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Rice Genetic
Resources through

Elcio Perpétuo Guimarães[1]
Marc Châtel[2]

Elcio Perpétuo Guimarães


With the rice crop (Oryza sativa L.), breeders probably have the widest range of choices for exploiting the genetic resources available in the genus. They have access not only to the crop’s genetic resources as found in different ecosystems, but also to the knowledge base of its classification among genetic groups. Hence, breeders can also use the African O. glaberrima Steud. and various wild species. Such broad inter and intra-species variability is used in conventional breeding methods for self-pollinating crops, with the additional possibilities of producing hybrids and improving populations with broad genetic bases. This chapter presents a general view of how Latin American breeders seek to exploit rice genetic resources to develop varieties, emphasizing the use of population improvement. The search for genes for resistance to diseases and insect pests, a new ideal plant type and hybrids is discussed as a strategy to increase yield and use genetic resources more effectively. We briefly describe the achievements of various countries in using population improvement, already presented in detail in several chapters of this volume. We highlight the commercial release in Brazil of cultivar SCSBRS 113-TioTaka, the first rice variety to be obtained from a line derived from a population with a broad genetic base and improved through recurrent selection. We conclude by recommending modifications to the evaluation methodology for population improvement, particularly for the trait yield.


El arroz (Oryza sativa L.) es quizás uno de los cultivos en el cual el fitomejorador posee las más diversas alternativas para explorar los recursos genéticos disponibles en el género. Se encuentran disponibles los recursos genéticos de la especie cultivada en los diferentes ecosistemas y el conocimiento de su clasificación en grupos genéticos. Así mismo están a disposición de los fitomejoradores la especie africana (O. glaberrima Steud.) y las varias especies silvestres. Esta gran variabilidad intra e inter-específica se utiliza a través de los métodos convencionales de mejoramiento de los cultivos autógamos, con la posibilidad adicional de producir híbridos y mejorar poblaciones de amplia base genética. Este capítulo presenta una visión general de cómo los fitomejoradores latinoamericanos buscan explorar los recursos genéticos del arroz para desarrollar variedades, con énfasis en la utilización del mejoramiento poblacional. La búsqueda de genes de resistencia a enfermedades y plagas; la de un nuevo tipo de planta ideal y la de producción de híbridos se mencionan como estrategias para incrementar los rendimientos de grano y el uso de los recursos genéticos. Se describen de manera breve los logros de los países que utilizan el mejoramiento poblacional (estos aparecen detallados en varios capítulos de esta publicación). Cabe resaltar el lanzamiento comercial en Brasil, de la variedad SCSBRS 113 - TioTaka, la primera de arroz de riego obtenida de una línea derivada de una población de amplia base genética mejorada por selección recurrente. El capítulo concluye con una recomendación para que se realicen ajustes en la metodología de evaluación en el mejoramiento poblacional, en especial, para el carácter rendimiento de grano.


In its 31st Session (November 2001), the FAO Conference approved the International Treaty on Plant Genetic Resources for Food and Agriculture. The approval came after 7½ years of discussion and negotiation among the 164 member countries of the Commission on Plant Genetic Resources for Food and Agriculture. By 5 November 2002, the European Community and 77 countries had signed the Treaty and, on the same date, 9 had ratified it. The Treaty will become effective 90 days after 40 have ratified it.

The Treaty is vitally important to the theme of conservation and sustainable use of the world’s plant genetic resources for food and agriculture (PGRFA). It is the document used for germplasm exchange, helping to distribute, justly and equitably, the benefits deriving from the use of this germplasm. It establishes the work priorities for these areas (FAO, 2001). The Treaty applies to all PGRFA and includes specific provisions for the multilateral access and distribution of benefits for the most important crops, including rice. Plant breeders therefore do not have to make contracts to access samples of rice genetic resources. Moreover, the Treaty establishes provisions for the use of genetic resources stored in the germplasm banks of the international centres of the Consultative Group on International Agricultural Research (CGIAR).

The Global Plan of Action (GPA) is the document that orients activities for countries to fully implement the Treaty. Chapters 9 to 14 of the Plan describe activities related to the use of PGRFA. Chapter 10 clearly indicates that prebreeding and broadening the genetic base of crops should be priorities of national genetic improvement programmes (FAO, 1996).

Rice breeders can consider themselves privileged with respect to the number of methodological alternatives with which they may exploit the genetic resources available in the 22 species of the Oryza genus (Vaughan, 1994). The two ecotypes of the cultivated species Oryza sativa L., occasionally denominated as subspecies indica and japonica, are autogamous and, as a result, their improvement has been characterized by the use of methods commonly employed for autogamous plants. Most of the varieties cultivated in different parts of the world started from the genetic variability generated by simple, triple or multiple combinations, and lines were developed by the pedigree method. Mass selection or modified mass selection methods, and backcrossing have been important under certain specific conditions.

