Genetic Structure and Diversity of Rice From Certied Cultivars and Farmer’s Fields in Burkina Faso

Background: In West Africa, two rice species are cultivated, the African rice Oryza glaberrima and the Asian rice Oryza sativa, the second one being much more frequent. Despite its importance for food security in West Africa, the genetic diversity of Oryza sativa in farmer’s elds remains understudied in this region. Documenting the dynamics of diversity in the elds between landraces and improved cultivars is of importance to ensure rice cultivation adaptation to global change. In this study, we genotyped 77 rice samples from Burkina Faso using the C6AIR SNP array from IRRI. Among the studied samples, 27 were certied cultivars and 50 were sampled in rice elds from three geographical zones in western Burkina Faso, each zone comprising one irrigated area and a neighboring rainfed lowland. Obtained data were analyzed in the frame of the worldwide rice genetic diversity by using the 3K genomes as reference. Results: Most of the certied cultivars clustered with the indica genetic group, with a minority (26%) assigned to the japonica group. All except one of the rice samples from farmer’s elds belonged to the indica group. The peculiar one unexpectedly clustered with the Aus genetic group and originated from Tengrela (rainfed lowland in Karguela zone). This site, already known to differ in terms of agronomic practices, showed the highest genetic diversity compared to the ve other sites, as well as highest genetic differentiation. Obtained genetic data conrmed the high global frequency of one cultivar, in accordance with the data from farmer’s interview. However, at the eld level, genetic data rarely corresponded to the cultivar’s names obtained from farmer’s interviews. Conclusions: Overall we found a high genetic diversity in the studied samples from Burkina Faso (certied and eld’s samples). We argue on the importance to document and preserve this agro-biodiversity as a prerequisite to face the current challenges of growing rice demand and global change. To this purpose, are required further scientic studies to rene our understanding of the dynamics of diversity in farmers’ elds, as well as a better knowledge of rice agrobiodiversity and awareness of its importance by rice farmers themselves. Our results offer a picture of rice genetic diversity in six sites from lowland and irrigated areas of western Burkina Faso. We conrmed that indica rice is by far the most frequently grown, but we identied a sample from the Aus genetic group. We globally did not notice major differences between lowland and irrigated areas, except for the lowland site of Tengrela, where rice is grown traditionally (low input) by women using traditional landraces. We conrmed the predominance of one certied cultivar in the ve other sites.

samples). We argue on the importance to document and preserve this agro-biodiversity as a prerequisite to face the current challenges of growing rice demand and global change. To this purpose, are required further scienti c studies to re ne our understanding of the dynamics of diversity in farmers' elds, as well as a better knowledge of rice agrobiodiversity and awareness of its importance by rice farmers themselves.

Findings
Crop genetic diversity is a component of agro-biodiversity, with high value for nutrition and adaptation to biotic and abiotic stresses (Zimmerer et al. 2019), particularly in the context of global changes (Pironon et al. 2019). It contributes to render farming systems more stable, robust, and sustainable. On the other hand, the development, dissemination and adoption of improved cultivars is a pathway to increase crop productivity and align on market demands. A deep knowledge of certi ed cultivars at genomic level, as well as crop genetic diversity actually grown locally, are important information to take into account for plant diversity management and crop improvement.
Rice is rapidly becoming a staple food in the African diet. In West Africa, average annual production is 10.098.106 tons (milled equivalent, 2009-2019 period, Soullier et al. 2020), and average annual growth of production (2009-2019) is higher than 10% (Soullier et al. 2020). However, it still does not meet the demand, the imports representing 46% of rice consumption on average annually over the 2009-2019 period (Soullier et al. 2020), so that the efforts to increase rice production in a sustainable manner have to be pursued.
