# Population structure and genetic diversity of cowpea germplasm from Senegal in light of a global panel

Amy Bodian, Awa Sarr, Sassoum Lô, Omar Diack, Demba Dramé, Daniel

Fonceka, Aissatou Sambou, Elisabeth A.M.C. Diop, Ivette Rachelle Djiboune,

Ndiaga Cissé, et al.

► To cite this version:

Amy Bodian, Awa Sarr, Sassoum Lô, Omar Diack, Demba Dramé, et al. Population structure and genetic diversity of cowpea germplasm from Senegal in light of a global panel. 2025. hal-05388174

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# Population structure and genetic diversity of cowpea germplasm from Senegal in light of a global panel

## Amy Bodian

miamybo@gmail.com

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Awa Sarr

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Sassoum Lô

University of California Riverside

## Omar Diack

Institut Sénégalais de Recherches Agricoles (ISRA), Centre National de Recherches Agronomiques (CNRA)

## Demba Dramé

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Daniel Fonceka

UMR AGAP

## Aissatou Sambou

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Elisabeth AMC Diop

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Ivette Rachelle Djiboune

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Ndiaga Cissé

Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

## Ndjido Ardo Kane
Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès

Philippe Cubry

Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis

## Article

**Keywords:** cowpea (Vigna unguiculata), germplasm, Senegal, SNP markers, genetic diversity

**Posted Date:** November 26th, 2025

**DOI:** https://doi.org/10.21203/rs.3.rs-7999275/v1

**License:** © Ⓟ This work is licensed under a Creative Commons Attribution 4.0 International License.

Read Full License

**Additional Declarations:** No competing interests reported.
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# Population structure and genetic diversity of cowpea germplasm from Senegal in light of a global panel

Amy Bodian¹*, Awa Sarr¹, Sassoum Lô²*, Omar Diack³, Demba Dramé¹, Daniel Fonceka⁴, Aissatou Sambou¹, Elisabeth AMC Diop¹, Ivette Rachelle Djiboune¹, Ndiaga Cissé¹, Ndjido Ardo Kane†¹, Philippe Cubry†⁵

1 Institut Sénégalais de Recherches Agricoles (ISRA), Centre d'étude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS) Thiès, Sénégal

2 Department of Botany and Plant Sciences, University of California Riverside, CA 92521, USA

‡Present address: Department of Plant Sciences, University of California Davis, CA 95616, USA

3 Institut Sénégalais de Recherches Agricoles (ISRA), Centre National de Recherches Agronomiques (CNRA) Bambey, Sénégal

4 Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, 34398 Montpellier, France

5 DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis, 34394 Montpellier, France

† These authors contributed equally to this work

*Corresponding author: miamybo@gmail.com; amy.bodian@isra.sn

## Abstract

Characterizing the genetic diversity of crop germplasm is essential for its effective use in breeding programs. In this study, we genotyped 95 cowpea (Vigna unguiculata) accessions from Senegal, including cultivated, intermediate, and wild types, using the Illumina Cowpea iSelect Consortium Array (51,128 SNPs). We first compared the genetic diversity of the Senegalese collection to that of the UCR minicore collection, which represents the global cultivated cowpea diversity, and then conducted a detailed analysis of the Senegalese accessions. Principal component analysis and population structure revealed the six clusters previously identified in the UCR minicore, as well as two to three additional groups unique to the Senegalese collection. The genetic diversity of Senegalese cultivated accessions ranked among the highest of all minicore subpopulations. These findings indicate that Senegalese cowpea germplasm represents a valuable and original genetic resource that can contribute to broadening global cowpea diversity. Within the Senegalese collection, population structure did not consistently reflect geographic origin, with the exception of the accessions from Saint Louis. Wild accessions formed a distinct and homogeneous cluster. Overall, the observed diversity highlights promising opportunities for identifying beneficial alleles that can be leveraged in cowpea breeding programs.

