Chapter 4: Simple sequence repeat (SSR) markers-based genetic diversity and population
4.5 Discussion
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Table 4.6: Eco-geographical partitioning of the Molecular Variance of the 264 Accessions Source of variation df Estimated variance Percentage of variation
(a)
Between zones of collection 3 -0.207 -2.451
Ecologies within each zone 8 0.953 11.283**
Groups within ecologies 6 3.477 41.167**
Within groups 500 4.223 50**
Total 517 8.446 100
(b)
Between groups 1 2.792 35.5**
Between sub-populations within
groups 2 0.774 9.8**
Accessions within subgroups 488 4.294 54.6**
Total 491 7.861 100
**: Values significant at P ≤ 0.001
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japonica), with high overall diversity in the world and Guinea samples, while there was only the indica subspecies in Niger. However, the gene diversity in Niger (D = 0.69) was similar to D = 0.7 found in the world collection of sativa species and the mean heterozygosity, Ho = 0.14, was twice as high as that of the collection of rice accessions of Maritime Guinea.
Regarding O. glaberrima accessions, the number of alleles found in the collection from Niger (Na=4.94) was higher than that found in the Maritime Guinea (Na=0.45). In contrast, a large number of alleles (Na= 9.4) was found in a collection of 198 rice accessions from 12 Africa countries (without Niger), when analysed at 93 SSR loci (Semon et al., 2005). Likewise, the African collection of O. glaberrima had slightly high PIC value (0.34), compared to that of the Niger collection presented here (PIC= 0.31), while the gene diversity was higher in Niger.
Girma et al. (2010) studied Ethiopian wild rice using inter-simple sequence repeat amplification (ISSR) and found for their sample of O. barthii a gene diversity value of 0.18, four times lower than the value of gene diversity (D=0.77) within the O. barthii sample from Niger. The number of allele per locus (Na = 4.06) in this study was double that found in a collection of 240 accessions of wild O. rufipogon, collected in China and south-eastern Asia, when they were evaluated by 24 pairs of SSR primers (Li et al., 2006). However, this collection of O. rufipogon displayed greater gene diversity. In addition, the value of gene diversity observed in the sample of O. barthii from Niger was higher that those from populations of O. rufipogon and O. officinalis from China, that were evaluated with seven SSR markers (Gao and Zhang, 2005).
4.5.2 Population structure and distribution
The results from the model-based population structure analysis showed the presence of two main genotypic groups. Nearly all O. sativa accessions belong to Group 1, while Group 2 consisted of O. glaberrima and its two wild relatives, O. barthii and O. longistaminata. The O. sativa accessions in the present study were only O.s. subsp. indica. The lack of japonica subspecies in the current study was not surprising because of the hot and dry climate of Niger. Indeed, in 1965 an attempt was made to introduce japonica varieties originating from Taiwan, but without success (Bonkoula and Miezan, 1982).
Rice cultivation in Niger is dominated by lowland production, with low to deep-water ecology (water level < 500 mm), floating ecology (water level up to 5 m) and irrigated ecology (full
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controlled water level). Thus, O. sativa subspp. indica (Gg1-2), corresponding to Group I identified by Glaszmann, (1987), was well represented in irrigated and lowland ecologies with both traditional accessions, landraces. Floating photosensitive O. sativa accessions (corresponding to Group III and IV identified by Glaszmann) were also cultivated in the country along the Niger River and other seasonal watercourses. In addition to local floating landraces like the "red Degaulle", intensive releases of deep-water and floating rice were achieved before the independence of the country. Some varieties of the subgroup Gg1-1, like Sintane Diofo and D5237, are representative of these varieties. The latter cultivar was found to be the most important floating rice variety of the country in the production area in the western part of the Niger River, while varieties El-Sambera and Sountan, two other floating accessions, were the most important in the south-eastern part of the Niger River region.
The Gg2 group was composed of O. glaberrima (Gg2-glab.) cultivated only in lowland and floating ecologies, plus the closely related wild annual O. barthii (Gg2-barthii) and one sample of O. longistaminata, which is the perennial ancestor from which O. barthii was supposed to have been derived. Apart from ecological information, genetic data was unable to separate the
"floating" ecotype from the "non-floating" described by Porteres (1970) and confirmed later (Semon et al., 2005). The floating ecotype of O. glaberrima was cultivated mainly in Tillabéry, bordering Mali, while the "non-floating" varieties appeared progressively in the proximity of Nigeria. However, few accessions of the "floating" glaberrima were found in the last village of Niger before entering Nigeria. In contrast, only a few accessions of glaberrima remained in the valley of the Komadougou Yobé, in the region of Lake Chad. Most of the glaberrima accessions from the central-south region, bordering Nigeria, were also 'non-floating" types. However, a few floating glaberrima varieties were still cultivated in Tafukka, a village near the city of Konni, very far from the Niger River and close to the Nigerian border. Apart from a few villages on the Niger River, this village had the largest number of accessions of O. glaberrima. It was probably due to germplasm exchange between autochthones and relatives living in the region of the Niger River in Niger or Nigeria.
