RICE CROP GERMPLASM COMMITTEE REPORT

- April 1, 1997 -

INTRODUCTION

Rice (Oryza sativa L.) is one of the major food crops of the world ranking second only to wheat in terms of annual production for food use. About 90% of the production is in Asia and only about 4% of the world's total rice production enters into international trade. Rice is grown on about three million acres in the U.S. in two major ecogeographic regions: the southern U.S. (Arkansas, Louisiana, Texas, and Mississippi with a small commercial production in Missouri and Florida), and California. U.S. rice production accounts for about 1% the world's annual rice crop, however, the U.S. is the 4th leading exporter providing about 20% of world exports. By contrast, Thailand, the leading exporter, is fifth in terms of total rice production and has 36% of world exports. Vietnam and India are now emerging as major rice exporters.

Virtually all rice is consumed as food, primarily as white rice. Rice is also used in cereals, snack foods, brewing, brown rice (not milled), and as flour. Annual per capita consumption exceeds 220 pounds in Asia with a 141 pounds world average consumption. U.S. per capita consumption is 26 pounds and has doubled since 1975 with more than 50% of U.S. production being used domestically. This is in response to a large influx of Asian immigrants, increased consumer interest in new foods, and increased use of rice in cereals, processed foods, and brewing. Rice has also received a prominent position in the base of the USDA dietary food pyramid which has certainly improved the image of rice and contributed to increased usage in the U.S.
Rice production in the U.S. is highly mechanized and grown under lowland conditions (flooded). Rice is direct seeded (drilled or water-seeded) and fertilizers and agrochemicals for weed, disease, and insect control are typically used to achieve high yields and quality. U.S. cultivars can be classified genetically as tropical japonica (long-grain types), and temperate japonica (medium- and short-grain types). The long-, medium-, and short-grain types are the primary U.S. market classes and have been associated with different cooking characteristics. Long grains cook dry and flaky whereas medium and short grains cook moist and sticky. Long-grain varieties are primarily grown in the southern U.S. and medium- and short-grain varieties have been produced in California. Rice varieties developed for the southern U.S. have not been used in California because of susceptibility to cool temperatures and California medium- and short-grain varieties have not been grown in the southern U.S. because of disease susceptibility. Interest in developing special purpose types of rice has increased. These rice types are in demand in ethnic or special quality markets. A summary of U.S. rice production is provided in Table 1.

Source: 1996 Annual Crop Summary USDA National Agricultural Statistical Service (http://www.gov.usda./nass/).

Since the formation of the Rice Crop Germplasm Committee and the 1987 committee report there have been many developments involving rice. Rice breeding activities have expanded in the U.S. in both the public and private sector. Biotechnology (tissue culture, genetic mapping, and genetic engineering) has blossomed with rice receiving a prominent position as a tool and target for this technology. Germplasm introduction, rejuvenation, storage, and evaluation have expanded and computer access to information is now available.

The use and manipulation of rice germplasm faces formidable challenges to meet the needs of the next century. Government rice support payment to growers are being phased out and free trade agreements are thrusting U.S. growers into a highly competitive marketplace. This will provide market opportunities as well as increased competition. Environmental concerns and regulations are restrictive and impact productivity. Budget constraints will also limit government supported research and extension. Finally, world population growth, population migration from farms, and loss of arable land are forecast. Improved agricultural productivity including increased yield and resistance to pests and environmental stress, has been identified as a necessary part of the solution necessary to meet future needs.

GERMPLASM ACTIVITIES

Introduction

Since cultivated rice originated in Asia, all U.S. rice varieties ultimately trace back to plant introductions. New rice germplasm and varieties must be grown in quarantine and there is an ever-increasing backlog of material for processing. Rice breeding programs have been active in the U.S. for some 70 years and have been expanded tremendously in the past 15 years in both the pubic and private sectors. An even greater growth is now unfolding in rice genetics with research developments and applications in gene mapping and genetic engineering. Germplasm manipulation and its use for variety development and research is rapidly increasing.