**Key words:** cowpea (Vigna unguiculata), germplasm, Senegal, SNP markers, genetic diversity

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## Introduction

Cowpea [*Vigna unguiculata* (L.) Walp.] is primarily self-pollinating, and is one of the most important grain legume crops for millions of smallholder farmers and consumers in sub-Saharan Africa ¹. Cultivated by both men and women, cowpea is a fast-maturing and nutritious food. Its grains are rich in protein and the leaves, stems, and immature pods are also edible ²,³, making it suitable for both human consumption and livestock fodder ⁴. Cowpea can be used in various dishes, including starters, lunch, dinner, desserts, and even coffee. It is an important source of income, particularly for women, who play an active role in the value chain (production, processing and marketing) ⁵. When effectively valued, cowpea can play an important role in combating malnutrition and reducing dependence on staples like rice, wheat or animal proteins.

In Senegal, cowpea has been cultivated for centuries ¹,⁶ with the introduction of local early maturity varieties from Nigeria, and late maturity varieties from Mali ⁷. In 1979, drought and heat-tolerant American breeding lines were introduced across various Senegalese agro-ecological zones ⁸. The best-adapted varieties from evaluation trials have been crossed with local varieties to transfer their tolerance or resistance traits ⁹,¹⁰. In 2005, the Senegalese breeding program developed new productive cowpea varieties with a potential yield of three tons per hectare ¹¹. However, actual average yields remain low, about 708 kg/ha ¹², due to biotic (diseases, pests, plant parasites, etc.) and abiotic (drought, low soil fertility, heat, etc) stresses and climate variability ¹. Improving yield requires developing varieties resistant to these constraints. The success and sustainability of breeding programs depend on access to sufficient genetic diversity ¹³. Characterizing the available genetic diversity is essential for effectively using germplasm to develop high-yielding, stress-tolerant varieties. Accordingly, several cowpea germplasm collections have been established, including the world's largest collection maintained by the IITA gene bank, which comprises over 15,000 accessions. From this collection, a representative minicore of 370 landraces was develop ¹⁴. The University of California, Riverside (UCR) minicore, consisting of 368 cultivated cowpea accessions from 50 countries worldwide ¹⁵, is also a valuable resource for cowpea research and breeding.

Several studies have investigated the genetic diversity of cultivated and wild cowpea using different type of markers, including biochemical ¹⁶,¹⁷, RAPD ¹⁸, AFLP ¹⁹, RFLP ²⁰, and SSR markers ²¹⁻²³. In particular, ²³ characterized cultivated and wild Senegalese accessions and found that wild cowpeas exhibited greater genetic diversity than cultivated ones, with no clear genetic structure linked to geographic origin.

Recent advancements in next-generation sequencing (NGS) have facilitated the increased use of single nucleotide polymorphism (SNP) markers in cowpea genetic studies ²⁴⁻²⁸, demonstrating their effectiveness in assessing diversity and structure ²⁹. For example, ³⁰ used over 1,200 SNPs to genotype global landraces and African wild cowpeas, revealing two major gene pools in West and East Africa, each closely related to local wild populations. ³¹ identified 5,828 SNPs in 768 accessions using genotyping-by-sequencing (GBS), uncovering three subpopulations, including one from West Africa. ¹⁴ analyzed 298 accessions from the IITA minicore and found three genetic clusters, none restricted to a single country. Using the Illumina Cowpea iSelect Array (51,128 SNPs, ³²), ³³ examined 96 global accessions and identified four subpopulations, with Iberian Peninsula accessions clustering with those from southern Europe and North Africa. Results also showed a subpopulation which was composed of only West African accessions while South and Southeast African accessions clustered with those from South America and Asia. ¹⁵ applied the same array to genotype the UCR minicore comprising 368 accessions from 50 countries and identified six subpopulations differentiated by cultivar group and geographic origin. Two subpopulations were predominantly West African, while others included breeding lines or landraces from the Mediterranean, Asia, and Southeastern Africa. Interestingly, nearly half of the accessions showed admixture, not aligning with any specific subpopulation. A similar genetic structure distinguishing West and East Africa was also observed in high-density SNP analysis of IITA's core collection, which includes 2021 cowpea accessions ³⁴.
Together, these studies underscore the value of SNP markers in elucidating cowpea's genetic diversity, population structure, and evolution.

