Resonator to Laser Cavity Decoupling Interface for Chemical Oxygen Iodine Laser

In the present work, the conventional chemical oxygen iodine laser (COIL) source has been technologically upgraded and successfully tested after implementation of decoupling interface between laser cavity and resonator. In the technique, anti-reflection coated fused silica windows mounted in suitable mechanical assemblies are placed between resonator mirrors and laser cavity in such a way that the generated laser beam is out coupled through the resonator during the laser operation. The implemented decoupling assemblies isolate the caustic environment produced in low pressure laser cavity from that of resonator mirrors. Thus requirement of using isolation valves and cavity limbs between laser cavity and resonator as in conventional COIL source is eliminated. Such decoupling mechanism therefore effectively reduces the number of associated components as well as overall length of the laser source which in turn further reduces the overall weight of the laser making it suitable for use onto a mobile platform. Moreover the technique provides accrued benefits in terms of reduction in readiness time and checking of optical alignment of the laser source at will in practical operation scenarios

Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense

Background Hordeum chilense, a native South American diploid wild barley, is a potential source of useful genes for cereal breeding. The use of this wild species to increase genetic variation in cereals will be greatly facilitated by marker-assisted selection. Different economically feasible approaches have been undertaken for this wild species with limited direct agricultural use in a search for suitable and cost-effective markers. The availability of Expressed Sequence Tags (EST) derived microsatellites or simple sequence repeat (SSR) markers, commonly called as EST-SSRs, for barley (Hordeum vulgare) represents a promising source to increase the number of genetic markers available for the H. chilense genome. Results All of the 82 barley EST-derived SSR primer pairs tested for transferability to H. chilense amplified products of correct size from this species. Of these 82 barley EST-SSRs, 21 (26%) showed polymorphism among H. chilense lines. Identified polymorphic markers were used to test the transferability and polymorphism in other Poaceae family species with the aim of establishing H. chilense phylogenetic relationships. Triticum aestivum-H. chilense addition lines allowed us to determine the chromosomal localizations of EST-SSR markers and confirm conservation of the linkage group. Conclusion From the present study a set of 21 polymorphic EST-SSR markers have been identified to be useful for diversity analysis of H. chilense, related wild barleys like H. murinum, and for wheat marker-assisted introgression breeding. Across-genera transferability of the barley EST-SSR markers has allowed phylogenetic inference within the Triticeae complex

Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis

Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2–10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of “K” genome, although distinct from both the “A” and “B” genomes, but more similar to “B” genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications

Perl module and PISE wrappers for the integrated analysis of sequence data and SNP features

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Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut

Sowing Legume Seeds, Reaping Cash

This open access book shares impact stories – testimonies from various value chain actors who have been part of the Tropical Legumes (TL) projects, over the past twelve years. The Tropical Legumes projects led by ICRISAT in three parts (TLI, TLII and TLIII), constitute a major international initiative supported by the Bill & Melinda Gates Foundation (BMGF) and jointly implemented by the International Center for Tropical Agriculture (CIAT), International Institute of Tropical Agriculture (IITA) and National Agricultural Research Systems (NARS) partners from Sub-Saharan Africa and India. The project developed improved cultivars of common bean, cowpea, chickpea and groundnut (but also soya bean and pigeon pea cultivars in its initial phases) and delivers their seed to smallholders in BMGF-focus areas. It also strengthens the NARS and CGIAR's breeding programs and seed platforms to enhance their ability to deliver high and sustained outputs to smallholder farmers. The book compiles the experiences of a diversity of actors within the grain legume value chains, with a focus on groundnut and common beans in Tanzania and Uganda, groundnut and cowpea in Nigeria, and groundnut in Ghana. All stakeholders involved share their thoughts on being part of a decade-long development project family. National agricultural research institutes, knowledge brokering organizations, NGOs, public and private seed companies, agro-dealers, individual seed entrepreneurs, farm-implement makers, farmer cooperatives, farmer groups, individual men and women farmers, middlemen, processors, traders and consumers were all involved in this project, and as such this book provides valuable insights for development workers, technical staff, and project managers

Genetic relationships among seven sections of genus Arachis studied by using SSR markers

<p>Abstract</p> <p>Background</p> <p>The genus <it>Arachis</it>, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the <it>Arachis </it>species are diploids (2<it>n </it>= 2<it>x </it>= 20) and the tetraploid species (2<it>n </it>= 2<it>x </it>= 40) are found in sections <it>Arachis</it>, <it>Extranervosae </it>and <it>Rhizomatosae</it>. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of <it>Arachis </it>by using simple sequence repeat (SSR) markers developed from <it>Arachis hypogaea </it>genomic library and gene sequences from related genera of <it>Arachis</it>.</p> <p>Results</p> <p>The average transferability rate of 101 SSR markers tested to section <it>Arachis </it>and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, <it>Arachis pusilla </it>exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (<it>A. duranensis</it>) and the B-genome accession ICG 8206 (<it>A. ipaënsis</it>) were found most closely related to <it>A. hypogaea</it>.</p> <p>Conclusion</p> <p>A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of <it>Arachis</it>, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of <it>A. monticola </it>and <it>A. hypogaea </it>as well as on the most probable donor of A and B-genomes of cultivated groundnut.</p