Breeding Programs

Cooperative rice breeding programs were established between the USDA and the state agricultural experiment stations starting in 1909. Breeders were based at the state agricultural experiment stations in Arkansas, California, Louisiana, and Texas by the USDA Agricultural Research Service. A rice breeding program funded entirely by state rice growers was established in California in 1969. The agricultural experiment stations have assumed responsibility for state breeding programs in Arkansas, Louisiana, Mississippi, and Florida. Rice breeding programs and activities have expanded markedly in the last 20 years. Over 60 new rice cultivars have been released since 1970 and they have played a primary role increasing U.S. rice yields. Public rice breeding programs are located at: Rice Research & Extension Center, Stuttgart, AR; Rice Experiment Station, Biggs, CA; Rice Research Station, Crowley, LA; Texas Agricultural Research & Extension Center, Beaumont, TX; Delta Branch Experiment Station, Stoneville, MS; and Everglades Research and Extension Center, Belle Glade, FL. Public cultivars have accounted for more than 90 % of the U.S. acreage. Private breeding programs are present in several states and have expanded their activities. Notable features of the privates programs include development of special quality varieties of rice, F 1 hybrids, and international seed marketing. The major private programs include Busch Agricultural Resources, Inc., Pleasant Grove, CA and Jonesboro, AR; RiceTec, Inc., Alvin, TX; Farmers Rice Cooperative, Sacramento, CA; and Rice Researchers, Inc., Glenn, CA.

Pedigree breeding has been and continues to be the mainstay of U.S. rice breeding programs. Backcrossing and some modified bulk methods are also used to a lesser extent. Induced mutation made a major contribution to rice improvement in California by supplying adapted semidwarf germplasm which was used directly as cultivars and more extensively in crossbreeding. Some induced mutation work is continuing in various U.S. rice programs. Somaculture has been used to generate mutants for agronomic traits and disease resistance. Anther culture has been used to produce a long-grain rice cultivar in Texas. A large rice anther culture program is in place in Louisiana and this technology is used to a lesser extent in other states. RiceTec has been pursuing the development of F 1 hybrids (which have been very successful in China) and is moving into commercial production with their first materials in 1996. Transgenic herbicide-resistant lines have been developed from U.S. rice cultivars and are being tested in Louisiana and other states. Gene mapping of rice may soon be used as an additional rice breeding tool. Winter nurseries in Hawaii and Puerto Rico are routinely used for generation advance, screening, and seed increase.

Breeding objectives in programs may vary from region to region but they focus in the areas of increased yield, disease and insect resistance, resistance to environmental stress, and quality. One notable trend in grain quality research is an expanded effort to develop special purpose rice to meet ethnic or specialty markets. These might include aromatics (basmati, Della, and Jasmine types), waxy rice, premium Japanese, and large-seeded Mediterranean types of rice.

Genetic studies

U.S. rice geneticists include USDA scientists at Stuttgart, AR (2), Beaumont, TX (2), Davis, CA (1), and a Louisiana State University scientist Baton Rouge, LA. Genetic research is often conducted by rice breeders, pathologists, and physiologists from land grant universities in rice producing states. Rice is serving as a model system for molecular genetics and is being studied by scientists in numerous institutions and private companies in the U.S. and worldwide.

There have been tremendous advances in the field of rice genetics over the last decade, largely as a result of new molecular technology. Rice was among the first crops for which a molecular linkage map was produced, and two saturated maps based on an interspecific and an indica/japonica cross have been published as well as a RAPD-based map from a cross between two japonicas. Because of its small genome size, rice is an ideal species for map-based cloning technology, and Xa21, conferring resistance to rice bacterial blight, was the first gene cloned by this method in a monocot. Rice is also the cereal crop most amenable to transformation with exogenous DNA. These qualities have given it the status of model species among crop plants for genetic Studies.

Gene mapping has proceeded rapidly. Much of this work is being done by the International Rice Research Institute (IRRI) in the Philippines, the Japan Rice Genome Program (RGP), and Cornell University. RGP has developed a high-density molecular map and is continuing work on physical mapping of the rice chromosomes and large-scale DNA sequencing. Researchers in California and in Texas have begun mapping genes of relevance to U.S. rice production systems. Priorities include seedling vigor, yield and quality-related traits, and resistance to blast, stem rot and rice water weevil. Quantitative trait loci (QTL) for maturity and plant height, sheath blight resistance, and seedling vigor have been mapped in U.S.-based populations. While most gene mapping has focused on indica/japonica crosses, newly developed markers (e.g. microsatellites and AFLPs) will allow gene mapping within the temperate and tropical japonica subspecies.