In this study, we used the Illumina Cowpea iSelect Consortium Array ³² to genotype a panel of cultivated, intermediate form and wild Senegalese accessions previously characterized with SSR markers ²³. We first compared the genetic diversity of the Senegalese accessions to that of the UCR minicore. We then conducted a detailed analysis of the genetic diversity and population structure found within the Senegalese collection.

## 102 Results

## 104 Population structure and genetic diversity in the whole dataset: Comparison of the Senegalese cowpea collection to the UCR minicore

## 107 • Principal Component Analysis (PCA) of the whole dataset (minicore and Senegalese collection accessions)

Principal-component analysis based on the whole SNP dataset showed that the groups previously inferred for the minicore (six subpopulations) are maintained. However, a lot of admixed genotypes can be observed for the minicore accessions (Fig S1). To better discriminate among the subpopulations, we perform a PCA with genotypes that are not identified as resulting from the admixed group (Fig 1). Axis one (V1) and axis two (V2) of the PCA explained 17% and 8% of the total variance respectively. Senegalese accessions were divided in two main subpopulations according to their biological status. The first subpopulation from Senegal comprised landraces and intermediate forms, which appeared mainly closely related to subpopulation 5 of the minicore. This alignment appeared to correspond with a genetic group from Western Africa, as reported in previous research by ¹⁵. The wild accessions formed a homogeneous group, constituting the second subpopulation which was also closely related to subpopulation 5 (though more distant than the cultivated one).

In addition, two landraces (NC2 and 20) from Thiès (Senegal) clustered with subpopulation 6 corresponding to accessions from Eastern Africa. In this subpopulation (6), there is also one accession of the minicore originating from Senegal (UCR3301/5820). One accession (552) collected in the South of Senegal (Sédhiou) was close to the subpopulation 4 of the minicore (Asia). This accession was among the shortest duration (less than 2 months, Bodian, unpublished) accessions of the Senegalese collection, with small seeds and pod shattering. Finally, some accessions from Senegal were found between the different subpopulations.

## 128 • Population structure of the whole dataset (minicore and Senegalese collection accessions)

Regarding the genetic structure analysis using sNMF, the cross-entropy plot showed a slight decline at k=9 (Fig 2A). For k=9, the six previously defined subpopulations were clearly identified, plus three other clusters corresponding to the Senegalese accessions (Fig 2B). One cluster encompassed only landraces (SL), one included both landraces and intermediate forms (SI+SL) and one only the wild accessions (Sw). The wild accessions appeared to be very well differentiated from the landraces found in both senegalese and minicore collections, consistently with the PCA.

Considering only eight clusters, the six subpopulations of the minicore were still well separated, two clusters from Senegal (SL and SI+SL) collapsed, and wild accessions clustered together (Fig 2B). At K=7, subpopulations 2 and 5 from the minicore collapsed (Fig S2). It was only at K=6 (Fig S2) that the Senegalese landraces and intermediate forms clustered together with subpopulations 2 and 5 from the minicore (West Africa accessions).
142 • **Dendrogram of the whole dataset (minicore and Senegalese collection accessions)**
143
144 As for the PCA and the structure analysis, the dendrogram showed the six subpopulations of the
145 minicore that were well differentiated as well as the three sub-populations from the Senegalese
collection. Moreover, subpopulation 5 was very close to Senegalese collection accessions and the wilds
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147 were differentiated from the cultivated and intermediate forms (Fig 3).