The new ideal plant type as proposed by Khush (1994) has contributed a new, although not methodological, alternative to the genetic improvement of rice by broadening the exploitation of the crop’s species and ecotypes. Its combination with methodological alternatives such as hybrids has made it possible to obtain significant gains in important traits such as yield.

In recent decades, the exploitation of rice genetic resources began including the alternative of hybrid development. Although this method is limited for some countries, it has shown potential, particularly in China (Yuan, 2002), and is spreading to other Asian countries (Tran, 2002).

Population improvement, a method typically used for allogamous species, is now part of the portfolio of alternative means of exploiting rice genetic resources, particularly in Latin America, with the creation of populations and training of scientists by CIAT, CIRAD and Embrapa Arroz e Feijão in the mid-1990s.

As well as these alternatives related to the use of different methods of improvement, rice is also the model crop for studies involving molecular markers. The rice genome has been one of the most studied by scientists around the world. Goff et al. (2002) present the genome sequence for the japonicas, and Yu et al. (2002) that of the indicas.

According to Brown and Brubaker (2002), the number of accessions in germplasm banks has grown continuously, but their use and maintenance are a problem. On analysing the alternatives described-new ideal plant type, hybrids, population improvement, and biotechnological tools-one concludes that, in recent decades, rice breeders have been extremely creative. They can also be considered as models for other breeders wishing to increase the exploitation of genetic resources available in the different species of their respective crops.

To create hybrids, for example, cytoplasmic- genetic male sterility has been sought for in O. sativa f. spontanea. To expand the capacity for crossing and facilitate the production of hybrid seeds, Taillebois and Guimarães (1988) describe how they used the species O. longistaminata A. Chev. et Roehr. Moncada et al. (2001) used species such as O. rufipogon Griffith to increase the yield of the crop under upland conditions in Latin America. With the same objective, Xiao et al. (1998), in China, worked with the wild species O. rufipogon and found genes responsible for increasing yield. Brondani et al. (2002) are using a species collected in Brazil (O. glumaepatula Steud.) to increase yield of irrigated varieties.

Population improvement allows the creation of populations involving varieties of different origins and possibly distinct genetic structures. Some examples of genetic variability grouped into available populations by Latin America plant breeders are:

This chapter presents an overview of how Latin American plant breeders are seeking to exploit rice genetic resources to develop varieties that respond better to the demands of different users along the crop’s production chain. Emphasis is given to the use of population improvement.

Introgression of resistance genes

One strategy that has most contributed to the expansion of using a crop’s genetic resources is the introgression of genes of resistance to diseases and insect pests. In rice, several examples show the use of this strategy for seeking, in wild species, resistance that is either nonexistent or existing at undesirably low levels in the cultivated species.

One early reported example is the introduction of resistance to grass stunt virus, an important viral disease in Asia, into varieties IR28, IR29 and IR30. The source of resistance came from O. nivara Sharma et Shastry. For resistance to the viral disease tungro, the source used was O. rufipogon (Khush, 1977).

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (ex Ishiyama 1922) is very important in Asia, with no adequate levels of resistance existing in the cultivated species. Khush et al. (1990) found a resistance gene in O. longistaminata and transferred it, by successive backcrossing, to variety IR24.

In Asia, the white-backed planthopper is an important pest of the rice crop. Jena and Khush (1990) introduced resistance genes found in O. officinalis Wall ex Watt into several lines developed by the International Rice Research Institute (IRRI). The authors noted that, in these crosses, genes of resistance to X. oryzae were also introduced.

These are only a few examples of how rice genetic resources have been used to introduce resistance into commercial varieties.

New gene combinations for obtaining varieties

IRRI has worked on developing a new plant type since the 1980s. The idea was to produce a rice plant that, compared with commercial varieties, presents fewer tillers; denser panicles, with a larger number of grains; and a higher percentage of filled grains per panicle (Khush, 1994).

The exploitation of different germplasm to generate these materials is a clear example of broadening the use of rice genetic resources. The new lines, which yield 20% to 30% more than the best commercial materials, originated from crosses between materials classified as ‘Bulu’ or javanicas (tropical japonicas from Indonesia), and temperate- climate indicas and japonicas from IRRI’s genetic improvement programme.

