Some are aromatic, some are colored including brown, red, purple and black and some are of medicinal value. The variation in characteristics makes one variety more popular in one region of the world than another.

Marker assisted selection in rice breeding

K K Vinod

Classical plant breeding is primarily of phenotypic selection of superior individuals, among segregating progenies following a hybridization, induced variability created through mutation, polyploidisation etc., and from a native outbreeding mixture of individuals. Though the idea seems simple, success of choosing a right kind of genotype is often hindered by genotype x environment interaction and the genetic nature of trait of interest itself.  In addition to testing procedures for selection of target traits in target environments are difficult, unreliable and expensive due to the nature of the traits themselves like biotic and abiotic stresses.

Latest advents in molecular marker technology, using tiny DNA fragments, that can distinguish individuals with slightest genetic variation, and unaffected by the environments, became a handy tool in providing information on selecting individuals possessing target trait genes. These DNA fragments are known as DNA markers.  These markers can be established through various molecular marker systems viz., restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites or simple sequence repeats (SSR), inter-simple sequence repeat (ISSR), retrotransposon based polymorphisms, sequence characterized amplified regions (SCAR), sequence related amplified polymorphisms (SRAP), single nucleotide polymorphisms (SNP) etc. Each of these systems has its own merits and demerits.

Molecular markers which are stable, unique and abundant can help us in study the linkage among themselves relating to their positions in the target genome.  When subjected to classical genetic analysis based on the segregating pattern of markers among individual segregating progenies obtained by crossing two homozygous individuals (purelines) which are genetically different, linkage distance between each of the segregating markers can be determined and drawn on a linkage map. When many markers are employed in this attempt covering the entire genome, we will be able to reconstruct individual linkage groups or chromosomes of that particular genome. This framework of chromosomes will provide us the information where individual markers are located and in consultation with classical cytogenetic maps we can assign individual chromosome designations to the constructed linkage groups. These populations used for molecular map construction are called mapping populations.

Further extending the marker segregation pattern and the linkage disequilibrium among themselves, on to the phenotypic segregation of quantitative traits, help us in identifying markers that closely follow the pattern of segregation of the target traits.  The simplest possible analysis for this is to carryout the simple regression between marker and phenotype segregation pattern. Alternatively we can use simple factor analysis of variance (ANOVA). This analysis is called single marker analysis (SMA). Extending further these analysis the model can be allowed to include more than one marker interacting, so that we can identify marker-by-marker interaction significantly influencing the phenotype. These markers can either be on the same chromosome (linked) or on different chromosome (epistatic). Locations of these markers which significantly influence the phenotype is called quantitative trait loci (QTL). Locations on these markers can be traced to the molecular linkage map, thereby the genomic location of the QTL.

However, one may be very conscious while referring the QTL as the gene responsible for the trait. Actually QTLs are putative locations of genes responsible for influencing the trait.  Actual gene may, therefore, be away from this location or at this location.  Nevertheless, the function how these genes influence the trait is also unknown.  Besides, there may be different degree of influence of QTLs to the traits. Some QTLs which show larger and conspicuous influence are called major QTLs, and those with minor effects are called minor QTLs.

Further extending concept of linkage analysis on multipoint mapping, the methods called interval mapping is designed. There are two types viz., simple interval mapping (SIM) and composite interval mapping (CIM). Compare to SIM, CIM is statistically robust and help in predicting more accurate QTL positions.  The procedures of interval mapping include extensive step-wise regression and predictions based on maximum likelihood ratios and/or best linear unbiased prediction (BLUP).  Mixed model mapping incorporating models of additive x additive, additive x epistatic interactions and phenotyping under varying environments are also employed currently. Many statistical predictions and sub-sampling are done using Bayesian methods or jackknifing procedures.

Location of QTLs, help us in closely looking at the chromosomal locations using closely placed markers. This is known as fine mapping of the target genomic locations, and once the exact location of the QTL is identified this genomic location can be sequenced to see whether this location code for a known or unknown protein that influence the trait. By doing this the exact influence of the gene located at this QTL can be understood.  If found extensively useful this QTL can be cloned and used for further genetic engineering programmes.