Genetic Engineering

Methods for introducing genes through direct DNA transfer have been refined and are becoming applicable in rice. At present there are two principal gene transfer techniques in rice and other monocotyledonous crop plants. In the first method, cells cultured in vitro are exposed to certain enzymes for removal of their cell wall. This treatment allows rapid uptake and stable expression of DNA in the cells, but the process is labor intensive and limited to a few lines with high regeneration capabilities. A recent alternative to this direct uptake method has been development of the "particle gun" or "biolistic device" where micron-size gold particles are coated with DNA and accelerated to velocities sufficient for non-lethal penetration of cell walls and membranes. Advantages of biolistic gene transfer over the first method include reduced labor investment, simpler laboratory procedures, and an increase in the number of cultivars than can be stabily transformed. Genes transferred to rice by this approach are generally incorporated into more than one position on the chromosomes. Recent experiments in different laboratories using the direct uptake or biolistic approach have resulted in "gene silencing" where some genes that are transferred remain genetically stable, but are not expressed. To overcome this problem, engineered strains of the soil microbe Agrobacterium tumefaciens are being evaluated in different laboratories as an alternative gene transfer agent in rice. Recent studies in Japan, United States and Europe show that this technique leads to stable incorporation and expression of foreign DNA in adult plants. With continued success and refinements, A. tumefaciens may serve as the preferred vehicle for gene transfer in rice.

This technology appears promising for introducing traits useful for U.S. rice production and is rapidly moving from initial tests in the laboratory only a few years ago to multi-state field evaluations of various transgenic lines conducted in 1996. Examples include resistance to broad-spectrum herbicides, fungal diseases and insect pests.

Weed control is a major concern for all rice growing areas in the U.S. In the southern rice belt, red rice is the primary noxious weed. Glufosinate, a broad-spectrum herbicide, was shown to effectively control red rice and other weeds. Recently the bar gene, which confers tolerance to glufosinate, was introduced into various U.S. and Japanese cultivars. Results from a four-year field trial in Louisiana indicate that elite cultivars carrying the bar gene express high levels of tolerance to glufosinate at rates that will effectively control red rice and most other weeds. A multi-state evaluation of the bar-containing cultivars is currently underway. Transgenic herbicide resistant rice varieties are in development by several agricultural/biotechnology companies.

Fungal diseases are also a chronic problem for most U.S. rice growing states. Field trials were initiated in Louisiana with engineered rice containing chitinase genes for resistance against sheath blight and blast diseases. Preliminary results show reduced fungal infection levels with engineered rice when compared with controls. Resistance to Lepidopteran insect pests has also been introduced to rice by cloned genes originally isolated from the bacterium Bacillus thuringiensis.

The promise of genetic engineering for rice improvement is now closer to reality for certain traits such as herbicide resistance. Further refinements in cell culture and gene delivery methods will make this technology more accessible to plant breeders who will apply this tool to rice improvement.

Plant Introduction

In 1899, USDA introduced 'Kyushu' rice from Japan and distributed it for on farm testing in southwest Louisiana and Texas and formally began rice improvement in the U.S. Introduction of varieties represented the first step in rice improvement and many of these introductions were either used directly or selections were made from original populations or accessions. These early varieties are the ancestors of our modem U.S. cultivars and they certainly had a major role in the evolution of U. S. rice grain quality. Examination of the ancestral relationships of the rice cultivars developed by the U.S. public rice breeding programs indicate that all parental germplasm can be traced back to 22 plant introductions in the southern region and 23 plant introductions in California. Calculations also showed that current rice cultivars are closely related. This lack of genetic diversity is considered undesirable because it increases the potential genetic vulnerability of the crop. However, it has allowed the continued development of improved cultivars with the required quality characteristics that are consistent with established market types. Considerable efforts are made to introduce foreign germplasm into rice improvement programs.

Oryza species can be introduced into the U.S. only under approved quarantine procedures by a plant introduction permit holder. Animal Plant Health Inspection Service (APHIS) issues quarantine introduction permits to a limited number of qualified scientists. Incoming material is inspected and treated by APHIS then forwarded to the permit holder for quarantine introduction. USDA operates a Plant Germplasm Quarantine Office (PGQO) which handles introduction for non-permit holders and PGQO has limited facilities and staff for introduction of rice and has been processing about 400 new introductions annually. The ability to continue this level of quarantine introduction by PGQO is in jeopardy. Over 3000 lines are being held at NSSL for introduction. In 1996, 5511 accession were transferred to other permit holders for introduction. This large number of accessions in 1996 was due to introduction of large genetic mapping populations. This placed heavy demands on APffiS, which has been forced to implement restrictions on introductions.

The issue of rice quarantine and plant introduction has been a continuing agenda item at Rice Crop Germplasm Committee (RCGC) meetings since its inception. Current procedures are old, expensive, time consuming, and may limit importation of germplasm for U.S. research. APHIS, USDA, and RCGC recognize the need to research, document, and revise U.S. rice quarantine procedures that prevent the importation of new rice pests into the U.S. and also expedite the safe and efficient flow of germplasm for research progress. This area has been identified as a primary challenge for the RCGC and U.S. rice germplasm management.