The progress made from directly using this strategy is still limited. However, crosses are already being made in several countries with lines originating from this strategy. Thus, the possibilities of obtaining new gene combinations and broadening the genetic base of the commercial varieties are increasing. The contribution of this germplasm to hybrids is significant as it deals with material of an origin different to that which has been used, thus opening doors towards obtaining combinations that are even more heterotic than the current ones.

The New Rice for Africa (NERICA) programme is another example of using rice genetic resources to develop commercial varieties that are more adapted to local cultivation conditions, which, in this case, emphasizes the upland system. To develop new varieties with increased vigour and greater capacity to compete with weeds, parental materials from the cultivated African (O. glaberrima) and Asian (O. sativa) species were combined. The potential increase in yield was 35%, compared with local varieties (M. Jones, personal communication, 2002, WARDA, Côte d’Ivoire).

Hybrid rice

The first scientist to report the phenomenon of heterosis in rice was Jones (1926). The idea of commercially exploiting hybrid rice was first mooted in India (Richharia, 1962) and China (Yuan, 1966), with the Chinese developing the strategy further. The mid-1970s saw the development of the first groups of lines possessing cytoplasmic-genetic male sterility, with their maintainers and restorers for commercial hybrid production via the three-line method (Lin and Yuan, 1980). The development of this methodology permitted plant breeders to exploit genetic resources that were distinct from the traditional ones. Even the gene of male sterility had to be introduced from a wild species, O. sativa f. spontanea (Lin and Yuan, 1980). This strategy made possible increasing yields by 20% to 30% (Yuan and Virmani, 1988).

Currently, the methodology to develop a genetic improvement programme emphasizing hybrid production has been carefully described in several publications. Yuan and Fu (1995) detail all the stages that should be followed to obtain male-sterile lines, restorers and maintainers. The search for higher levels of heterosis requires using distantly related germplasm from the genetic viewpoint.

Today, we can say that hybrid rice is a reality in China, India, Viet Nam, Philippines, Bangladesh, Indonesia and Sri Lanka (Manicpic, 2002).

Although the genetic resources exist and the technique for their use is well described, one constraint is the methodology to commercially produce hybrid seeds. Despite considerable progress in recent years, it continues to be a major limitation to the technology’s broader dissemination. Virmani (2002), in commenting on the orientation of research programmes for hybrid rice, refers to seed production in four of nine areas of research.

A possible solution to this problem is to use hybrids of two lines, in which the need for cytoplasmic-genetic male sterility is eliminated, and temperature and day length are used to sterilize the female lines. According to Yuan (2002), in China, about 2.5 million hectares are already planted to hybrids with two lines. Their yields are 5% to 10% higher than the three-line hybrids.

Population improvement

The original direction of population improvement was very different to the one it follows today. As Châtel and Guimarães (1993) mentioned, the initial idea was to develop hybrid rice with competitive advantages under drought. That is, to produce materials with more efficient root systems than those of the germplasm available in the 1980s. These populations were used as a basis on which to launch population improvement programmes, using recurrent selection. That is, the populations would permit the creation of other populations better adapted to different cultivation conditions. They would also solve the problems of Latin America as mentioned above and discussed in several chapters of this volume.

The initial idea was to use these populations as vehicles for broadening the genetic base of commercial varieties, which, as Cuevas-Pérez et al. (1992) pointed out, is very narrow. This is particularly true for those varieties released in Latin America between 1971 and 1989. However, other literature suggests that genetic improvement does not necessarily reduce diversity (Donini et al., 2000; Manifesto et al., 2001).

Because of the diversity of the parental materials involved in the composition of these populations, exploiting the crop’s genetic resources through this methodology was believed to be an interesting alternative with which to achieve the objective. The population improvement method was also readily accepted by national breeding programmes in Latin America, because it contributes a constant source of variability. Such variability stems from the presence of the recessive nuclear gene for male sterility, which permits the constant recombinations needed to manage the recurrent cycles. The region’s genetic improvement programmes began looking at the possibility of routinely obtaining improved lines that could be evaluated for their potential as new varieties for farmers.

The more structured programmes sought, in addition to lines for their trials on grain yield, parental materials for their conventional programmes for crosses and generating new variability (e.g. Venezuela; C.E. Gamboa (R.I.P.) and DANAC Foundation, personal communication, 2002).

Hence, the methodology was rapidly adopted in the region and, after a little more than 6 years, significant results are being produced, not only for the breeding programmes themselves but also for the farmers. Such is the case of the recent release of the variety SCSBRS 113-TioTaka, recommended for irrigated conditions in the State of Santa Catarina, the second largest producer of irrigated rice in Brazil.