148
149 **Genetic diversity of observed subpopulations in the whole dataset (minicore and Senegalese**
150 **collection accessions)**
151
152 Considering the nine (9) subpopulations identified by structure analysis, the genetic diversity was
153 higher in subpopulation 6 (0,23), followed by subpopulation 4 and landraces from Senegal (0,21). The
154 lowest genetic diversity was observed among the wild species from Senegal (0,08) and in
155 subpopulation 3 (0,10). The Senegalese intermediate forms also had a low genetic diversity (0,14)
156 (Table 1).

157
158 **Genetic diversity of cowpea accessions from Senegal**
159
160 In order to better understand the genetic diversity in Senegalese collection and its dynamic and spatial organization, this analysis was done only within this subset.

161 • **PCA and Structure analysis for Senegalese collection accessions**
162
163 The genetic diversity and structuration of Senegalese cowpea accessions were investigated using PCA
164 and population structure inference with varying cluster numbers (K). PCA revealed that wilds formed
a homogeneous group, while intermediate forms were genetically closer to landraces (Fig 4).

165 The structure analysis indicated that seven genetic groups best explained our data (Fig 5). At K=7, wilds
166 formed a distinct group, and there were six groups for landraces and intermediate forms. Among these,
one group was primarily constituted by Saint Louis accessions, while the remaining were a mix from
167 various regions, with no clear geographic structuring. At K=6, one group of six accessions disappeared,
168 with most collapsing into the intermediate group. At K=3, there was a group for wilds, one for landraces
169 and the last was constituted by intermediate forms and some landraces. At K=2, there was one group
170 composed of wilds and one intermediate form collected in Kolda, and another one constituted of
171 landraces and the other intermediate forms. This structure of wilds compared to landraces and
172 intermediate forms confirmed the PCA results.
173

174
175 • **Dendrogram of Senegalese collection**
176
177 As for the PCA and Structure results, the dendrogram showed that wilds formed a homogeneous
group. The other groups were constituted by landraces and intermediate forms. There is one
178 intermediate form (S90) from Kolda that was localized between wilds and landraces (Fig 6).
179

180 • **Geographical representation**
181
182 We observed no clear geographic determinism of genetic structure either with K=6 or K=7. However,
a genetic group seems to be more prevalent in northern populations from Saint-Louis (V5 Fig 7 and V3
183 Fig S3). This genetic group is the only one detected in the most northern spatial group, and is the most
184 frequent in the two closest ones. It is apparently absent or at very low frequencies in the central or
185 southern groups. Another group (V1 in Fig 7, V7 in Fig S3) also seems to have some differential spatial
186 patterns, being at high frequencies in three central groups close to Bambey, and at far lower
187 frequencies in the others, with the exception of the westernmost group from the Kédougou region
188 Discussion

189
190 Global, and especially climate changes continue to threaten biodiversity and crop productivity. In this
191 context, the genetic diversity contained within crop germplasm is essential for breeding programs
192 aiming to develop improved varieties with enhanced tolerance to biotic and abiotic stresses ³⁵.
193 Characterizing and preserving this diversity is thus an essential step and a prerequisite for efficient
194 germplasm use. This study represents the first high-density SNP genotyping of a Senegalese cowpea
195 collection, including cultivated, intermediate, and wild types, and the first assessment of its genetic
196 diversity and population structure in comparison with a worldwide panel representative of known
197 cultivated diversity.

198 The genetic diversity of the Senegalese collection was compared to that of the UCR minicore composed
199 of 368 accessions of cultivated cowpea¹⁵ representative of the worldwide cultivated diversity. PCA and
200 neighbor-joining clustering analyses conducted on both datasets showed that some Senegalese
201 accessions were clustered distinctly from the genotypes of the minicore and represent an original
202 reservoir of diversity. Indeed, some of the Senegalese accessions did not belong to any identified
203 subpopulation of the minicore. These results were confirmed by the structure analysis which allowed
204 the identification of nine subpopulations: six from the UCR minicore previously identified in the study
205 of ¹⁵, and three for the Senegalese collection (one subpopulation comprising only landraces, one both
206 landraces and intermediate forms and one only wild types). These results indicate that the Senegalese
207 cowpea collection contains variation levels not currently represented in the minicore and can be useful
208 for cowpea breeding programs.

