Identification of groundnut (Arachis hypogaea) SSR markers suitable for multiple resistance traits QTL mapping in African germplasm

AbstractBackgroundThis study aimed to identify and select informative Simple Sequence Repeat (SSR) markers that may be linked to resistance to important groundnut diseases such as Early Leaf Spot, Groundnut Rosette Disease, rust and aflatoxin contamination. To this end, 799 markers were screened across 16 farmer preferred and other cultivated African groundnut varieties that are routinely used in groundnut improvement, some with known resistance traits.ResultsThe SSR markers amplified 817 loci and were graded on a scale of 1 to 4 according to successful amplification and ease of scoring of amplified alleles. Of these, 376 markers exhibited Polymorphic Information Content (PIC) values ranging from 0.06 to 0.86, with 1476 alleles detected at an average of 3.7 alleles per locus. The remaining 423 markers were either monomorphic or did not work well. The best performing polymorphic markers were subsequently used to construct a dissimilarity matrix that indicated the relatedness of the varieties in order to aid selection of appropriately diverse parents for groundnut improvement. The closest related varieties were MGV5 and ICGV-SM 90704 and most distant were Chalimbana and 47–10. The mean dissimilarity value was 0.51, ranging from 0.34 to 0.66.DiscussionOf the 376 informative markers identified in this study, 139 (37%) have previously been mapped to the Arachis genome and can now be employed in Quantitative Trait Loci (QTL) mapping and the additional 237 markers identified can be used to improve the efficiency of introgression of resistance to multiple important biotic constraints into farmer-preferred varieties of Sub-Saharan Africa

Aflatoxin B1 levels in groundnut products from local markets in Zambia

In Zambia, groundnut products (milled groundnut powder, groundnut kernels) are mostly sold in under-regulated markets. Coupled with the lack of quality enforcement in such markets, consumers may be at risk to aflatoxin exposure. However, the level of aflatoxin contamination in these products is not known. Compared to groundnut kernels, milled groundnut powder obscures visual indicators of aflatoxin contamination in groundnuts such as moldiness, discoloration, insect damage or kernel damage. A survey was therefore conducted from 2012 to 2014, to estimate and compare aflatoxin levels in these products (n = 202), purchased from markets in important groundnut growing districts and in urban areas. Samples of whole groundnut kernels (n = 163) and milled groundnut powder (n = 39) were analysed for aflatoxin B1 (AFB1) by competitive enzyme-linked immunosorbent assay (cELISA). Results showed substantial AFB1 contamination levels in both types of groundnut products with maximum AFB1 levels of 11,100 μg/kg (groundnut kernels) and 3000 μg/kg (milled groundnut powder). However, paired t test analysis showed that AFB1 contamination levels in milled groundnut powder were not always significantly higher (P > 0.05) than those in groundnut kernels. Even for products from the same vendor, AFB1 levels were not consistently higher in milled groundnut powder than in whole groundnut kernels. This suggests that vendors do not systematically sort out whole groundnut kernels of visually poor quality for milling. However, the overall contamination levels of groundnut products with AFB1 were found to be alarmingly high in all years and locations. Therefore, solutions are needed to reduce aflatoxin levels in such under-regulated markets

Global distribution of genotypes containing linked-marker allele(s) for different economically important traits in peanut.

<p>An attempt has been made to show passport-based geographical distribution of genotypes that had favourable alleles for markers showing association and explaining >20% phenotypic variation for the trait. Genotypes containing favourable alleles for different traits have been represented by circles in different colors.</p

Linkage disequilibrium (LD) decay in the peanut ‘reference set’ based on mapped SSR marker data.

<p>The simulation trend line within 20 cM showed that the LD declined to below 0.1 within 20 cM. Hence, the estimated LD decay in the ‘reference set’ is 15.0 cM.</p

Selected genotypes possessing desirable allelic combination for multiple traits.

<p>Selected genotypes possessing desirable allelic combination for multiple traits.</p

Genomewide distribution of trait-associated markers for different traits.

<p>Mapped SSR markers that showed trait association are represented on linkage groups (A01 to A10 and B01 to B10) while unmapped DArT features are assigned to A0 linkage group for representation.</p

Genetic and population structure of the peanut ‘reference set’.

<p>This figure shows (a) grouping of genotypes based on SSR and DArT marker genotyping data, (b) principle co-ordinate analysis (PCoA) based on SSR and DArT marker genotyping data. In the case of SSR as well as DArT based PCoA, cultivated genotypes are clustered in two groups and the wild species genotypes are clustered in one group. (c) the population structure in the reference set at different values of K (K = 1 to K = 15), and (d) presence of three subgroups based on mean Fst values.</p