However, more useful and practical approach a breeder is interested in is using the QTL information and the looking for presence of them in a population using the linked markers, help him in selecting the target QTLs carrying individuals which will in turn contain the target trait itself.  This procedure of selection is called marker assisted selection (MAS).  However, marker assisted selection is not much confined to QTLs as it can be extended to any molecular marker linked to any major gene. Best examples are single genes conferring resistance to diseases. Also there can be the involvement of more than one major genes to which MAS can be targeted.  Another avenue MAS is extensively used is the selection among the transgene derived populations. Here, when the MAS is exercised on the target trait directly (herbicide tolerance) it is called foreground selection and when done on the marker trait (antibiotic resistance) it is called background selection.

The success of MAS depends on location markers with respect to the gene of interest. Three kinds of relationships are common, (i) marker lie within the gene, which is most favourable situation for positive selection (ii) marker is in linkage disequilibrium with the gene of interest in the whole population, where there will be the tendency of the marker to inherit closely with the gene of interest, and (iii) the marker in linkage equilibrium with the gene of interest, in which case the success of MAS is unpredictable.  Another challenge in MAS using QTL is the interaction of QTL with the target environments. QTL x environment (QE) interaction is a serious problem in MAS.  Here it is more prudent to look for environment specific QTL or widely adapted QTLs depending upon the objective of the selection programme.

Marker assisted selection in rice

MAS has been successfully employed in rice crop. Successful marker assisted screening and selection for root traits (Price and Curtois, 1999) resulted in better drought tolerance in upland rice. Selection was done based on RFLP and SSR markers for QTLs that determined root traits. Successful MAS based backcrossing also was done to transfer early season drought resistance and aroma from a japonica variety Azucena to Kalinga III, a high yielding height grain quality indica variety (Steel et al., 2002).  Participatory plant breeding using MAS bulks and purelines were successfully carried out in backcross progenies of Kalinga III x Azucena, following schemes given below:

Another approach was to develop purelines out of the BC3 population and evaluating them for the presence of individual root QTLs and also for the combination of more than one QTLs. As many as four root QTLs were pyramided in successful lines.

A great advantage of these selections is that many are done at farmers holdings and selections were done by the farmers themselves.  Predominantly lines selected by the farmers were accumulating the targeted QTLs confirming the success of MAS. As many as 24 lines from upland, 12 from medium upland and 16 lines from lowland conditions were selected by these participatory plant breeding approach using MAS from crosses using Kalinga III as one parent, and IR 64, Radha 32, IR 36 and Vandana as other parent (Steele et al., 2002).

Many successful attempts for MAS in rice is reviewed in Babu et al., (2004). These include resistances to blast, bacterial blight, rice tungro virus, gall midge, brown plant hopper and green leaf hopper, tolerance to submergence and salt accumulation, wide compatibility, temperature sensitive male sterility, garin aroma, amylase content, photoperiod sensitivity, semi-dwarf stature and shattering tolerance.

References

Babu, R., Nair, S.K., Prasanna, B.M., and Gupta, H.S. (2004) Integrating marker-assisted selection in crop breeding – Prospects and challenges. Current Science, 87: 607-619.

Steele, K.A., Virk, D.S., Prasad, S.C., Kumar, R., Singh, D.N., Gangeswar, J.S., and Witcombe. J.R. (2002) Combining PPB and marker assisted selection: Strategies and experiences in rice. In: Quality Science in participatory plant breeding. Workshop at IPGRI, Sept 30- Oct 4, 2002,Rome, Italy.

Price, A.H., and Curtois, B. (1999) Mapping QTLs associated with drought resistance in rice: Problems, progress and prospects. Plant Growth Regulation, 29: 123-133.

Price, A.H., Steele, K.A., Moore, B.J., and Wyn-Jones, G. (2002) Upland rice grown in soil filles chambers and exposed to contrasting water deficit regimes. II. Mapping QTLs for root morphology and distribution. Field Crops Research, 76:25-43.

About Rice (Oryza sativa L.)