Two rice species are cultivated in West Africa: the African rice Oryza glaberrima Steud., and the Asian rice Oryza sativa L. Asian rice is nowadays by far the more cultivated in West African farming elds, with O. glaberrima being restricted to small areas, grown in places that are unsuitable for O. sativa, maintained mainly for social reasons (Linares 2002). African rice is known for its resistance to biotic and abiotic stresses and was consequently included to O. sativa genetic improvement programs, led by AfricaRice (Africa Rice Center) at the continental scale, to create improved cultivars named NERICA (New Rice for Africa), and some of the cultivars named ARICA (Advanced Rice for Africa) (Sarla and Swamy 2005;Ndjiondjop et al. 2018a As expected, considering that upland ecology is not very common in Burkina Faso, only 11 accessions were assigned to O. sativa japonica genetic group; the indica group was consequently by far the most abundant and could be subdivided into three genetic groups (Kam et al. 2017b).
Considering the recent rise in areas cultivated in rice in Burkina Faso (three-fold between 2006 and 2016, FAO), and the intensi cation of rice cultivation (Demont et al. 2013), it is likely that the rice genetic diversity in the elds is rapidly evolving as well, rendering important to get a more recent picture of rice genetic diversity in this country.
Among the four rice production systems existing in West Africa (rainfed upland, rainfed lowland, irrigated and Faso. To this purpose, we selected two sets of samples for genotyping: cultivars certi ed in Burkina Faso or West Africa and samples from farmer's elds located in six study sites in western Burkina Faso, in order to address the following questions: (1) What is the genetic diversity of rice from Burkina Faso compared to worldwide rice diversity ?
(2) What is the genetic diversity and differentiation of rice actually grown by the smallholder rice farmers in irrigated and rainfed lowland sites in western Burkina Faso ? (3) What is the correspondence between certi ed cultivars, genetic assignation of eld samples and cultivar's names as known by the farmers ?
We selected 27 certi ed cultivars from INERA Farako-Bâ, to represent the diversity of certi ed cultivars including some already adopted by the farmers in Burkina Faso, and recent elite varieties from African breeding programs. The information related to each of them appears in Table 1.
For each cultivar, are indicated potential synonym, the country or organism of origin, the date of introduction in Burkina Faso and the genetic group, based on a priori knowledge. Most of the cultivar's names begins with 'FKR' for 'Farako-Bâ Riz'.
In addition, we took advantage of a sampling previously performed in six sites in western Burkina Faso (Barro et al. 2021). These six sites are located in three geographical zones (Bama, Banzon and Kar guela), each zone comprising one irrigated area and a neighboring rainfed lowland ( Fig. 1a and https://dataverse.ird.fr/dataset.xhtml? persistentId=doi:10.23708/8FDWIE). The present study focused on the 50 elds studied in 2018 (7-11 elds per site, 8,33 on average, see Table 2). A map of the studied elds is presented in Fig. 1a. Each sample used in this study corresponded to one leaf per eld, and was collected between September and December 2018. In 40 out of these 50 elds (80%), we interviewed the farmer and asked for the rice cultivars grown. We also performed farmer's interviews  Datasets from the chip genotyping and from the 3K genome data were merged prior to apply genomic lters. In order to keep best-quality SNPs, we applied the following lters SNPwise: less than 15% of missing data considering only the accessions from Burkina Faso, less than 10% missing data considering the whole dataset and an additional lter on heterozygosity which get rid of positions with more than 45% heterozygosity. We ended up with a nal dataset including 5,247 SNPs.
