Chapter 3: Agro-morphological variability of rice species collected from Niger
3.3 Material and Methods
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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.
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recognized as disappeared or abandoned, questions were asked of the community about the reasons that led to the disappearance or abandonment. In addition to this, farmers were also asked to advise the collection team about another village where the absent accessions might be found.
Generally, an identified accession was re-sampled again in one to two villages following its first appearance in order to confirm the name. However, if a name, already recorded, appeared later (in very distant villages, eco-geographical zones or ethnic groups), it was sampled again.
Additionally, if an accession already identified and sampled appeared again under a different name in another village, it was re-sampled and all related information was taken again from the farmer. Overall 202 rice accessions were collected, of which nine samples of wild O. barthii were collected at sites far from any cultivated rice farm.
The collection was then brought to AfricaRice, where the seeds of each identified sample were visually separated from off-types to constitute "pure" samples for each identified accession. If the off-types derived from a sample did not correspond to any identified accessions, they were kept.
The accessions were then coded using the initials of the region where they were collected, and followed by a number corresponding to the order of collection (e.g. TH3 corresponded to the third accession collected in the region of Tahoua, while DF13 was the thirteenth sample collected in the region of Diffa). The kept off-types were named after their samples code followed by an alphabetic letter (e.g. DS14-E was the fifth off-type in the fourteenth sample collected in the region of Dosso). Finally, 370 rice accessions, including 168 off-types derived from each sample, plus 5 checks were grown in the first trial in 2008 (a purification-characterisation trial). From the purification-characterization field, 270 accessions, comprising 202 accessions and 68 ‘unique’
off-types were selected for the second field trial in 2009 (characterisation trial). This study then focused on the 270 accessions, which represent the observed phenotypic diversity of rice in Niger, plus eight Control varieties, including four O. sativa varieties, comprising two irrigated indica (IR64, B6144), one traditional deep-water floating indica variety (RAM63), and one upland japonica variety (Moroberekan), together with two O. glaberrima varieties including the upland CG14 and the lowland TOG7106, and two interspecific varieties (NERICA14 (upland) and NERICAL41 (lowland)).
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The purified accessions, as well as all related unique off-types and seven control varieties (Total N= 370) were sown at the AfricaRice research station (Togoudo, Benin) during the rainy season of 2008. The field was regularly watered if there was no rain. An augmented experimental design with five replicated checks (ITA212, NERICA4, NERICA14, B6144 and TOG7106) in ten blocks was used. When enough seed was available, the elementary plot for each accession was 0.6 x 1.5 m with 3 rows, with a spacing of 200 mm between and within rows and a distance of 400 mm maintained between plots, at the rate of 3 plants per hill by direct seeding. Thinning to one plant/hill was done 20 days after sowing (DAS). Fertilizer rate used was NPK (15-15-15) at 200 kg ha-1 applied just after thinning. Urea was also applied at a rate of 100 kg ha-1 three weeks after thinning. Regular weeding was done when necessary. Data was recorded on five to 10 plants of the inner row from seedling stage to harvest. For each accession, panicles of five well- identified plants from the inner row were individually harvested and the remaining ten were bulk- harvested.
From the 2008 purification-characterization field, 270 accessions were selected after eliminating accessions that were similar in the field. Accessions and the eight control varieties were directly sown during the rainy season of 2009 in plastic buckets of 5 litre capacity at a rate of two plants per bucket. Buckets were laid out in a randomized complete block design (RCBD) with two replications. For each accession, three buckets was used per replication. Thus, a total of 12 plants were sown per accession. Fertilizers were applied as NPK (15-15-15) at 20 DAS, and Urea was applied at panicle initiation. The trial was watered during days without rain. Only 44 traits that were found discriminating our accessions, after a factorial analysis on the previous year's data set, were recorded on five plants per accession.
3.3.3 Data collection and analysis
All the data was recorded using a descriptor for wild and cultivated rice species (Bioversity International et al., 2007). During the trials 44 agro-morphological traits were measured (Appendix 3.2). A factorial analysis was performed on the data set, and the 34 traits that contributed the most to the different factors (when the correlation was > 0.45) were selected for analyses.
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In addition to data collection, the accessions were classified into O. sativa L. or O. glaberrima Steud., based mainly on the ligules length and shape. O. sativa species have long ligules while O. glaberrima has short ligules (Sarla and Mallikarjuna Swamy, 2005). Similarly, awns length, texture and consistency, as well as grain length (Besancon, 1993) (Appendix 3.3) were used to classify the intermediate forms into O. glaberrima or O. barthii, in addition to the samples of O.
barthii collected in wild populations far from cultivated fields.
A Pearson Principal Component Analysis (PCA) was performed on the standardized quantitative data (18 traits), followed by the assignment of the different accessions into groups by Agglomerative Hierarchical Clustering (ACH). Dissimilarities were computed based on the Euclidian distance and aggregation of accessions was based on the Ward method (Ward, 1963).
Discriminant Analyses (DA) were conducted using groups identified by cluster analysis plus eco- geographical zones, agrosystems, and species as categorical variables. Thirty four traits (18 quantitative and 16 qualitative traits) were used. These analyses were performed using XL-STAT 2010 application package.
The diversity of phenotypic traits was estimated using the Shannon-Weaver Index (Shannon, 1948), computed under Microsoft Excel 2010 application package. The Shannon Index was computed of all the 44 traits. However, only the results from the 33 most expressive traits (15 quantitative and 18 qualitative traits) were presented. Quantitative continuous data were transformed into categorical data by creating for each phenotypic trait classes based on either the rice descriptors of Bioversity, IRRI, and AfricaRice, or as described by Sanni et al. (2008). When information was not available, three classes were created, based on the mean, median and quartiles. The Shannon Diversity Index H' was computed as:
Where, k: the number of phenotypic classes for a character and Pi, the relative abundance of individuals in the ith class, calculated as the proportion of individuals in the phenotypic class i to the total number of individuals (N). However, to keep the value of the Shannon-Weaver Index between 0 and 1, H' was divided by its maximum value, log2k (Abdi et al., 2002; Sanni et al., 2008).
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