K K Vinod

[Following is the text of my short presentation made to my class at UNIVERSITY OF NEBRAKSA-LINCLON]

Rice is a semiaquatic annual grass belonging to the genus Oryza. The genus oryza includes 24 species, of which 22 are wild and two namely Oryza sativa and Oryza glaberrima are cultivated. O. sativa is grown all over the world while Oryza glaberrima has been cultivated in West Africa for about 3500 years. There are more than 120,000 varieties of cultivated rice (IRRI, 2001). It is believed that rice domestication occurred independently in China, India and Indonesia, thereby giving rise to three races of rice: sinica (also known as japonica), indica and javanica (also known as bulu in Indonesia).

Cultivated rice is diploid (2n=24) and belongs to AA genome. The sativa rice varieties of the world are commonly grouped into three subspecies namely indica, japonica and javanica. Rice grown in India belongs to the indica subspecies. They are characterised by having leaves slightly pubescent and pale green in colour. Indicas are awnless or possess short and smooth awns. The rice grown in Japan belongs to japonica subspecies. Japonicas are adapted for cultivation in the subtropical and warm temperate regions. Japonica varieties mostly have oval and round grains. They may be awned or awnless. Leaves are narrow and dark green in colour. Subspecies javanica is characterised by a stiff straw, long panicle with awned grains, sparse tillering habit, long duration and low sensitivity to difference in day length. These are found mainly in Indonesia.

Rice was domesticated more than 10,000 years ago is possibly one of the oldest domesticated species. Huke and Huke (1990) observes that the domestication of rice ranks as one of the most important developments in history, for this grain has fed more people over a longer period of time than has any other crop. Rice is the staple cereal for more than 50% people (~3.25 billion) around the world, cultivated in about 9% of the earth's arable land, which is the largest single use of land for producing food. Rice provides 25 to 85 percent of the calories in the daily diet and 15% of per capita protein (IRRI, 2002). In Asia, where rice is the major energy providing food, it accounts for 50-80% of daily caloric intake, especially among the poor (IRRI, 2001). Unlike other major cultivated grains like wheat and corn which are also used for feeding livestock, rice is exclusively used for human consumption.

With China, India and Indonesia producing the most of the world’s rice, Asia accounts for over 90% of the world's production of rice. Only 6-7% of the world's rice crop is traded in the world market. Production of rice in The United States accounts to 1.5% of the world's production, with Arkansas, California and Louisiana producing 80% of the U.S. rice. Thailand, Vietnam, China and the United States are the world's largest exporters (IRRI, 2002).

Rice is the only cereal that can be grown for long period in standing water. Even though predominantly semi-aquatic, rice is grown under many different conditions and production systems, including upland and dry conditions. (FAO, 2004a). 57% of the world’s rice is grown on irrigated land, 25% on rainfed lowland, 10% on the uplands, 6% in deepwater, and 2% in tidal wetlands (Chopra and Prakash, 2002). The flooded rice paddy sustains rich aquatic biodiversity, providing a home for fish, plants, amphibians, reptiles, mollusks, and crustaceans (FAO, 2004b).

Rice has many characteristics, making it useful in various ways to be included in cereals, snack foods, brewed beverages, flour, oil, syrup, flakes and religious ceremonies. Rice grains can be short, medium and long or waxy (sticky) or non-waxy. Some are aromatic (Alford and Duguid, 1998; Chaudhary et al., 2001), some are colored including brown, red, purple and black (FAO, 2004c) and some are of medicinal value. The variation in characteristics makes one variety more popular in one region of the world than another.

Rice breeding

The primary breeding objective in rice growing countries has been high yield potential. Plant breeders have greatly contributed to the development of high-yielding crop varieties and have changed the morphology and physiology of crop plants, and incorporated desirable traits and resistant gene(s) into traditional varieties while stabilizing or increasing crop production. Dramatic advancement in productivity has achieved by incorporation of the semi-dwarf gene from Dee-Gee-Woo-Gen into traditional tall, leafy rice. The semi-dwarf rice varieties are now planted in 60% of the world's rice land.

High-yielding varieties have made a great contribution to the world's food supply, but they also have several major problems. The high yields of these varieties can only be attained with a high level of inputs, in particular heavy applications of fertilizer. This has led to problems associated with pest outbreaks in certain areas, while increased rice production has resulted in lower rice prices.

