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BackgroundAccurate identification of crop cultivars is crucial in assessing the impact of crop improvement research outputs. Two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, have inherent uncertainty levels. Genotyping-by-sequencing (GBS) was used in a case study as an alternative method to track released varieties in farmers’ fields, using cassava, a clonally propagated root crop widely grown in the tropics, and often disseminated through extension services and informal seed systems. A total of 917 accessions collected from 495 farming households across Ghana were genotyped at 56,489 SNP loci along with a “reference library” of 64 accessions of released varieties and popular landraces.ResultsAccurate cultivar identification and ancestry estimation was accomplished through two complementary clustering methods: (i) distance-based hierarchical clustering; and (ii) model-based maximum likelihood admixture analysis. Subsequently, 30 % of the identified accessions from farmers’ fields were matched to specific released varieties represented in the reference library. ADMIXTURE analysis revealed that the optimum number of major varieties was 11 and matched the hierarchical clustering results. The majority of the accessions (69 %) belonged purely to one of the 11 groups, while the remaining accessions showed two or more ancestries. Further analysis using subsets of SNP markers reproduced results obtained from the full-set of markers, suggesting that GBS can be done at higher DNA multiplexing, thereby reducing the costs of variety fingerprinting. A large proportion of discrepancy between genetically unique cultivars as identified by markers and variety names as elicited from farmers were observed. Clustering results from ADMIXTURE analysis was validated using the assumption-free Discriminant Analysis of Principal Components (DAPC) method.ConclusionWe show that genome-wide SNP markers from increasingly affordable GBS methods coupled with complementary cluster analysis is a powerful tool for fine-scale population structure analysis and variety identification. Moreover, the ancestry estimation provides a framework for quantifying the contribution of exotic germplasm or older improved varieties to the genetic background of contemporary improved cultivars.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0273-1) contains supplementary material, which is available to authorized users.

Groundnut is the most important legume in Ghana. The crop is grown in all the agroecologies in the country; from the dry savannah regions to the moist forest areas. Several food preparations incorporate groundnut to improve the protein level, taste and flavour. Despite the importance of the crop, the chemical compositions of the varieties grown by farmers have not been analyzed according to their nutritional quality. Oil, fatty acids, protein, oleic/linoleic (O/L) acid ratio, iodine value and free soluble sugars were studied in 20 groundnut varieties grown in Ghana to determine their nutritional quality and to inform endusers which variety to choose for maximum benefit. Results indicated a significant difference (p<0.05) in oil content among the varieties. Oil content ranged from 33.60 to 54.95%. Mean oil content of the subspecies hypogaea (49.7%) was higher than in subspecies fastigiata (47.3%). The major fatty acids were oleic and linoleic which accounted for 77.89% of the total fatty acids. The subspecies hypogaea had significantly higher (p<0.01) content of oleic acid (55.9%) than the subspecies fastigiata (43.3%). The sum of three fatty acids oleic, linoleic and palmitic acid constitute 89.35% of the total fatty acids of the seeds. The mean O/L ratio ranged from 1.14 to 3.66; the mean for subspecies hypogaea was 2.59 as compared to 1.28 for subspecies fastigiata. There was high correlation between oleic and O/L acid ratio (r 2 =0.983) and negative correlation between oleic acid and linoleic acid (r 2 =-0.996). The iodine value ranged from 85.77 to 98.43% and total soluble sugars from 9.20 to 13.30%. Protein of defatted portion ranged from 39.65 to 53.45%. Subspecies fastigiata had higher mean protein content than subspecies hypogaea. Generally, there were significant variations in the parameters measured in the groundnut varieties. Five varieties with O/L ratio more than 2.0 were identified and their oils would be further tested for their stability.

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