We rst made a Principal Component Analysis (PCA, Fig. 2 S2). We then restrained our analysis on the accessions from this study (samples from Burkina Faso) and rst computed a genetic tree within these samples (Fig. 3). Genetic distances between the accessions were computed using the dist.gene function and the resulting Neighbor-Joining tree was computed using the ape R package v5.5 (Paradis and Schliep 2019). Graphical representation was made using the "fan" option of the ggtree R package v3.1.2 (Yu 2020). A PCA was then computed considering only the eld genotypes (with or without a peculiar accession, Fig.   3 and Fig. S1) with the dudi.pca function of ade4 R package v1.7-17 (Dray and Dufour 2007). Finally basic population genetics descriptive statistics (gene diversity and populations pairwise Fst) considering different levels of hierarchy were computed using hierfstat ( Table 2 and Table 3). The PCA analysis including both this study's samples and the 3K rice genomes (Fig. 2), as well as the DAPC analysis (Fig. S2), showed that the vast majority of the samples corresponds to indica group. This was expected as none of the samples came from upland growing systems, where japonica are generally found (Ndjiondjop et al. 2018a). Also, Diop et al. (2020) found that indica was the most widely cultivated type of lowland rice in West Africa; with very few of their samples revealed as japonica.
On the other hand, seven reference cultivars (FKR45N, FKR59, FKR33, FKR21, FKR61, NERICA4, NERICA8, see Fig. 2, Fig. 3) were attributed to the japonica group. These cultivars were known to be japonica or Nerica upland (Table 1, Fig. 3) so that this result is congruent with expectations. The japonica group do not contain any of the analyzed samples from farmer's elds (Fig. 2, Fig. 3). The cultivar FKR04, a cultivar introduced from Casamance (Senegal) in 1960 belonged to admix (Table 1, Fig. 2, Fig. 3). Finally, one eld sample, from the eld labelled 'TG02', belong to Aus group (Fig. 2, Fig. 3). The Aus genetic group does not seem to be common in West Africa in general, as it does not appear in the two studies cited previously ( Global gene diversity estimated in the 27 certi ed cultivars from Burkina Faso was 0.282. It represented various genetic groups (indica, japonica and admix, Fig. 2). Within-group diversity was also apparent as we noticed the certi ed cultivars from Burkina Faso are not so closed from each other's within indica and japonica diversity groups (Fig. 2). We argue however that the diversity used for the certi ed cultivars in Burkina Faso could still be enlarged by mobilizing more genetic diversity of the rice worldwide germplasm.
Global gene diversity estimated in the 50 analyzed eld samples from Burkina Faso was 0.137, and within-site genetic diversity was the highest in Tengrela site (0.132; Table 2). On the other hand, Banzon irrigated site presented the lowest genetic diversity (0.108; Table 2). Tengrela was also involved in all highest pairwise genetic differentiation values ( Table 3, Table S1). Highest between site genetic differentiation was between Tengrela rainfed lowland and Banzon irrigated perimeter (F ST = 0.328 [0.311-0.347]). Such a speci city of this site of Tengrela, compared to others study sites, was also evidenced in a previous study on agricultural practices, showing that rice was mostly grown by women, for self-consumption only, with low frequency of chemical fertilization but often manure from household waste (Barro et al. 2021).
Tengrela was also the only site among the six where only landraces were grown (no use of certi ed cultivars, Fig. 1b, Barro et al. 2021) and where a sample was attributed to Aus group (Fig. 2, Fig. S1). The farmer named its cultivar 'Samperema'. We note that the six other samples from Tengrela (whose names include ETP, Bedankaki, Bandakadi / Debale, Tchombiais) are also differentiated from the samples found in the ve other sites (Fig. 3, and see the point aspect in Fig. 4 and Fig. S1). They could derive from hybridization between the locally grown landrace belonging to the Aus diversity group and introduced indica varieties, as suggested by their a nity in the PCA with TG02 (Fig. S1).
In terms of rice growing systems, we note that the samples from irrigated areas (in blue, Fig. 3) and rainfed lowlands (in orange, Fig. 3) do not speci cally differ from each other, with the exception of Tengrela village, as previously mentioned (TG samples in Fig. 3). Rainfed lowlands considered as a whole (three sites) had a higher gene diversity (0.149) compared to irrigated areas (0.125). The genetic differentiation between all rainfed lowlands elds and all irrigated areas was estimated to F ST = 0.030 [0.027-0.034]. This is likely due to the peculiarity of Tengrela site, as we note that the Fst obtained between rainfed lowlands and irrigated areas from the geographic zones of Banzon and Bama both do not differ from zero (Table 3 and Fig. S1).