Our data also revealed the presence of admixed accessions between O. sativa and O. glaberrima in different regions (the Niger River, the Dallol Maouri and in the village of Tafukka). Despite
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the sterility barrier, such natural recombination between the two cultivated species was widely reported. After the first case of identified natural interspecific variety in Guinea (Barry et al., 2007b), a study conducted recently on 315 rice samples from seven West-African countries revealed the occurrence of natural interspecific hybrids between the African and Asian rice in farmers' fields, leading to the emergence of a new genetic group (Nuijten et al., 2009). It was suggested that spontaneous backcrossing events were driving the process. Such possibilities were suggested long before the creation of New RIce for Africa (NERICA) by AfricaRice (Pham, 1992; Ghesquiere et al., 1997; Jones et al., 1997). Similarly natural hybrids have occurred between O. sativa and O. barthii, the wild progenitor of African rice. Their progenies were called O. stapfii. Chev. but in the absence of clear discriminating morphological traits and a continuous variation of traits between the two parents, progenies were subsequently classified with the barthii species (Chevalier, 1932; Bezançon, 1993). Thus, the prevalence of weedy O. barthii types (collected near cultivated rice fields) in our O. barthii samples could explain the low differentiation observed between Gg2-glab. and Gg2-barthii in the present study. Another hypothesis is that the marker set used in this study could not separate O. glaberrima from O.
barthii, with most of their genome being common. To confirm this information, the genetic data of 2757 accessions genotyped with 50 SSR by the GCP to constitute its rice core collection was downloaded from Internet and analysed to test the concept (http://gcpcr.grinfo.net/index.php?app=datasets&inc=files_list). Similar to our study, O. glaberrima, O. barthii and O. glumaepatula (a floating South American wild rice species) were not separated by this set of markers, in the same way O. sativa was not separated from its wild ancestors, the annual O. rufipogon and the perennial O. nivara. A more recent study was conducted to investigate the domestication history of O. glaberrima using multiple sequences from 14 genes (Li et al., 2011). Analyses of the population structure of 20 accessions of O. glaberrima and 20 accessions of O. barthii species, from 16 African countries showed that some O. barthii samples, originating from the supposed centres of domestication of O. glaberrima (Niger River upper delta and Sahelian rivers), shared a high level of ancestry and clustered with the O. glaberrima group, which was homogenous, regardless the inferring methods applied.
A farmer variety collected in Tafukka is named "Chinkafa Djado", meaning "rice of the warthog"
in Hausa. It has intermediate spikelets and awns characteristics similar to O. barthii and has very
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high shattering incidence. This variety could be considered to be the result of either a natural interspecific between the two species or a variety in the process of domestication. Chen et al.
(2004) reported gene flow frequencies to vary from 0.011% to 0.046%, from cultivated rice to weedy forms of O. sativa; and 1.21% to 2.19% from cultivated rice to wild rice O. rufipogon, under field conditions.
When partitioned, most of the observed genetic variance remained between the two main groups and within related subgroups, suggesting that accessions were highly differentiated within subgroups. Additionally, 12 accessions were admixed between the two sativa subgroups.
However, they are randomly scattered and have no grouping pattern, and may correspond to independent gene flow event in farmers' field.
The overlapping of the three different rice ecosystems in Niger and the flat geographical pattern of the country provide the most plausible hypothesis explaining the low to moderate genetic differentiation between the main eco-geographical zones. High levels of seed exchange take place within, and between farmers in the regions, regardless of whether the accession being traditional or improved. Rice cropping intensification has reached all rice growing areas, except for some villages in the central-south zone. Agricultural extension officers have been disseminating new, improved, high-yielding varieties to replace landraces because the country is facing the third major food insecurity situation during the last decade. This could explain the very low genetic differentiation observed between the Niger River region and the Lake Chad region despite the large geographical distance (more than 1000 km). However, regarding the small number of samples collected across the Lake Chad zone, the diversity could be considered as relatively high and deserving of particular attention due to the presence of various endangered natural populations of wild O. barthii with long and well-filled grains. Moreover, they were very early maturing, thus could be used in breeding programmes for earliness and various traits. Such an approach has been demonstrated to be efficient in the improvement of O. sativa, from using genes from its wild progenitor O. rufipogon for numerous traits (McCouch et al., 2007).
The present study is the first reporting an exhaustive collection and evaluation of rice species from the major rice-growing regions of Niger. The analysis of the extent of the diversity revealed that a relatively high genetic diversity of O. glaberrima could be found, even far from the centre of diversification. The interpenetration of different ecologies and the easiness of varietal
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movement promoted the dual cultivation of the two cultivated rice species, together with the wild relative, O. barthii species. This provides the opportunity for the occurrence of natural interspecies hybridizations. The study also revealed that Niger has much more rice diversity than the few O. sativa varieties currently used in modern breeding programmes in Niger. Indeed, all the varieties released the last 25 years are clustered in the Gg1-2 subgroup. Thus modern rice breeding is not exploiting the full genetic potential of Niger rice germplasm. Therefore, great progress could be made by widening the gene pool of the nationalofficial rice breeding programmes with the glaberrima and barthii compartments. The hierarchical partitioning of the genetic diversity according to the main eco-geographical zones, and genetic structures revealed that most of the variance was distributed between groups, within subgroups and within ecologies, suggesting that analyses of a collection should consider different species of rice accessions and ecologies rather than eco-geographical zones to capture the maximum diversity.
This collection is stored for ex-situ conservation but this provides only a short-term solution.
Therefore, prior to initiating a long-term rice breeding plan, a thorough study of rice diversity in some villages should be undertaken, in order to prioritise the social network involved in the maintenance and the evolution of this diversity. This may provide a framework for an appropriate in-situ conservation programme.