Preservation

The USDA-ARS National Small Grains Collection (NSGC) presently maintains more than 17,250 accessions of Oryza. In addition to the cultivated species, sativa and glaberrima, accessions are maintained for six other Oryza taxons. Accessions have origins in about 110 countries or regions of the world. More than half of the accessions were donated via IRRI.

Rice accessions are maintained and distributed from the USDA-ARS National Small Grains Germplasm Research Facility, Aberdeen, Idaho, as part of the NSGC. Storage conditions are 6°C and 25% RH. Nearly all accessions are backed-up at the National Seed Storage Laboratory (NSSL). Regeneration and descriptor data collection are coordinated and performed by the USDA geneticist at Stuttgart, AR.

Evaluation and Enhancement

Ground breaking for the $11.2 million National Rice Germplasm Evaluation and Enhancement Center (NRGEEC) was on April 12, 1996, at Stuttgart, Arkansas. Completion of construction is anticipated by the winter of 1997.

The mission of the NRGEEC is to conduct germplasm-based research directed at meeting the need of the U.S. rice industry, in the rice producing states of Arkansas, California, Florida, Louisiana, Mississippi, Missouri, and Texas. The research needs include high yield, superior grain quality, pest resistance, and stress tolerance.

The NRGEEC is a 46,000 square foot facility containing offices, laboratories, seed storage, and greenhouse space. When completed and fully staffed, the NRGEEC will have ten USDA- ARS rice scientists, and will provide shared laboratory space for seven University of Arkansas rice scientists. Current USDA-ARS staff includes a director, research geneticist, research plant physiologist, and two support scientists. Future staffing priorities are for a molecular geneticist, a cereal chemist, a molecular plant pathologist, a cytogeneticist, and another plant physiologist.

As part of the National Plant Germplasm System, the NRGEEC complements the activities of the working collection of cereals in the National Small Grains Collection at Aberdeen, Idaho, and the base collection of all seed crops at the NSSL at Ft. Collins, Colorado.

STATUS OF CROP VULNERABILITY

Genetic

The two major rice growing regions of the U.S. have historically utilized different gennplasm pools. Recent genetic research has shown the southern U.S. long~grain varieties comprise a tropical japonica rice pool and the California medium and short grains a temperate japonica pool. Indica material has been used as a donor source of semidwarfing genes in both regions, but only after extensive backcrossing to adapted material. Breeding programs have relied on their own adapted gennplasm pools for cultivar development. This is due to the need to satisfy established grain shape, milling, cooking, and processing quality characteristics required for traditional U.S. markets. Cold tolerance and water-seeded seedling vigor in California and resistance to blast (Pyrcularia grisea) in the southern U.S. have also limited use of other gene pools.

In recent decades there have been notable shifts in selection of parents in U.S. breeding programs. First, the development of adapted cold tolerant vigorous long grains in California (L-201, L-202) have been extremely popular and successful parents for the southern U.S. This has opened a new genetic pool for the southern U.S. High quality southern long grains have also been used in developing improved California long grains. There has been an increase in the number of crosses made in the U. S., including more crossing of materials from different U.S. rice breeding programs.

Secondly, a strong breeding effort has begun to try capture the very high yield potential demonstrated in indica hybrids and inbred lines from of China. This high yield potential has not been successfully recombined with the high milling yield and cooking characteristics of U.S. long grains. This objective is receiving considerable interest and effort in the southern U.S. in both the public and private sectors.

Additional gennplasm pools for the U.S. are being used to develop rice with special cooking and processing characteristics. This would include basmati, Jasmine, Della, waxy, premium quality Japanese, large-seeded Mediterranean types, and "Calrose" quality medium-grain rice. To recover the desired quality breeders are accessing different gennplasm pools. A recent first-time outbreak of blast in California has also resulted in breeders seeking new gennplasm pools in search of resistance. These objectives pose significant breeding challenges and may aid in broadening the U.S. gennplasm base for rice, thereby reducing genetic vulnerability. Conversely, it may also increase risk because of adaptation problems not experienced in the traditional gennplasm pool.

Industry

The U.S. rice industry is facing major challenges for survival. Government price supports are being phased out. International markets offer trade opportunities as well as low cost competitors that have increased U.S. rice imports. Enviromnental concerns and urban encroachment are impacting the industry. High grain quality levels are being demanded and production costs continue to rise. Rice production is gaining support from wildlife advocates because of its value to waterfowl and contribution to wetland habitat. Rice growers have increased their direct financial support for rice research and improvement, however, public research is experiencing significant budgetary restrictions.

