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The potential of cowpea to address food security in Burkina Faso in particular is well established. However, there is limited information on drought tolerance and diversity in the germplasm in Burkina Faso and farmers’ perceptions on the effects of drought and their varietal preferences are not known. The present study was, therefore, conducted to: (1) identify farmers’ perceptions on the impact of drought on cowpea production and identify their preferences regarding cultivars and traits, (2) identify drought tolerant varieties in cowpea germplasm, (3) determine single nucleotide polymorphisms (SNPs) based genetic diversity in the cowpea germplasm, and (4) implement markerassisted backcrossing to transfer yield and stay-green QTLs and striga resistance into a farmer preferred landrace. A participatory rural appraisal (PRA) was conducted to identify farmers’ perceptions on the impact of drought on cowpea production. This study established that farmers have a deep knowledge about cowpea production constraints. Limited access to seed of improved variety was ranked as the most important constraint in all the areas where the study was conducted. Drought was classified among the four most important constraints to cowpea production in the three districts where the PRA was conducted. The preferred grain traits for all regions were white colour, large seeds with a rough texture for food and market purposes, except for the northern region where brown grain colour was preferred for food. The identification of drought-tolerant varieties in cowpea germplasm through field screening of fifty genotypes and the use of selection indices revealed wide genotypic variability among the tested germplasm. Biplot displays indicated that the genotypes could be grouped into four categories according to their drought tolerance and yielding ability as indicated below: high yielding-drought tolerant (group A), high yielding-drought susceptible (group B), low yielding-drought tolerant (group C), and low yielding-drought susceptible (group D). Genotypes like Djouroum local, KVx404-8-1, IT98K-1111-1, Gorom local, CB27, IT93K- 693-2, Mouride, and KVx61-1 were clustered in group A, that is they were high yielding and drought tolerant. The stress tolerance index was the best criterion for assessing genotypes for variability to drought tolerance because it enabled the identification of high yielding and drought tolerant genotypes. Genetic diversity was assessed using 177 SNP markers on 50 cowpea lines. The phylogenetic pattern of this germplam revealed seven clusters. The lines were almost grouped based on their geographical origin, and the breeding background. Thus, materials which originated from Burkina Faso were clustered in the same group while those from IITA/Nigeria were also almost all clustered in the same group. The genetic distance was low (≤0.29) suggesting a narrow genetic base in the cowpea germplasm used in this study. SNPs were efficient in the study of the diversity and a core collection of 20 lines was generated for further use in the breeding programme. Marker-assisted backcrossing (MABC) was used to transfer QTLs for yield under drought and stay-green and striga resistance gene into Moussa local, a farmer preferred landrace. Two backcrosses assisted by SNP markers in foreground and background selections were sufficient to select for QTLs presence and to recover the background of Moussa local, the recurrent parent. The BC3F1s were selfed and six BC3F2s were evaluated for preliminary yield under stress and non-stress conditions. Out of the six, three MABC selected lines were promising and yielded better than the check and the parents. From these recombinant lines, several high yielding lines are likely to be developed for release in the near future. Most of them could be used in intercropping which will make great impact on cowpea production in Burkina Faso.

In general, potential parents for genetic improvement for yield and drought tolerance were identified. However, further studies for assessing yield stability of cowpea genotypes are necessary and could be achieved by including more seasons and sites to get a better understanding of the genotype × environment interaction and yield stability of cowpea in Burkina Faso for all the materials identified including the MABC lines.