In the phylogenetic tree (Fig. 3), as well as PCA analyses ( Fig. 4 and Fig. S1), we also note that many eld samples (from ve sites: Senzon, Banzon, Kar guela, Badala, Bama) are identical to each other's and to the reference cultivar FKR64 (commonly named TS2 in Burkina Faso, see Table 1). This cultivar, originating from Taïwan (Table 1), was frequently mentioned by the farmers from all sites, except in the peculiar site of Tengrela (Fig. 1b). Consequently, genetic data and farmer's responses were in agreement in that this rice cultivar is the most frequently grown in the studied sites from western Burkina Faso. However, at the eld level, the genetic assignation of samples did not always correspond to the cultivar given names according to farmers' interviews (see the color of labels in Fig. 4 and Fig. S1). This likely re ects the dynamics of rice genetic diversity in farmer's eld and illustrates that genetic pool is not xed but still evolving.
Our results offer a picture of rice genetic diversity in six sites from lowland and irrigated areas of western Burkina Faso. We con rmed that indica rice is by far the most frequently grown, but we identi ed a sample from the Aus genetic group. We globally did not notice major differences between lowland and irrigated areas, except for the lowland site of Tengrela, where rice is grown traditionally (low input) by women using traditional landraces. We con rmed the predominance of one certi ed cultivar in the ve other sites.
Further research is required to encompass rice agrobiodiversity actually grown in this country and in West Africa in general. As a perspective of this study, we rst propose to include more certi ed varieties and to extend the geographic areas to cover all important rice production areas from Burkina Faso. For instance, it would be interesting to study samples from other regions in Burkina Faso, such as the Boucle du Mouhoun, that was shown to be the most diversi ed in a previous study (Kam et al. 2017a). In addition, it could have been interesting to include rainfed upland rice elds, although this rice production system is minor in Burkina Faso (10% of the rice land area and 5% of national rice production, MAHRH 2011). Third, deciphering potential within-eld rice genetic diversity is also an interesting research question for future work, that was not addressed in our study where only one plant sample from each eld was analyzed (but see Gouda et al. 2020).
We also documented the genetic diversity of 27 certi ed cultivars, including indica, japonica and Nerica. This may offer the perspective (not straightforward though) to try to design easy-to-use genetic markers (see Ndjiondjop et al. 2018b) for markers discriminant for rice species) useful for quality control and seed certi cation. Finally, we argue for more studies combining rice genetic diversity with human and social science to understand further the rationale behind rice farmer's seed choice. This would allow understanding the apparent discrepancies between genetic assignations and naming of the cultivars in the elds, and more importantly getting useful information to design suitable strategies for rice genetic diversity management.
Indeed, while genetic improvement is very important to increase yield and ght poverty and food insecurity (Arouna et al. 2017), it is also critical to preserve agrobiodiversity and to include landraces, especially the preferred by farmers and consumers, in breeding programs and dissemination projects. This is especially pertinent in the context of global changes because farmer rice varieties in West Africa were shown to be robust / tolerant to sub-optimal conditions (Mokuwa et al. 2013 Ethics approval and consent to participate In every case, we obtained permission from the farmers to work in their elds, and the management of the entire project followed the guidelines of the Nagoya protocol regarding access and bene t sharing.

Consent for publication
Not applicable. Figure 1 represented with blue scares and surrounded in blue; while rainfed lowland (SZ: Senzon; TG: Tengrela, BL: Badala) places are represented similarly but in orange. 1b. Frequency of rice cultivars according to farmer's interviews in the different study sites and the different years (2016-2019 dataset). Each plot corresponds to one site and each bar to a particular year and colors correspond to rice cultivars cited by the farmers.