209 Interestingly, a majority of Senegalese accessions (cultivated, intermediate and wild types) clustered
210 most closely with West African accessions in the UCR minicore, consistent with the study of ³³. The
211 genetic structure based on geographical origin was also identified by ³⁶ by using GBS to analyze the
212 genetic diversity of the cowpea core collection of the United States Department of Agriculture (USDA).
213 The geographic structuring mirrors the two majors gene pools (a western and an eastern gene pool) in
214 African cowpea reported by ³⁰. Indeed, ³⁰ showed the presence of two major gene pools in cultivated
215 cowpea in Africa. Each gene pool is most closely related to wild cowpea in the same geographic region,
216 underscoring the importance of these regions in the history and development of this crop. Gene flow
217 between cultivated and wild cowpea ³⁷ likely contributes to the observed pattern.

218 While most Senegalese accessions grouped with West African subpopulations, some were clustered
219 with southeastern African and Asian accessions. This could reflect historical germplasm exchange,
220 including the exchange of genetic materials between Senegal and the rest of the world ⁷,⁸.

221 The genetic diversity of the Senegalese landraces (He = 0,21) was high and comparable to
222 subpopulation 4 of the UCR minicore (He = 0,21), and only slightly lower than that of subpopulation 6
223 (He = 0,23). This underlines the rich diversity preserved in Senegalese landraces, which can serve as
224 valuable resources for cowpea improvement. This genetic diversity was found to be higher than that
225 in the Iberian Peninsula accessions ³³, and even when comparing the whole collection (He = 0,22).
226 These results confirm that Senegalese accessions exhibit a high level of diversity, further supporting
227 the utility of Senegalese germplasm in breeding. Surprisingly, low genetic diversity was observed in the
228 wild accessions compared to the landraces, despite the high agro-morphological variability found ³⁸.
229 This contrasts with earlier studies using other types of markers, which reported that the genetic
230 diversity of cultivated cowpea is smaller than that of wild types ¹⁹,²³,³⁹. However, our results were
231 consistent with studies utilizing SNP markers. For instance, ³⁰ found 57% polymorphism for wild
232 cowpea accessions compared to 73% for landraces using 1536 SNPs. This discrepancy could likely be
233 explained by the fact that the markers used are subject to ascertainment bias in SNP array design, as
234 the array was developed from cultivated lines ¹⁵, limiting its ability to capture wild-specific
235 polymorphism. Consequently, PCA and Structure results showed that all the wild accessions were
236 clustered together in the same and homogeneous group. This underscores the necessity for whole-
237 genome sequencing of the Senegalese collection to better capture and describe the diversity of the
238 wild types. The intermediate forms exhibited low genetic diversity (He = 0,14), possibly due to limited
239 sample size (13 accessions). According to ¹³, differences in SNP quality and performance observed in
240 various studies could be attributed to the differences in the number of genotypes, the types of markers
241 used, and the type of germplasm investigated.

242 When analyzing only the Senegalese collection data, PCA, Structure, and dendrogram clustering clearly
243 separated wild accessions from cultivated and intermediate forms.

244 For the cultivated accessions, clustering was not based on the geographical origin, except for
245 accessions from Saint Louis. These accessions are grown in the post-rainy season (November to
246 February) on flood-recession soils, a practice unique to this northern region ²³. The distinct growing
247 season likely limits gene flow with cowpeas grown during the rainy season (July to September),
248 explaining their genetic differentiation.

