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Background: For sustainable improvement of wheat-based farming systems in the North Africa, there is a need to improve plant health, soil health and fertility. One approach to achieve this is by integrating subsidiary crops (SC) as living or dead mulches or cover crops with the main crops in rotations, which will increase plant species and microbial diversity and reducing water demand in dry climates. Methods: A collaborative research project funded by EU FP 7 (Project No. 289277) was initiated in April 2012, in partnership with European Union (public research organizations and private sector small and medium enterprises of Germany, Norway, Sweden, Denmark, the Netherland, UK, Poland, Switzerland and Italy), Brazil and Morocco (INRA-Morocco and ICARDA), in order to enhance understanding and use of SC systems, develop suitable farm technologies, increase the range of SC species, and enhance understanding of impact of SC on soil ecology, biology and microbial diversity and crop pests and diseases. Results: Based on two field experiments in Morocco (Sidi AI-Aidi and Sidi Allal-Tazi), the project will assess the economic and ecological impact including legume root health and soil health, fertility and microbial diversity and compare the results with other sites in Europe. Screening of new species and genotypes will result in identification of range of potentially useful plant species for SC for the North Africa and Europe. The identified SC species will be tested for their potential as forage and for extraction of useful biochemicals. Conclusion: The results of the project as a whole will be of use for and improve sustainability in low-input, organic, and conventional farming systems in the North Africa, Latin America and Europe.

Chickpea is the fourth largest grain legume crop globally. A composite collection of 3000 accessions was formed and genotyped using 50 SSR markers. The accessions were also field evaluated for seven qualitative traits. Analysis of 48 SSR markers data on 2915 accessions detected 1683 alleles, of which 935 were rare and 748 common. Gene diversity varied from 0.533 to 0.975. Kabuli chickpea as a group were genetically more diverse than other seed types. Several group-specific unique alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in West Asia and Mediterranean, 117 in South and South East Asia, and 10 in African region accessions. A genotype-based reference set captured 1315 alleles compared to 1237 alleles in the reference set based on qualitative traits or 1354 alleles based on SSRs and qualitative traits data. The relative usefulness of these reference sets in chickpea breeding and genomics studies are being further investigated.

Background Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directi