Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species

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

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

BACKGROUND: Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N(2)-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. RESULTS: Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. CONCLUSION: An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties

Development and characterization of novel microsatellite markers from the olive ridley sea turtle (Lepidochelys olivacea)

Olive ridley turtles, although widely distributed globally and in Indian coastal waters, have undergone declines in recent years due to anthropogenic factors, particularly fishery-related mortality. Assessment of genetic variability in existing populations is critical to the development of effective conservation strategies. Here we describe the development of six highly polymorphic microsatellite loci from a simple sequence repeat-enriched genomic DNA library of olive ridley turtle. Characterization of five of these loci using 83 individual olive ridley turtles revealed eight to 24 alleles per locus, high observed and expected heterozygosity values and broad cross-species amplifications. The sixth microsatellite was found to be monomorphic in the olive ridley samples but was polymorphic in two related marine turtle species. These microsatellites thus provide efficient genetic markers to understand the population structure, phylogeography and species relationships of olive ridley and other marine turtle species

The future of food: domestication and commercialization of indigenous food crops in Africa over the third decade (2012–2021)

This paper follows the transition from ethnobotany to a deeper scientific understanding of the food and medicinal properties of African agroforestry tree products as inputs into the start of domestication activities. It progresses on to the integration of these indigenous trees as new crops within diversified farming systems for multiple social, economic and environmental benefits. From its advent in the 1990s, the domestication of indigenous food and non-food tree species has become a global programme with a strong African focus. This review of progress in the third decade is restricted to progress in Africa, where multi-disciplinary research on over 59 species has been reported in 759 research papers in 318 science publications by scientists from over 833 research teams in 70 countries around the world (532 in Africa). The review spans 23 research topics presenting the recent research literature for tree species of high priority across the continent, as well as that in each of the four main ecological regions: the humid zone of West and Central Africa; the Sahel and North Africa; the East African highlands and drylands; and the woody savannas of Southern Africa. The main areas of growth have been the nutritional/medicinal value of non-timber forest products; the evaluation of the state of natural resources and their importance to local people; and the characterization of useful traits. However, the testing of putative cultivars; the implementation of participatory principles; the protection of traditional knowledge and intellectual property rights; and the selection of elite trees and ideotypes remain under-researched. To the probable detriment of the upscaling and impact in tropical agriculture, there has been, at the international level, a move away from decentralized, community-based tree domestication towards a laboratory-based, centralized approach. However, the rapid uptake of research by university departments and national agricultural research centres in Africa indicates a recognition of the importance of the indigenous crops for both the livelihoods of rural communities and the revitalization and enhanced outputs from agriculture in Africa, especially in West Africa. Thus, on a continental scale, there has been an uptake of research with policy relevance for the integration of indigenous trees in agroecosystems and their importance for the attainment of the UN Sustainable Development Goals. To progress this in the fourth decade, there will need to be a dedicated Centre in Africa to test and develop cultivars of indigenous crops. Finally, this review underpins a holistic approach to mitigating climate change, as well as other big global issues such as hunger, poverty and loss of wildlife habitat by reaping the benefits, or ‘profits’, from investment in the five forms of Capital, described as ‘land maxing’. However, policy and decision makers are not yet recognizing the potential for holistic and transformational adoption of these new indigenous food crop opportunities for African agriculture. Is ‘political will’ the missing sixth capital for sustainable development

FTA Highlight No.2 – Tree Seed and Seedling Systems for Resilience and Productivity

The work of the CGIAR Research Program on Forests, Trees and Agroforestry (FTA) on tree seed systems — the authors’ shorthand for the means through which growers obtain access to tree-planting materials, either seeds or seedlings — has sought to address significant constraints in the diversity and genetic quality of the tree seeds and seedlings that are being supplied. These concerns are exacerbated by an increase in demand for germplasm to meet huge global forest landscape restoration commitments and other tree-planting targets. Over the last decade, FTA has worked on twin concerns in this regard: first, how to make available quality tree-planting material; and second, how to ensure that tree seeds and seedlings are planted in the right places for the right purposes. It has addressed availability through building stakeholder partnerships and model tree seed systems; delivering improved “orphan” (under-researched) tree crops through supporting breeding and its impact; mainstreaming food trees through nurseries; conserving and making available diverse tree germplasm to support delivery and use; and developing policies to support the effective supply of tree seeds and seedlings. It has supported better decision making through building information platforms to support tree-planting choices and tree seed system operations; designing maps to guide tree seed and seedling distribution that is suited to current and predicted future climatic conditions; and releasing statistical packages to guide appropriate tree planting and assess the impacts of this planting in terms of benefits such as additional carbon sequestered and extra soil protected. This work is the foundation of local and global economic and environmental benefits of huge significance. It supports climate change mitigation and adaptation, restores landscapes and conserves biodiversity, and provides healthy foods and other products for local and global communities. This publication focuses on FTA’s work in these areas. Future directions for work identified include a closer analysis of the relative importance of supply side versus demand-side measures for mainstreaming improved tree genetic materials by growers; working with investors to improve tree seed quality at the project design stage of tree-planting programmes; and scaling up existing tree seed systems experience to burgeoning forest landscape restoration and broader tree planting initiatives. This scaling up will involve further engagement with major global initiatives such as the Bonn Challenge, the UN Decade on Ecosystem Restoration 2021–2030, and the Global Plan of Action on Forest Genetic Resources

FTA Highlight No.16 – Capacity Development

Capacity development is a key component of the pathways from research to impact, from upstream research to downstream outcomes. The term covers a typology of different activities to increase the capacities of various ranges of actors, in order to enable them to act for positive, sustained change. In the CGIAR Research Program on Forest, Trees and Agroforestry (FTA), capacity development was mainstreamed into the 25 operational priorities, and supported by a central coordination component. This FTA highlight summarizes the evolution of the concept of capacity development (CapDev), from the inception of the programme in 2011 through the FTA Capacity Needs Assessment (2018–2019) to the final FTA CapDev Plan of Action 2020–2021 (FTA 2020a). It provides an overview of the key activities undertaken in FTA and reflects on the relevant findings from related CGIAR and FTA evaluations