In rice breeding, the ideal plant type sought by breeders have been high yield potential; resistance to major diseases and insects; and improved grain and eating quality. However, there are few conflicting objectives like, high grain quality tends to result in unstable yields and also, too much emphasis on disease and insect resistance and stable yields leads to poor grain quality. Hence, breeding efforts should be fashioned in a way to sustain the yield under unfavorable conditions, and to maximize yields when conditions are favorable. 

The following breeding approaches should be emphasized in producing varieties for sustainable rice production.

·         - High-yield potential under low inputs.

·         - Heterotic F₁ hybrid

·         - New plant type

·         - Premium grain and eating quality to meet consumer demand, and to provide grain suitable for processing.

·         - More genetic diversity.

·         - Durable host resistance to major diseases and insects.

·         - Wider range of growth duration for various purposes.

·         - Proper levels of tolerance to environmental and climatic stresses in specific areas.

Common breeding method used in rice is pedigree breeding method.  Other than the introduction of semi-dwarf gene (sd1), popularization of male sterile systems in early 1980’s, hybrid rice production has met dramatic increase in rice yields in China. Three line breeding of hybrid rice carrying wild-abortive cytoplasmic male sterility has been utilized in commercial scale (Kim and Rutger, 1988). The advent of environmentally sensitive male sterility systems (TGMS and PGMS) paved way for the development of two-line hybrid breeding in rice.  Transfer of cytoplasm from wild species to cultivated backgrounds used backcross procedures widely.

Host resistance to various biotic stresses is a very important aspect of high yields, and can be expected to play a significant role in sustainable rice production. There are now numerous varieties resistant to rice blast, bacterial blight, various virus diseases, and plant hoppers and some possess multiple resistance to diseases and insects. Varieties with the Xa4 gene resistant to bacterial wilt have been grown in the Philippines for the last 15 years, and continue to be resistant. It is extremely difficult to identify polygenic resistance and incorporate it into improved germplasm (Khush and Virmani, 1985). Current studies on host resistance to crops emphasize the durability of resistance (Ikehashi and Kiyosawa, 1981; Ahn, 1982; Lee et al., 1989). Polygenic traits rather than absolute resistance would be preferable in sustainable agricultural production (Hauptli et al., 1990).

Improvements in rice quality are very important in meeting the demands of consumers for healthy, high-quality food. Many traditional varieties in both the tropics and the temperate zone have excellent cooking and eating quality, but a low grain yield (Khush and Juliano, 1985). For many years, breeders have focused their attention on quality improvement, but there seems to be some unknown genetic barrier to incorporating this trait into high-yielding varieties.

Biotechnological Advances

Modern day crop breeding in rice is supplemented with biotechnological tools.  Success stories are fast emerging with the development of golden rice (Ye et al., 2000), and many efforts are on to develop transgenic rice with various incorporated traits, including resistance to pests, herbicides etc.  Successfully the Xa21 gene conferring resistance to Bacterial leaf blight has been cloned. The deciphering the entire rice genome has been completed. Marker assisted frameworks of quantitative trait loci are being developed intensively which will help in developing strong target trait directed marker assisted selection programs.

References:

Ahn, S.W. 1982. The slow blasting resistance. Proceedings, Symposium on Resistance to Rice Blast. IRAT/GERDAT, Montpellier, France, pp. 343-70. 

Alford, J. and N. Duguid, 1998. Seductions of Rice. Artisan Publishers, NY, NY

Chaudhary, R., et al., eds., 2001. Speciality rices of the world. Science Publishers, Inc, NH, USA. 

Chopra, V.L. and S. Prakash, 2002. Evolution and Adaptation of Cereal Crops. Science Publishers Inc, NH, USA. 

Food and Agriculture Organization, 2004a. Rice and water: a long and diversified story, International Year of Rice, 2pp.

Food and Agriculture Organization, 2004b. Aquatic biodiversity in rice fields, International Year of Rice, 2pp.

Food and Agriculture Organization, 2004c. Rice and human nutrition, International year of rice, 2pp. 

