Lessons from community engagement to improve COVID-19 diagnosis and treatment in Cochabamba, Bolivia.

BACKGROUND: Community engagement is recognized as a vital component of health-related research and programs, particularly during infectious disease outbreaks and epidemics. Despite the importance of engaging communities in the response to COVID-19, relatively little research has examined how this was (or was not) achieved, and even less in low- and middle-income countries. This article describes the community engagement that accompanied efforts to strengthen COVID-19 diagnosis and treatment as part of the ECO Project in Cochabamba, Bolivia and highlights lessons for future pandemic response. METHODS: Community engagement involved formative assessment, co-creation to develop a health information campaign, ongoing community listening and evaluation. Qualitative data were collected during workshops, project meetings and focus groups. Questionnaire-based surveys were conducted to assess COVID-19-related attitudes, knowledge and practices. RESULTS: The collected data highlighted the value of working closely with well-established community health committees and involving community members with social media skills in the design of COVID-19-related messages to address on- and offline misinformation. Co-creation sessions enabled the adjustment of the information campaign in terms of content and approach based on the needs and preferences of community members and health staff. The continuous listening with community and health personnel facilitated the ongoing adaptation of project activities. CONCLUSION: Through a stepped and multi-pronged approach, incorporating co-creation and community listening, the engagement could respond to emerging local challenges during the pandemic. The project created spaces for dialogue and opportunities for collaboration that strengthened links between the community and the health services.

Main findings Key elements of community engagement to improve COVID-19 diagnosis and treatment in Cochabamba, Bolivia, included working closely with well-established community health committees, involving community members with social media skills in the co-design of COVID-19-related messages, and continuous listening with community and health personnel facilitated the ongoing adaptation of project activities.Added knowledge With little research on community engagement for COVID-19 diagnosis and treatment in Latin America, this study reports the results of mixed methods research on the impact of a comprehensive approach to engagement that highlights lessons for future health emergencies.Global health impact for policy and action Lessons for engagement in health emergencies include the need for a multi-pronged approach, incorporating co-creation and community listening, to respond to emerging local challenges.

Traces of Introgression from cAus into Tropical Japonica Observed in African Upland Rice Varieties.

BACKGROUND: Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. METHODS: We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. KEY RESULTS: Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions.

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate.

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

Implementación de un modelo de comunicación en Chagas basado en la estrategia de educación por pares / Implementation of a communication model in Chagas based on the peer education strategy

OBJETIVOS: el presente estudio evalúa el cambio en las perspectivas, conocimientos, actitudes y prácticas de los familiares de un grupo de pacientes capacitados con la estrategia de educación por pares que fueron tratados en la Plataforma de atención integral de Chagas, y si ese cambio se traduce en un aumento de la demanda de atención integral de Chagas en los servicios de salud del Valle Alto de Cochabamba. MÉTODOS: se comparó los resultados de la encuesta realizada en 32 familiares de 8 pacientes capacitados en 2018 (grupo A) con una encuesta similar realizada en 64 familiares de 16 pacientes tratados en 2017 (grupo B) que no fueron capacitados, pero en cambio recibieron la consejería que provee el personal de salud de forma rutinaria. RESULTADOS: los resultados obtenidos muestran que los familiares de pacientes educadores pares han modificado sus conocimientos, actitudes, prácticas y percepciones sobre la enfermedad de Chagas y este cambio ha influido positivamente la demanda de atención de servicios integrales para dicha enfermedad. CONCLUSIÓN: la estrategia de educación por pares ha demostrado ser eficaz, fácil de aplicar por un personal de enfermería en los 1º y 2º niveles de atención, y que permite llegar a las familias afectadas a un costo relativamente bajo.(AU)

OBJECTIVES: this study aims to identify changes in the perspectives, knowledges, attitudes and practices of the relatives of a group of patients treated in the Platform of integral care of Chagas, and trained as peer educators, and if that changes led to an increase of the Chagas demand in the health services of Valle Alto, in Cochabamba department. METHODS: we compared the results of the survey conducted on 32 relatives of 8 patients trained in 2018 (group A) with a similar survey conducted on 64 family members of 16 patients treated in 2017 (group B) who were not specifically trained, but received the counseling routinely provided by the health staff. RESULTS: the results show that relatives of peer educators have modified their knowledge, attitudes, practices and perceptions about Chagas disease and this change has influenced the demand for diagnosis of this disease. CONCLUSIONS: the strategy of peer education has proven to be effective, easy to apply by a nursing staff in the 1ª and 2ª levels of care, and allows reaching affected families at an affordable cost.(AU)

Fine Scale Genomic Signals of Admixture and Alien Introgression among Asian Rice Landraces.

Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behavior of this classifier is studied under scenarios of varying genetic divergence, admixture, and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica, and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus, and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication.

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation.

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives.

We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.

New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

PREMISE OF THE STUDY: Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. METHODS AND RESULTS: A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19. CONCLUSIONS: The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management.

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies.

Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets thanks to next-generation sequencing methods. In this study, we develop an easy and cost-effective protocol for in-solution enrichment hybridization capture of complete chloroplast genomes applicable at deep-multiplexed levels. The protocol uses cheap in-house species-specific probes developed via long-range PCR of the entire chloroplast. Barcoded libraries are constructed, and in-solution enrichment of the chloroplasts is carried out using the probes. This protocol was tested and validated on six economically important West African crop species, namely African rice, pearl millet, three African yam species and fonio. For pearl millet, we also demonstrate the effectiveness of this protocol to retrieve 95% of the sequence of the whole chloroplast on 95 multiplexed individuals in a single MiSeq run at a success rate of 95%. This new protocol allows whole chloroplast genomes to be retrieved at a modest cost and will allow unprecedented resolution for closely related species in phylogeography studies using plastomes.

Achievements and challenges upon the implementation of a program for national control of congenital Chagas in Bolivia: results 2004-2009.

Bolivia is one of the most endemic countries for Chagas disease. Data of 2005 shows that incidence is around 1.09‰ inhabitants and seroprevalence in children under 15 ranged from 10% in urban areas to 40% in rural areas. In this article, we report results obtained during the implementation of the congenital Chagas program, one of the biggest casuistry in congenital Chagas disease, led by National Program of Chagas and Belgian cooperation from 2004 to 2009. The program strategy was based on serological results during pregnancy and on the follow up of children born from positive mothers until one year old; if positive, treatment was done with Benznidazole, 10 mg/Kg/day/30 days with one post treatment control 6 months later. Throughout the length of the program, a total of 318,479 pregnant women were screened and 23.31% were detected positive. 42,538 children born from positive mothers were analyzed at birth by micromethod, of which 1.43% read positive. 10,120 children returned for their second micromethod control of which 2.29% read positive, 7,650 children returned for the serological control, of which 3.32% turned out positive. From the 1,093 positive children, 70% completed the 30 day-treatment and 122 returned for post treatment control with 96% showing a negative result. It has been seen that maternal-fetal transmission rates vary between 2% and 4%, with an average of 2.6% (about half of previously reported studies that reached 5%). In this work, we show that it is possible to implement, with limited resources, a National Congenital Chagas Program and to integrate it into the Bolivian health system. Keys of success are population awareness, health personnel motivation, and political commitment at all levels.

Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources.

Large ex situ collections require approaches for sampling manageable amounts of germplasm for in-depth characterization and use. We present here a large diversity survey in sorghum with 3367 accessions and 41 reference nuclear SSR markers. Of 19 alleles on average per locus, the largest numbers of alleles were concentrated in central and eastern Africa. Cultivated sorghum appeared structured according to geographic regions and race within region. A total of 13 groups of variable size were distinguished. The peripheral groups in western Africa, southern Africa and eastern Asia were the most homogeneous and clearly differentiated. Except for Kafir, there was little correspondence between races and marker-based groups. Bicolor, Caudatum, Durra and Guinea types were each dispersed in three groups or more. Races should therefore better be referred to as morphotypes. Wild and weedy accessions were very diverse and scattered among cultivated samples, reinforcing the idea that large gene-flow exists between the different compartments. Our study provides an entry to global sorghum germplasm collections. Our reference marker kit can serve to aggregate additional studies and enhance international collaboration. We propose a core reference set in order to facilitate integrated phenotyping experiments towards refined functional understanding of sorghum diversity.

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping.

BACKGROUND: Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a 'Mediterranean' mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. RESULTS: Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between 'Mediterranean' mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. CONCLUSIONS: A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the 'Mediterranean' mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents.

A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae).