249 The intermediate forms collected in North Central Senegal (Louga, Fatick, and Diourbel regions) are
250 more similar to cultivated cowpea. They germinated spontaneously in farmers' fields and are called
251 "Kodj" in Ouolof, the local language. They may have undergone gene flow with cultivated cowpea in
252 the fields over time which could account for their high similarity with cultivated cowpea and in the
253 structure analysis, they clustered with cultivated cowpea for k=2. After harvest, farmers did not mix
254 hybrid seeds with their own seeds. They sort the hybrid seeds and discard them because they take
255 longer to cook due to their harder seed coats compared to the cultivated ones. The hybrids also have
256 smaller seed size than that of the cultivated cowpea, but still larger than that of the wild species. These
257 intermediate forms can be compared to the weedy rices observed in rice, which derived from
258 introgression between wild and cultivated forms ⁴⁰. In addition to these rices, other weedy forms have
259 appeared, displaying many of the same characteristics as wild rice ⁴⁰, such as dormancy, shattering,
260 organ pigmentation, etc. This is the case of accession 90 in this study, which was between
261 landraces and wilds but closer to the least ones, in Fig 4 and 6. This accession was the only intermediate
262 form from the southern part of the country (Kolda). It was collected along the road in the bush, far
263 from habitations unlike other intermediate forms that were found in farmer's fields. It shares similar
264 characteristics with wild cowpeas, such as pod shattering, smaller seed size, and a creeping growth
265 habit, distinguishing it from to other intermediate forms and cultivated types. Moreover, since it was
266 found outside of cultivated fields, this accession was likely isolated from gene flow with cultivated
267 cowpea and therefore genetically closer to wild types, unlike other intermediate forms from north
268 central Senegal.

269 The results of this study show that Senegalese cowpea germplasm contains substantial genetic
270 diversity, including unique alleles and population structure not found in widely used global panels.
271 Cultivated and intermediate types display diversity patterns influenced by geography and farming
272 methods. Finding accessions with genetic profiles different from global subpopulations emphasizes the
273 importance of preserving local germplasm and incorporating it into breeding programs. However, the
274 limited diversity seen in wild accessions, probably due to marker ascertainment, underlines the need
275 for additional genomic tools such as whole-genome sequencing to fully capture genetic variation,
276 especially in underrepresented groups. Also, wider sampling across regions and ecotypes would help
277 improve understanding of population dynamics and gene flow in cowpea.

278
279 Methods

280
281 Plant material

282 Ninety-five accessions that represent the geographical, morphological, and genetic diversity of the
283 Senegalese cowpea collection, were used. Detailed passport data for the accessions is provided in
284 Table S1. These accessions were collected during surveys conducted in eight regions (Thiès, Louga,
285 Diourbel, Fatick, Saint Louis, Sédhiou, Kédougou, and Kolda) in Senegal between 2015 and 2016. The
collection includes 67 cultivated cowpea accessions (seven from Diourbel, eight from Fatick, four from Kédougou, 11 from Louga, 15 from Saint Louis, six from Sédhiou, 11 from Thiès, and five from Kolda), 13 intermediate forms (including eight from Louga, two from Diourbel, two from Fatick, and one from Kolda), and 15 wild relatives, which comprise 13 *Vigna unguiculata* var. *spontanea* (five from Thiès, four from Fatick, three from Kolda and one from Diourbel), and two *Vigna racemosa* from Kolda. The intermediate forms are accessions that could not be classified strictly as either cultivated or wild based on phenotypes. The samples examined in this study are part of a larger collection of Senegalese cowpeas genotyped using SSR markers<sup>23</sup>, and are representative of the genetic diversity obtained with these markers.

295

## 296 DNA extraction and SNP genotyping

Genomic DNA from the 95 accessions was extracted from young leaves using the MATAB (Mixed Alkyl Trimethyl Ammonium Bromide) method<sup>41</sup> at CERAAS (Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse) genotyping laboratory. These accessions were genotyped using the Cowpea iSelect Consortium Array<sup>32</sup>, containing 51,128 SNPs. Genotyping was conducted at the University of Southern California Molecular Genomics Core facility (Los Angeles, California, USA). SNPs were called using GenomeStudio software V.2011.1 (Illumina, Inc. San Diego, CA).