Hauptli, H., K. David, B.R. Thomas, and R.M. Goodman. 1990. Biotechnology and crop breeding for sustainable agriculture. In: Sustainable Agricultural Systems, A. Edwards, R. Lal, P. Madden, R.H. Miller,and G. House. (eds.). Soil and Water Conservation Society, U.S.A., pp. 142-156. 

Huke, R.E. & Huke, E.H. 1990. Rice. then and now. Manila, International Rice Research Institute. 44 pp.

Ikehashi, H., and S. Kiyosawa. 1981. Strain-specific reaction of field resistance of Japanese rice varieties revealed with Philippine strains of rice blast fungus, Pyricularia oryzae Cav.. Jap. J. Breed. 31, 3: 293-301. 

International Rice Research Institute, 2001. Rice Research and Production in the 21st Century. 

International Rice Research Institute, 2002. Rice Almanac, 3rd Edition. 

Khush, G.S., and B.O. Juliano. 1985. Breeding for high-yielding rices of excellent cooking and eating qualities. In: Rice Grain Quality and Marketing, International Rice Research Institute, College, Laguna, Philippines, pp. 61-69. 

Khush, G.S., and Virmani. 1985. Breeding rice for disease resistance. In: Progress in Plant Breeding. Vol. 1. Butterworths, United Kingdom, pp. 240-279. 

Kim, C.H., and J.N. Rutger. 1988. Heterosis in rice. In: Hybrid Rice. International Rice Research Institute, College, Laguna, Philippines, pp. 39-54. 

Lee, E.J., Qi Zhang and T.W. Mew. 1989. Durable resistance to rice disease in irrigated environments. In: Progress in Irrigation Rice Research. International Rice Research Institute, College, Laguna, Philippines, pp. 93-100. 

Ye, X, Al-Babili, S., Kloti, A., Zhang, J., Lucca, P., Beyer, P and Potrykus, I. 2000. Engineering the Provitamin A (b-Carotene) Biosynthetic Pathway into (Carotenoid-Free) Rice Endosperm, Science, 287: 303-305.

UV-B Radiation Stress in Rice

K.K.Vinod

Rice is grown mostly in tropical and subtropical countries. It is known that UV-B radiation is highest in tropical regions where rice is grown, because the stratospheric ozone layer in high latitudes, and solar angles are higher. The current information on rice is insufficient to conclude the potential risks of UV-B exposure to rice production. UV-B radiation would also have indirect effects on rice production through indirect effects on other components of rice ecosystem such as weeds, diseases and nitrogen-fixing cyanobacteria. Increased UV-B radiation induces a significant reduction in the total biomass in a number of rice cultivars, accompanied by a reduction in tiller number and photosynthetic capacity of plants. The prolonged exposure of UV-B light affects plant height, leaf area, dry weight, net assimilation rate and relative growth rate in some rice cultivars.

Evidence were shown for that UV-B mediates photoinduction of anthocyanin synthesis in seedlings of a cyanic rice cultivar, Purple puttu, which is associated with PAL biosynthesis. They observed that sunlight triggered the photoinduction of anthocyanin in shoots of purple puttu seedlings, whereas seedlings exposed to sunlight filtered through window glass showed little formation of anthocyanin. In addition to UV-B receptor the anthocyanin level was also modulated by phytochrome. However, the anthocyanin photoinduction was restricted to only a few cultivars of rice, indicating variability within the cultivars with respect to anthocyanin induction. 

The stresses imposed by UV-light irradiation can cause reactive oxygen species generation (ROS) such as O^2- and H₂O₂. Though H₂O₂ is an innocuous metabolite present in cells irradiation with UV-light breaks it down to extremely deleterious hydroxyl free radicals (OH^•). Since H₂O₂ can easily diffuse through cell membranes it is extremely deleterious to cellular constituents such as DNA. Studies have indicated that in vitro anthocyanins could act as effective antioxidants as anthocyanins prevent ascorbic acid (AsA) against metal induced oxidation by forming a stable AsA-metal-anthocyanin co-ordinate complex. Above complex protected AsA from H₂O₂ and OH^•, and also anthocyanins from damage.