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Though an important crop, the yield of groundnut has been decreasing for years because of a lack of a strong breeding programme in Togo. In recent years, efforts are going on for establishing a well-functioning breeding programme to develop improved groundnut varieties for improving productivity and production of groundnut. The main aims of this study were understanding farmers’ perceptions of production constraints and preference criteria, characterizing cultivated groundnut varieties and understanding genetic mechanisms for priority traits. Results will be useful to exploit genetic diversity among the cultivated groundnut accessions and to integrate farmer knowledge and expectations in the development of high yielding and adaptable groundnut varieties that are preferred by farmers, marketers, processors and consumers in Togo. The investigation on production constraints and farmer preferences showed that yield related traits such pod yield (66.66%) and pod size (12.12%) were the most valued selection criteria of farmers. According to the farmers, groundnut production is mainly constrained by the diseases (37.77% of the respondents). Important economic loss and various causes were associated to late leaf spot (LLS) in the surveyed area. Diversity assessment of 94 accessions from Togo, Senegal and ICRISAT, using agro-morphological and molecular markers, revealed that many quantitative traits such as LLS incidence, number of pods per plant and yield displayed an adequate variability (coefficient of variation > 20%). The most diverse qualitative traits based on Simpson index were primary seed colour (0.75), stem pigmentation (0.60), and Growth habit (0.59). Moreover, principal component analysis underscored quantitative traits such as hundred seed weight, days to maturity, and LLS incidence, as the main traits contributing to the divergence. Correlation analysis and path analysis showed that the number of pods per plant was the main yield-related trait positively affecting yield (PC=0.84; p=0.01). Overall, SNP markers revealed high genetic variability in the genotypes and the percentage of heterozygous genotypes varied from 0 to 50 % for all loci. AMOVA
revealed that only 1.1% of the total molecular variance accounted for geographical contribution to the diversity. Cluster analysis delineated three clusters harbouring useful alleles and interesting phenotypic features such as LLS resistance, a high number of pods per plant and early maturity. Structure co-analysis of phenotypic and SNP data showed that differences observed at the phenotypic level are underlined by genotypic differences. The phenotypic and genotypic diversity revealed appreciable diversity that could be exploited for the identification of parent with preferred traits for use in the breeding program in Togo. The linkage disequilibrium (LD) in Togo groundnut collection was found to be high (0.36). Mean r2 ranged from 0.058 to 0.99 with the genomic distance between loci ranging from 0 to 148 Mbp for intrachromosomal linkage disequilibrium. The interchromosomal LD was found to be significant at p = 0.01 with a certain number of loci located on different chromosomes exhibiting r2 above 0.1. Association study revealed that out of 31 agro-morphological traits analyzed, significant associations between SNPs and agronomic traits of interest (p ≤ 10-7) were established for nine traits. Chromosome A02, A03, A05 and B10 were found to be significantly associated with LLS resistance with r2 ranging from 0.50 to 0.57. Hundred seeds weight, pod width, pod length, seed length, seed with, growth habit and pod reticulation were also associated with various genomic regions. Genetic mechanism analysis for LLS using sixteen F2 progenies from full factorial design crosses indicated additive gene and maternal effect for LLS resistance with 48,3 % and 3.86 % of the phenotypic variance explained, respectively. Non-additive genetic variance was close to zero for LLS resistance. In contrast to LLS resistance, non-additive gene effect played the most important role in the pod weight per plot (21.79 % phenotypic variance explained). For the other yield-related traits, additive genetic variance was more important than the other variance components. Accession 43AH and ICG 7878 with the highest general combining ability could be considered as the best parents for high yielding LLS resistant lines development.