## 303 Analysis of the genotypic data

In this study, we also utilized the SNP genotyping data of 368 cowpea accessions from the UCR minicore<sup>15</sup> to compare the genetic diversity of Senegalese cowpea in a global context. The UCR minicore included landraces and breeding materials from 50 countries in Africa, Asia, North and South America, Europe, and Australia.

Among the 51,128 SNPs used to genotype the 95 accessions from Senegal, the 48,425 polymorphic SNPs retained by<sup>15</sup> to measure the genetic diversity of 368 accessions from the UCR cowpea minicore were considered in this study. To check the quality of the data, the Senegalese and UCR minicore data were merged, and stringent thresholds were applied to filter out missing data using the snpReady package in R software 4.1.3. The first filter consisted of removing loci and individuals that had more than 5% of missing data. This filtered out four individuals (TVu-4097 and TVu-6968 from the minicore and S79 and S81 from Senegalese collection) and 2,334 loci. The two filtered accessions from Senegal belonged to *Vigna racemosa* and came from Kolda and Sédhiou regions. As we focused our analysis on the Senegalese accessions, a filter of 5% missing data was applied to this subset. Thus, 1,129 loci that exhibited more than 5% missing data were filtered out from the global dataset. Finally, we applied thresholds of 10% for the heterozygosity and 5% for minor allele frequency (MAF) in the global set. After applying various filters, we ended up with a dataset comprising 39,555 loci and 459 genotypes for further analysis.

## 321 Statistical analysis

All analyses were conducted using R software (v 4.1.3)<sup>42</sup>. The functions pca and sNMF from the R package LEA<sup>43</sup> were employed to perform the Principal Component Analysis (PCA) and population structure analysis<sup>44</sup>, respectively, on the entire filtered dataset (minicore and Senegalese collection accessions). For clarity, the accessions categorized as "Admixed" in the minicore were removed. The resulting principal components were plotted using the ggplot function from the ggplot2 package in R<sup>45</sup>. A diversity tree was constructed using the pairwise distances from the R package ape<sup>46</sup> the Neighbor-Joining method. Then, we conducted the same analysis using only the accessions from the Senegalese collection. To calculate the diversity index (genetic diversity, *Fst*), basic.stats function from the hierfstat R package v0.5-10<sup>47</sup> was used.

To evaluate whether the genetic structure of the Senegalese landraces display a geographic pattern, we established artificial populations based on sampling coordinates. This was achieved using a k-
333 means clustering in conjunction with a rejection algorithm (R custom script, ⁴⁸) with the following
334 parameters: at least 16 populations, each with a minimum of three individuals. We then calculated the
335 average ancestries for each population based on the ancestries inferred for each accession within that
336 population. This procedure was repeated for various values of K, ranging from two to the optimal
337 number of clusters identified with the sNMF analysis. Geographic plotting was subsequently conducted
338 using pie-charts generated with the geom_scatterpie function from the scatterpie R package (version
339 0.1.8), overlaid on a ggplot2 graphic featuring Natural Earth geographic shapefiles. The size of the pie
340 charts was made proportional to the population size.

341

342 Funding

343 Feed the Future Innovation Lab for Climate Resilient Cowpea (USAID Cooperative Agreement AID-OAA-
344 A-13-00070)

345

346 References

347

348 1. Omomowo OI, Babalola OO. Constraints and Prospects of Improving Cowpea Productivity to Ensure Food, Nutritional Security and Environmental Sustainability. *Front Plant Sci.*
349 2021;12:751731. doi:10.3389/fpls.2021.751731
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## Acknowledgements

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## Author contributions statement

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A.B., D.F. and N.C. conceived the project, A.B. and A.S. wrote the first draft manuscript, A.B., A.S. P.C., S.L., D.D., A.S. and D.F. significantly contributed on writing manuscript, A.S. and O.D. contributed to preliminary data analysis, A.B. and P.C. analyzed the data. A.S., E.A.M.C.D. and I.R.D. did the DNA extraction and prepared the samples for genotyping. All the authors reviewed and approved the final manuscript.