Other countries have promising lines ready for official release into favoured uplands (e.g. Bolivia; R. Taboada Paniagua, personal communication, 2003, CIAT-Bolivia), and temperate-climate, irrigated-rice ecosystems (e.g. Chile; S.I. Hernaiz-L., personal communication, 2003, INIA, Quilamapu).

Progress achieved with the methodology

On reviewing the chapters of this book, the reader will clearly see the level of commitment assumed by Latin American breeders to use the new rice improvement method. The reader will also appreciate the progress achieved by most of the institutions working in the region.

Venezuela, for example (Chapter 10, this volume), in the first semester of 2003, completed the second recurrent cycle with population PFD-1. In the field, the phenotypes of S0:2 families clearly showed improvement when compared with the same generation from cycle 1. The conventional crossing programme is now using lines originating from the populations as parental materials an objective proposed for implementing the project.

The Bolivian programme has successfully developed lines from the populations it handles. These lines are now undergoing final yield evaluation trials, and showing potential for commercial release in the following year. Moreover, after the initial mass selection, the S0:2 families routinely underwent completed recurrent cycles and evaluation in multisite trials (Chapter 12, this volume).

Chile is concentrating on managing, under temperate conditions, two site-specific populations that were created by introducing local lines into introduced populations with broad genetic bases (Chapter 8, this volume). This country has developed a specific methodology to improve levels of cold tolerance in the populations and already has advanced lines in regional yield evaluation trials.

The programmes carried out by Embrapa Arroz e Feijão and the CIRAD/ CIAT Rice Project, by their nature and levels of experience, are the ones that have made the most progress.

As already mentioned, the Brazilian improvement programme for irrigated conditions has just released the variety SCSBRS 113-TioTaka and has several other advanced lines in final multisite yield evaluation trials.

The CIRAD/CIAT Rice Project developed an early maturing line that has been the most productive of all the materials so far planted under acid-soil conditions in Colombia. As Guimarães (2000) noted in his description of future needs, the researchers have begun studying the gains produced by using this methodology. Ospina et al. (Chapter 17, this volume) present results of evaluations of genetic gains after a selection cycle for yield and flowering under acid-soil conditions, and the effect of recombination cycles after selection.

Badan et al. (Chapter 16, this volume) describe the genetic gains achieved by using the methodology to improve levels of blast resistance in a population of upland rice. In Chapter 6, Trouche proposes an alternative to involve the participation of different actors in the production chain in managing the populations. Courtois et al. (Chapter 4) and Ramis et al. (Chapter 5) suggest some possibilities for using biotechnological tools in population improvement.

Methodological adjustments

Although the achievements are so far preliminary, one can see that the researchers who work with population improvement must begin studying methodological alternatives to better evaluate the traits they are selecting, particularly, yield. The increasing use of rice genetic resources, by creating populations with broad genetic bases, has enabled several authors to consider as attainable the broadening of the genetic base of commercial varieties and the breaking of yield ceilings. The materials that are in the final stages of evaluation in different national programmes yield more than the commercial checks and the programmes continue improving their populations.

Despite all the above, constraints continue, especially in the evaluation of progenies to decide on selection for the recombination phase and development of the new improved population. These constraints are:

Improvement programmes that are more advanced in the use of the methodology should give special priority to these themes, for example, by encouraging postgraduate students to conduct the work for their theses.

Final comments

The rice crop is an example of the creativity of researchers in combining the exploitation of genetic resources available in germplasm banks and using them in genetic improvement programmes by applying various and innovative methods for the crop.

The combination of improvement methods for autogamous and allogamous plants allows taking advantage of traits of agronomic interest that are present in lines belonging to different species and groups. Moreover, it permits the combination of parental materials of different origins to produce heterosis or create populations with broad genetic bases.

The priorities described in the GPA to encourage countries to sustainably use genetic resources have been implemented for the rice crop over several years, as can be seen in the comments made in different sections of this chapter.

Overall, this volume attempts, although with a focus on population improvement, to stimulate the creativity of plant breeders who work with other crops, particularly autogamous, to seek alternatives among the genetic resources available to them to sustainably broaden their use for the benefit of farmers.


We would like to take this opportunity to express our thanks to the national institutions and rice breeders of Latin America for their confidence, support and commitment to the implementation of a regional approach to rice population improvement.


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[1] Embrapa Arroz e Feijão, currently at FAO, Viale delle Terme di Caracalla, 00100 Rome. E-mail: [email protected]
[2] CIRAD/CIAT Rice Project, CIRAD-CA, A.A. 6713, Cali, Colombia. E-mail: [email protected]

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