PREMISE OF THE STUDY: Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers. METHODS AND RESULTS: One hundred seventeen markers were selected along the genome to provide coverage across the length of all 10 sorghum linkage groups. They were tested for polymorphism and reproducibility across two laboratories (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement [CIRAD], France, and International Crops Research Institute for the Semi-Arid Tropics [ICRISAT], India) using two commonly used genotyping technologies (polyacrylamide gel-based technology with LI-COR sequencing machines and capillary systems with ABI sequencing apparatus) with DNA samples from a diverse set of 48 S. bicolor accessions. CONCLUSIONS: A kit for diversity analysis (http://sat.cirad.fr/sat/sorghum_SSR_kit/) was developed. It contains information on 48 technically robust sorghum microsatellite markers and 10 DNA controls. It can further be used to calibrate sorghum SSR genotyping data acquired with different technologies and compare those to genetic diversity references.

Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers.

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.

Development of nuclear microsatellite markers for the fonio, Digitaria exilis (Poaceae), an understudied West African cereal.

PREMISE OF THE STUDY: We developed nuclear microsatellite primers to explore the genetic diversity, population genetic structure, and evolutionary history of the fonio (Digitaria exilis), an understudied cereal cultivated in West Africa. METHODS AND RESULTS: We used a microsatellite-enriched library approach to isolate and characterize 38 nuclear primer pairs (31 di-, five tri-, and two tetranucleotide repeats), of which 21 were polymorphic and exhibited a clear pattern in 36 accessions from West Africa. The number of alleles per locus ranged from two to 22, with a mean of 4.71, and expected heterozygosity ranged from 0.03 to 0.93. CONCLUSIONS: The developed set of 21 polymorphic SSR markers will provide tools for population and evolutionary genetics studies of the cultivated fonio.

The relationship between population structure and aluminum tolerance in cultivated sorghum.

BACKGROUND: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the Alt(SB) locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. METHODOLOGY: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking Alt(SB) and SbMATE expression was undertaken to assess a possible role for Alt(SB) in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. CONCLUSION/SIGNIFICANCE: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. Alt(SB) was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.

Population genetic relationships between Casearia sylvestris (Salicaceae) varieties occurring sympatrically and allopatrically in different ecosystems in south-east Brazil.

BACKGROUND AND AIMS: Species delimitation can be problematic, and recently diverged taxa are sometimes viewed as the extremes of a species' continuum in response to environmental conditions. Using population genetic approaches, this study assessed the relationship between two Casearia sylvestris (Salicaceae) varieties, which occur sympatrically and allopatrically in the landscape of south-east Brazil, where intermediate types are also found. METHODS: In total, 376 individuals from nine populations in four different ecosystems were sampled, and nine microsatellite markers were used to assess the relative effects of the ecosystems and varieties on the distribution of genetic diversity among populations of this species. KEY RESULTS: As a by-product of this study, several PCR products with more than two alleles were observed. The possibility that extra bands represent non-specific amplification or PCR artefacts was discarded by sequencing a sample of these bands. We suggest that (partial) genome duplication in C. sylvestris most probably explains this phenomenon, which may be a key factor in the differentiation of the two taxa, as it was markedly more frequent in one of the varieties. AMOVA indicated that approx. 22 % of the total genetic diversity was found between the two varieties. Bayesian analysis identified varieties and ecosystems as evolutionary units, rather than the individual populations sampled. CONCLUSIONS: The results are in agreement with field observations and support the recognition of two varieties, as well as documenting the occurrence of hybridization between them.

Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives.

Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.

Development and characterization of nine polymorphic microsatellite markers in the Chilean kelp Lessonia nigrescens.

A total of nine microsatellite loci were isolated and characterized in the Chilean kelp Lessonia nigrescens Bory. Using two different enriched libraries, we observed 1-14 alleles per locus in two samples of 21 kelp individuals each. The observed heterozygosities ranged from 0.05 to 0.80 and all loci are in Hardy-Weinberg equilibrium for one or both samples. Seventeen samples collected from different sites showed high allele diversity along the species distribution. The variation detected at these markers is currently being used for the study of populations of Lessonia nigrescens at different geographical scales.

SAT, a flexible and optimized Web application for SSR marker development.

BACKGROUND: Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. RESULTS: SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries.SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. CONCLUSION: The SAT Web application is available at http://sat.cirad.fr/sat, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator tropgene@cirad.fr to request a login and password.