54 research outputs found
An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms
The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of
intra- and interspecies single nucleotide polymorphisms
(SNPs). In the case of model organisms, the data available are
numerous, given the degree of redundancy in the deposited EST
data. There are several available bioinformatics tools that
can be used to mine this data; however, using them requires a
certain level of expertise: the tools have to be used
sequentially with accompanying format conversion and steps
like clustering and assembly of sequences become
time-intensive jobs even for moderately sized datasets. We
report here a pipeline of open source software extended to run
on multiple CPU architectures that can be used to mine large
EST datasets for SNPs and identify restriction sites for
assaying the SNPs so that cost-effective CAPS assays can be
developed for SNP genotyping in genetics and breeding
applications. At the International Crops Research Institute for
the Semi-Arid Tropics (ICRISAT), the pipeline has been
implemented to run on a Paracel high-performance system
consisting of four dual AMD Opteron processors running Linux
with MPICH. The pipeline can be accessed through user-friendly
web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is
available on request for academic use. We have validated the
developed pipeline by mining chickpea ESTs for interspecies
SNPs, development of CAPS assays for SNP genotyping, and
confirmation of restriction digestion pattern at the sequence
level
Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms
Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNAseq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein (Araip.3WN1Q) and another SNP from gene coding for the lipid transfer protein (Aradu.03ENG) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes
Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome
This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago
Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)
Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes
Genome-Wide Identification, Characterization, and Expression Analysis of Small RNA Biogenesis Purveyors Reveal Their Role in Regulation of Biotic Stress Responses in Three Legume Crops
Biotic stress in legume crops is one of the major threats to crop yield and productivity. Being sessile organisms, plants have evolved a myriad of mechanisms to combat different stresses imposed on them. One such mechanism, deciphered in the last decade, is small RNA (sRNA) mediated defense in plants. Small RNAs (sRNAs) have emerged as one of the major players in gene expression regulation in plants during developmental stages and under stress conditions. They are known to act both at transcriptional and post-transcriptional levels. Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDR) constitute the major components of sRNA biogenesis machinery and are known to play a significant role in combating biotic and abiotic stresses. This study is, therefore, focused on identification and characterization of sRNA biogenesis proteins in three important legume crops, namely chickpea, pigeonpea, and groundnut. Phylogenetic analysis of these proteins between legume species classified them into distinct clades and suggests the evolutionary conservation of these genes across the members of Papillionidoids subfamily. Variable expression of sRNA biogenesis genes in response to the biotic stresses among the three legumes indicate the possible existence of specialized regulatory mechanisms in different legumes. This is the first ever study to understand the role of sRNA biogenesis genes in response to pathogen attacks in the studied legumes
Explaining Differences in the Acceptability of 99DOTS, a Cell Phone–Based Strategy for Monitoring Adherence to Tuberculosis Medications: Qualitative Study of Patients and Health Care Providers
Hybrid Energy Efficient Secured Attribute based ZRP Aiding Authentic Data Transmission
The modern furtherance in mobile Ad-hoc networks with evolving technology is challenging the researcher’s calibre in several aspects concerning routing MANETS with dynamic structure rely on the routing factor for reliable transmission. Routing protocols dictate the performance of networks in Wireless environments. Practitioner’s research introduces routing protocols falling into categories like Proactive, Reactive and Hybrid routing protocols. Zone Routing Protocol (ZRP), a multicast routing protocol is gaining attention as it fusions the features of both proactive and Reactive protocols. Our work addresses the energy consumption issues and security breaches in the routing process of ZRP, thereby furnishing with a Hybrid Approach. The proposed Model leverages transmission efficiency by periodically reducing the number of unwanted nodes consuming energy and providing additional security instances using ABE-based encryption. Various Qualities of Service (QoS) parameters like throughput, end-to-end delay (E2ED), load balancing, energy consumption, and delivery ratio have shown that the hybrid technique is effective compared to the traditional ZRP
Hybrid Energy Efficient Secured Attribute based ZRP Aiding Authentic Data Transmission
69-75The modern furtherance in mobile Ad-hoc networks with evolving technology is challenging the researcher’s calibre in
several aspects concerning routing MANETS with dynamic structure rely on the routing factor for reliable transmission.
Routing protocols dictate the performance of networks in Wireless environments. Practitioner’s research introduces routing
protocols falling into categories like Proactive, Reactive and Hybrid routing protocols. Zone Routing Protocol (ZRP), a
multicast routing protocol is gaining attention as it fusions the features of both proactive and Reactive protocols. Our work
addresses the energy consumption issues and security breaches in the routing process of ZRP, thereby furnishing with a
Hybrid Approach. The proposed Model leverages transmission efficiency by periodically reducing the number of unwanted
nodes consuming energy and providing additional security instances using ABE-based encryption. Various Qualities of
Service (QoS) parameters like throughput, end-to-end delay (E2ED), load balancing, energy consumption, and delivery ratio
have shown that the hybrid technique is effective compared to the traditional ZRP
Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers
Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding
Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms
Drought is one of the main constraints in peanut production in West Texas and eastern New Mexico regions due to the depletion of groundwater. A multi-seasonal phenotypic analysis of 10 peanut genotypes revealed C76-16 (C-76) and Valencia-C (Val-C) as the best and poor performers under deficit irrigation (DI) in West Texas, respectively. In order to decipher transcriptome changes under DI, RNAseq was performed in C-76 and Val-C. Approximately 369 million raw reads were generated from 12 different libraries of two genotypes subjected to fully irrigated (FI) and DI conditions, of which ~329 million (90.2%) filtered reads were mapped to the diploid ancestors of peanut. The transcriptome analysis detected 4,508 differentially expressed genes (DEGs), 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms (SNPs) among the identified DEGs. The comparative analysis between the two genotypes revealed higher and integral tolerance in C-76 through activation of key genes involved in ABA and sucrose metabolic pathways. Interestingly, one SNP from the gene coding F-box protein (Araip.3WN1Q) and another SNP from gene coding for the lipid transfer protein (Aradu.03ENG) showed polymorphism in selected contrasting genotypes. These SNPs after further validation may be useful for performing early generation selection for selecting drought-responsive genotypes
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