## Data availability

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The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

## Additional Information

**Supplementary information:** The data analyzed in this study are included in the submitted manuscript (Supplemental Information).

**Competing Interests:** The authors declare no competing interests.
<figure><img src="image_2.png" /><figcaption>**Figure 1:** Principal Component Analysis of 294 accessions from minicore (without admixed) and Senegalese collection based on SNP markers. Each subpopulation is mainly made up of accessions from one region.</figcaption></figure>
<figure><img src="image_3.png" /><figcaption>**Figure 2:** (A) Graph of cross entropy against number of ancestral populations for the minicore and Senegalese collection; (B) Admixture ancestry cluster of 294 accessions from the minicore and Senegalese collection (k=9 and k=8)</figcaption></figure>

<figure><img src="image_4.png" /></figure>
<figure><img src="image_5.png" /><figcaption>**Figure 3:** Neighbor-Joining tree based on genetic distances computed from SNP data from the minicore and Senegalese collection accessions</figcaption></figure>

<figure><img src="image_6.png" /></figure>
<figure><img src="image_7.png" /><figcaption>**Figure 5:** (A) Graph of cross entropy against number of ancestral populations for the Senegal collection samples; (B) Population structure Admixture ancestry cluster of 93 accessions from Senegalese collection samples (K=7; K=6; K=3; K=2)</figcaption></figure>

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<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /><figcaption>**Figure 6:** Neighbor-Joining tree based on distances computed from SNP data from the 93 Senegalese collection samples</figcaption></figure>
<figure><img src="image_10.png" /><figcaption>**Figure 7:** Geographical distribution of genetic groups (k=6). The pie charts represent the average proportions from each genetic group for samples in each region. Pie chart sizes are proportional to the number of samples</figcaption></figure>

<table><caption>**Table 1:** Genetic diversity of the whole dataset (minicore and the Senegalese collection) for different observed subpopulations</caption><thead><tr><td>Sub populations</td><td>Genetic diversity</td></tr></thead><tbody><tr><td>Subpopulation 1</td><td>0.17</td></tr><tr><td>Subpopulation 2</td><td>0.16</td></tr><tr><td>Subpopulation 3</td><td>0.10</td></tr><tr><td>Subpopulation 4</td><td>0.21</td></tr><tr><td>Subpopulation 5</td><td>0.18</td></tr><tr><td>Subpopulation 6</td><td>0.23</td></tr><tr><td>Senegalese Landraces</td><td>0.21</td></tr><tr><td>Senegalese Intermediate forms</td><td>0.14</td></tr><tr><td>Senegalese wilds</td><td>0.08</td></tr></tbody></table>

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**Legend Figure 1:** subpopulation 1 (West Africa); subpopulation 2 (breeding lines from West Africa); subpopulation 3 (Mediterranean, Egypt); subpopulation 4 (Asia and Oceania); subpopulation 5 (West Africa); subpopulation 6 (Southeastern Africa)

● Senegal Intermediate form

● Senegal Landrace

● Senegal wild

● Subpopulation 1

● Subpopulation 2

● Subpopulation 3

● Subpopulation 4

● Subpopulation 5

● Subpopulation 6

**Legend Figure 2:**

SL: Senegalese landrace

S1: Senegalese intermediate

Sw: Senegalese wild

S1: subpopulation 1

S2: subpopulation

S3: subpopulation

S4: subpopulation

S5: subpopulation

S6: subpopulation

**Legend Figure 3:**

Subpopulation 4

Subpopulation 6

Subpopulation 2

Subpopulation 3

Subpopulation 1

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Senegal landrace

Senegal intermediate forms

Subpopulation 5
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<figure><img src="image_11.png" /></figure>

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**Supplementary Files**

This is a list of supplementary files associated with this preprint. Click to download.

* Supplementaryinformations.pdf