Chapter 3: Agro-morphological variability of rice species collected from Niger
3.2 Introduction
Globally, plant breeding has played an important role in the yield increase and quality improvement of many crops essential to human and animal nutrition. However, the widespread adoption rate of modern cultivars, combined with changing patterns in cropping, such as changes in cultural practices, crop intensification and sometimes natural disasters, tend to induce erosion of genetic diversity of cultivated crop species. This threatens long term global agricultural production (Hammer and Teklu, 2008). Indeed, preserving the genetic diversity of plants is important for the survival of species as well as their evolution in a rapidly changing environment, but also for small-scale farmers to be able to produce food under various climatic, biotic and
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edaphic factors. Additionally, that observed diversity is essential for future breeding programs (Gao, 2003). Generally, genetic erosion refers to the quantitative reduction of discrete representatives of a species in a region or ecosystem (Solbrig, 1991). However, for plant breeders, genetic erosion refers to the decrease of genetic variability, due to the loss of entities carrying specific genes or alleles (Esbern, 1999). By extension, it could also be defined as the disappearance of named varieties in regions or ecosystems where they have been reported previously (Hammer et al., 1996).
Two methods are being used to prevent the loss of genetic variability in crop species:
- In-situ conservation, based on farmers' involvement, has the advantages of keeping the species in their natural ecosystems or appropriately managed ecology. In that way, the crop species will evolve in their local environment and will thus undergo natural selection and adaptation (Tin et al., 2001);
- Ex-situ conservation, which involves collecting and storing seeds, cultured tissues or cloned DNA fragments in a genebank. However, seed collection is the most commonly used. Based on the duration of the conservation and the use of the material, a base collection, an active collection or a working collection could be established (Balick, 1991).
To support the global effort of plant genetic resource conservation, several world collections were developed for various crops, including pigeon pea (Reddy et al., 2005), and pearl millet (Bhattacharjee et al., 2007). Additionally, several national and regional collecting expeditions have been undertaken in several countries. These have included both cultivated crops (Lasa et al., 2001; Reddy et al., 2005; Mahalakshmi et al., 2007) and related wild species (Nooryazdan et al., 2010; Shakhatreh et al., 2010). These collections were evaluated for agro-morphological traits, documented, stored and are now being used to broaden breeding programs.
Likewise, collections have been conducted in many countries and regions to collect, evaluate and store rice genetic resources. Only two of the 23 species comprising the genus Oryza are cultivated (Vaughan et al., 2003), while the remaining are wild species. However, because of their adaptation to harsh biotic and abiotic environmental conditions, these wild species bear traits that may be useful for the improvement of cultivated rice (Khush, 1997) and they have therefore also been included in the conservation of the genus Oryza. The cultivated Asian rice
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Oryza sativa L. was domesticated in Asia, around 10,000 years ago from the wild annual O.
rufipogon, followed by a later, differentiation into two main subspecies: indica adapted to tropical and subtropical floating, lowland and irrigated agrosystems, and japonica adapted to temperate and tropical upland ecosystems (Chang, 1984; Khush, 1997). These two main subgroups have been differentiated based on morphological traits such as grain shape, apiculus hair length, leaf width and colour, or through biochemical assays for reaction to phenol (Kovach et al., 2007). In addition, isozymes have been used to classify the species into six varietal groups with indica and japonica as major groups (Glaszmann, 1987). With the advent of rice genome sequencing, simple sequence repeats (SSR) and microsatellites have been used to divide O. sativa into five groups consistent with the structure obtained using the isozymes (Garris et al., 2005).
African rice, O. glaberrima, was domesticated 3,500 year ago in the inner delta of the Niger River and later in the West African coastal regions (Portères, 1956; Chang, 1976; Second, 1985).
It was domesticated from the annual wild species O. barthii, itself derived from perennial wild species O. longistaminata (Sarla and Mallikarjuna Swamy, 2005). Several studies have concluded that African rice is less diverse than Asian rice (Chang et al., 1977; Second, 1985;
Barry et al., 2007a). Nevertheless, three subgroups, including a floating photosensitive ecotype (adapted to deepwater agrosystem), a non-floating ecotype (adapted to rainfed lowland agrosystem) and an upright ecotype (adapted to rainfed upland agrosystem) have been identified in African rice accessions using SSR markers (Semon et al., 2005). While Asian rice is being cultivated in all other parts of the world, Africa is the only continent where the two cultivated rice species have been cropped together since the 15th or the 17th century (Linares, 2002). Major rice collections were assembled during the sixties in most African countries and seeds were stored with three major research institutions: IRAT-ORSTOM, IITA, IRRI and the Japanese Institute of Genetics (Oka, 1977). Recently, collection of cultivated rice species was conducted in West Africa (Barry et al., 2007b; Nuijten et al., 2009), but Niger was not included, although the country is the nearest bordering of the primary centre of diversification of O. glaberrima, on the downstream part of the Niger River. On the other hand, rice species in Guinea, Mali and Nigeria were collected, studied and stored in genebanks (Bezançon et al., 1977; Semon et al., 2005; Barry et al., 2007b). In addition, in 2007 research conducted online on the AfricaRice Genetic Resources Unit database, which revealed that only 32 accessions had ever been collected from Niger, (1982), but were no longer available from 2007 to 2010. Thus, Niger did not benefit from
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the global effort to conserve local rice diversity ex-situ, although rice is the primary crop of people along the Niger River and other marshes from the central-south to the south-eastern part of the country around the Lake Chad and the Komadougou River. Moreover, major irrigated areas were constructed in the country, promoting high yielding O. sativa rice cultivars at the expense of O. glaberrima. Rice agrosystems in Niger include a diverse range, including rainfed lowland, deepwater flooding and irrigated (Bonkoula and Miezan, 1982). The present study was undertaken firstly, to create the first exhaustive collection of rice species from Niger, and secondly to evaluate the collection for agro-morphological traits, as well as identifying their geographical and ecological distribution.