Genic microsatellites or EST-SSRs derived from expressed sequence tags (ESTs) are desired because these are inexpensive to develop, represent transcribed genes, and often a putative function can be assigned to them. In this study we investigated 2,553 coffee ESTs (461 from the public domain and 2,092 in-house generated ESTs) for identification and development of genic microsatellite markers. Of these, 2,458 ESTs (all >100 bp in size) were searched for SSRs using MISA--search module followed by stackPACK clustering that revealed a total of 425 microsatellites in 331 (13.5%) non-redundant ESTs/consensus sequences suggesting an approximate frequency of 1 SSR/2.16 kb of the analysed coffee transcriptome. Identified microsatellites mainly comprised of di-/tri-nucleotide repeats, of which repeat motifs AG and AAG were the most abundant. A total of 224 primer pairs could be designed from the non-redundant SSR-positive ESTs (excluding those with only mononucleotide repeats) for possible use as potential genic markers. Of this set, a total of 24 (10%) primer pairs were tested and 18 could be validated as usable markers. Sixteen of these markers revealed moderate to high polymorphism information content (PIC) across 23 genotypes of C. arabica and C. canephora, while 2 markers were found to be monomorphic. All the markers also showed robust cross-species amplifications across 14 Coffea and 4 Psilanthus species. The apparent broad cross-species/genera transferability was further confirmed by cloning and sequencing of the amplified alleles. Thus, the study provides an insight about the frequency and distribution of SSRs in coffee transcriptome, and also demonstrates the successful development of genic-SSRs. It is expected that the potential markers described here would add to the repertoire of DNA markers needed for genetic studies in cultivated coffee and also related taxa that constitute the important secondary genepool for coffee improvement.

A set of 16 expressed sequence tag (EST)-derived simple sequence repeat (SSR) and 15 EST-derived single nucleotide polymorphism (SNP) markers together with 4 amplified fragment length polymorphism (AFLP) primer combinations were analyzed on 43 wild (Hordeum vulgare ssp. spontaneum -HS), 35 cultivated (H. vulgare ssp. vulgare -HV) and 12 elite (H. vulgare ssp. vulgare -from EU) barley lines. SSR markers were found most polymorphic with an average PIC value of 0.593 and eight alleles per marker, while AFLP markers showed the highest effective multiplex ratio (26.4) and marker index (5.042). The effective marker index (EMI) was recorded highest (0.468) for AFLP markers and lowest (0.341) for the SNP markers while the SSR markers had an intermediate EMI (0.442). Cluster analysis on combined set of SSR, SNP and AFLP genotyping data classified wild, cultivated and elite barley lines in three distinct groups. The present study suggests the SNP markers as the best class of markers for characterizing and conserving the genebank materials and the AFLP and SSR markers more suitable for diversity analysis and fingerprinting. #

Background The expanding world population is expected to double the worldwide demand for food by 2050. Eighty-eight percent of countries currently face a serious burden of malnutrition, especially in Africa and south and southeast Asia. About 95% of the food energy needs of humans are fulfilled by just 30 species, of which wheat, maize, and rice provide the majority of calories. Therefore, to diversify and stabilize the global food supply, enhance agricultural productivity, and tackle malnutrition, greater use of neglected or underutilized local plants (so-called orphan crops, but also including a few plants of special significance to agriculture, agroforestry, and nutrition) could be a partial solution. Results Here, we present draft genome information for five agriculturally, biologically, medicinally, and economically important underutilized plants native to Africa: Vigna subterranea , Lablab purpureus , Faidherbia albida , Sclerocarya birrea , and Moringa oleifera . Assembled genomes range in size from 217 to 654 Mb. In V. subterranea , L. purpureus , F. albida , S. birrea , and M. oleifera , we have predicted 31,707, 20,946, 28,979, 18,937, and 18,451 protein-coding genes, respectively. By further analyzing the expansion and contraction of selected gene families, we have characterized root nodule symbiosis genes, transcription factors, and starch biosynthesis-related genes in these genomes. Conclusions These genome data will be useful to identify and characterize agronomically important genes and understand their modes of action, enabling genomics-based, evolutionary studies, and breeding strategies to design faster, more focused, and predictable crop improvement programs.

Main conclusion The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.

Summary Especially in low‐income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low‐input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop ‘rewildings’.

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The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Genetic improvement of coffee ( Coffea arabica L.) is constrained by low genetic diversity and lack of genetic markers, suitable screening tools, information on the genetic makeup of available gene pool and long generation time. In this context, use of DNA markers such as microsatellites that provide high genetic-resolution becomes highly desirable. Here, we report the development of nine new microsatellite markers from partial genomic library of an elite variety of Coffea arabica . The developed microsatellites revealed robust cross-species amplifications in 17 related species of coffee, and their Polymorphic Information Content varied from 0 to 0.6, 0 to 0.78 and 0.67 to 0.90 for the arabica, robusta genotypes and species representatives, respectively. The data thus suggest their potential use as genetic markers for assessment of germplasm diversity and linkage analysis of coffee.