Sorghum germplasm from West and Central Africa maintained in the ICRISAT genebank: Status, gaps, and diversity

The genebank at ICRISAT maintains 8020 accessions of sorghum from 16 West and Central African countries. Geographical gaps and diversity were assessed in the collection. Using the passport data of 3991 accessions for which georeferenced data were available, a total of 386 districts (gaps) located in 11 West and Central African countries were identified as geographical gaps. Burkina Faso with 140 and Nigeria with 118 districts were identified as countries with major geographical gaps. The collection of 43 accessions of wild species represented only three species belonging to Sorghum bicolor ssp. drummondii and ssp. verticilliflorum, S. hevisonii, and S. macrochaeta, highlighting the need for collection missions aimed exclusively at enriching the collection of wild relatives. Accessions having characterization data (7630) were used to assess diversity. The first three principal components contributed to > 60% of variation. Maximum diversity was observed in the collection from Nigeria for both qualitative and quantitative traits. Mean values indicated significant differences between basic and intermediate races for the traits studied. Among the races, accessions of guinea-caudatum for qualitative traits and those of caudatum for quantitative traits were highly diverse. The low intensity of the sorghum collection and the many geographical gaps in the collection underline the importance of launching collection missions to fill the gaps, particularly in regions of predominantly guinea sorghums. Genotyping of possible duplicate accessions is needed to identify duplicates in the collection. It is suggested that all passport information including georeferenced data of collection sites should be collected when samples are collected in gaps

Status, genetic diversity and gaps in sorghum germplasm from South Asia conserved at ICRISAT genebank

The genebank at ICRISAT, India that serves as a world repository for sorghum germplasm conserves 39,234 accessions from 93 countries, including 6249 from seven South Asian countries: Afghanistan (6), Bangladesh (9), India (6101), the Maldives (10), Nepal (8), Pakistan (90) and Sri Lanka (25). A total of 5340 georeferenced accessions were used to identify gaps, and 5322 accessions that were characterized at ICRISAT were used to assess the diversity in the collection. Accessions of basic races varied widely than those of intermediate races for flowering in the postrainy season, plant height in both rainy and postrainy seasons, panicle exsertion, panicle length and width, seed size and 100 seed weight. Landraces from India were late flowering, tall and produced stout panicles and larger seeds. Landraces from Pakistan flowered early in both seasons and produced stout panicles and those from Sri Lanka were late flowering and tall in both seasons, produced more basal tillers and stout panicles. A total of 110 districts in 20 provinces of India, 13 districts in three provinces of Pakistan, three districts in Bangladesh and five districts in four provinces of Sri Lanka were identified as geographical gaps. Sorghum bicolor subsp. verticilliflorum, S. halepense and S. propinquum were identified as taxonomic gaps in the collection. Therefore, it is suggested to explore the districts identified as gaps to enrich the variability in the world collection of sorghum at ICRISAT

MiMiR - an integrated platform for microarray data sharing, mining and analysis

Background: Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.Results: A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.Conclusion: The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies

Geographical distribution, diversity and gap analysis of East African sorghum collection conserved at the ICRISAT genebank

The aim of the investigation was to assess the geographical distribution, diversity and gaps in sorghum collection from East African countries conserved at the ICRISAT genebank. The collection represents a total of 12,750 accessions including 11,672 landraces, 877 breeding materials, six improved cultivars, and 195 wild accessions. Passport data and FloraMap, a GIS software were used to assess geographical distribution and identify gaps. Range, mean, variance and phenotypic diversity index were estimated using GENSTAT 13.1. to assess the diversity in the collection. Cultivated sorghums classified into races and intermediate races based on spikelet and panicle morphology differed significantly, and races showed more variation than intermediate races for days to 50% flowering in postrainy season, plant height in rainy season, basal tillers per plant, panicle length, seed width and 100 seed weight. A total of 153 districts located in 50 provinces of 10 East African countries were found as the geographical gaps. Probably due to large variation for maturity, timing of collecting mission, and accessibility to the area under sorghum cultivation, both North and South Sudan were found as the major gaps with seven and 50 districts, respectively. The wild sorghum collection from East African countries belongs to S. bicolor, S. halepense, S. lanceolatum, S. macrochaeta, S. purpureosericeum and S. versicolor. Remaining species of genus sorghum were considered as taxonomic gaps. The gaps identified in the present study need to be explored on a priority basis to collect and conserve most diverse sorghum germplasm

A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset

Background: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. Results: Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a “subpopulation aware” 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). Conclusions: This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment. © 2024, The Author(s).Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

eQTL Explorer: integrated mining of combined genetic linkage and expression experiments

The development of computational resources to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. eQTL Explorer stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer provides a new and powerful tool to interrogate these very large and complex datasets

Effect of salinity on growth and proteomic changes in two cultivars of mulberry (Morus alba L.) with contrasting salt tolerance

508-518The effect of salinity on growth and proteomic changes was studied in two cultivars of mulberry (Morus alba L.) with contrasting salt tolerance. Three-month-old mulberry plants were subjected to 0.0 (control), 1.0, 1.5 and 2.0% NaCl stress for 7 d. Salt treatment did affect the growth, dry matter and leaf area in both the cultivars. The cultivar S1 showed a lesser rate of decrease in growth, dry matter and leaf area than cultivar ATP which indicated that cultivar S1 is better tolerant than cultivar ATP to salt stress. Soluble proteins extracted from leaves were analyzed by two-dimensional electrophoresis in order to detect salt stress induced changes in the polypeptide patterns. Salt stress resulted in differential changes in protein level qualitatively and quantitatively in both the cultivars. More than 150 protein spots that were detected in leaves of both cultivars showed reproducible abundance within replications and significant response to salt treatment compared to unstressed. In cultivar S1, 33 proteins increased and 21 proteins decreased by different salt stress levels. Among these, protein spot # 10, 32, 33, 46 to 48 and 53 were specifically induced by NaCl treatments in S1 cultivar. In ATP cultivar, eight proteins increased and 43 proteins decreased and one protein spot (# 55) found to be specific to this cultivar. In general, salt stress resulted a much decrease in growth and total polypeptide profiles in the susceptible cultivar ATP, than tolerant cultivar S1