In summary, the number of U.S. rice breeding programs has increased, the programs are larger in size, and are clearly increasing their utilization of genetic material from outside their adapted germplasm pools. The collection, preservation, distribution, evaluation, enhancement, and exchange of rice germplasm is going to be essential for success. The U.S. rice industry is certainly economically at risk and rice improvement is clearly identified as a major priority for the preservation and continued prosperity of the U. S. rice industry.

GERMPLASM PRIORITIES

NRGEEC

The successful identification, evaluation, and enhancement of the rice germplasm for U.S. rice improvement will playa pivotal role in the speed, progress, and success of U.S. rice breeding efforts and ultimately the U.S. rice industry. This activity is consistent with the mission of the NRGEEC. Facilities are scheduled for completion in the Winter of 1997. Thus, it is the position of the RCGC that the funding for staffing and operation be identified as the highest priority to move the NRCEEC forward on its mission, to serve its role in U.S. rice improvement.

Rice Quarantine

Rice quarantine regulations and procedures have been identified as needing review and revision by rice research scientists and APHIS for many years. Quarantine regulations do not reflect current scientific concerns about rice pests. Current procedures are expensive, time consuming, may limit genetic variability, are increasing quarantine backlogs, may encourage illegal introduction, and slow the movement of rice germplasm in U. S. research and commerce. Rice pathologists have developed revisions to the current protoco~ for the Rice Crop Germplasm Committee but are unable to prepare an appropriate referenced proposal for quarantine revision for consideration by APHIS. APHIS staff are overwhelmed with work on other critical projects. Thus, it is the position of the RCGC that funds and personnel should be secured to research, document, and submit to APHIS a new revised U.S. rice (Oryza spp.) quarantine procedure to minimize the risk of importation of rice pests of the world and meet the needs of the U.S. rice research community and industry.

Areas For Germplasm Research And Improvement

Four broad areas were identified by RCGC for germplasm research and improvement. They are interconnected and can be used to characterize a rice cultivar or germplasm line. All areas offer opportunities for research, enhancement, and application for rice variety improvement.

1. Yield is a broad category which remains one of the primary objectives for breeders and an identified need of U.S. rice growers. High, stable yields help reduce unit costs, provide a reliable commodity supply, and make cost effective use of agricultural inputs like water, fertilizer, and pesticides. This would include new genetic traits and mechanisms for yield advances.
2. Quality holds a very high position as a research priority. There is a clear increased emphasis on all aspects of rice quality (shape, appearance, milling, cooking, and processing) in U.S. rice research, experimentation, and marketing. Quality tends to limit yield and vice versa.
3. Pest management offers the potential to genetically protect rice with obvious benefits to yield, quality, and to the environment. This may be accomplished through genetic resistance to the major U.S. rice diseases [blast (Pyrcularia grisea), sheath blight (Rhizoctonia solani), and stem rot (Sclerotium oryzae)] and to insect pests like the rice water weevil (Lissoroptrus oryzophilus K). Other germplasm sources may provide "new" methods for weed control like herbicide resistance, herbicide tolerance, and alleopathy. All of these possibilities benefit producers and consumers by controlling pest damage, increasing yield and quality, reducing inputs and costs, and reducing environmental impacts.
4. Adaptation to the environment poses many challenges to rice production. The stress rice plants in the U.S. endure include high and low temperatures, water and soil quality, abiotic diseases and disorders, and pollutants. Some of these stress factors may be of greater importance in the future.

RCGC suggests the following activities as areas of emphasis for U.S. rice germplasm.
1. Collection and Preservation

A. Revise rice quarantine to expedite the flow of valuable germplasm into the
collection.
B. Survey rice collections of U.S. rice scientists and add available material to the national collection.
C. Identify and fill gaps in the national collection and limit redundancy in collection and introductions.
D. Obtain materials for "at risk collections" for preservation.

2. Evaluation

A. Resume the evaluation of the U.S. rice working collection for desirable milling,
cooking, processing, and nutritional characteristics using new technologies (e.g. NIR).
B. Continue evaluation for disease and insect resistance important to U. S. rice production.
C. Continue evaluation for sources of herbicide resistance and alleopathy.
D. Evaluate collection for important physiological traits (e.g. N use efficiency).

3. Enhancement

A.Identify useful genes for yield, quality, pest control, and adaptation.
B. Determine the inheritance of these important genes.
C. Develop improved germplasm through the use of conventional and molecular
methods.