1
|
Ruperao P, Gandham P, Odeny DA, Mayes S, Selvanayagam S, Thirunavukkarasu N, Das RR, Srikanda M, Gandhi H, Habyarimana E, Manyasa E, Nebie B, Deshpande SP, Rathore A. Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources. Front Plant Sci 2023; 14:1143512. [PMID: 37008459 PMCID: PMC10063887 DOI: 10.3389/fpls.2023.1143512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.
Collapse
Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, LA, United States
| | - Damaris A. Odeny
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research (ICAR) - Indian Institute of Millets Research, Hyderabad, India
| | - Roma R. Das
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Manasa Srikanda
- Department of Statistics, Osmania University, Hyderabad, India
| | - Harish Gandhi
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Baloua Nebie
- International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
| | | | - Abhishek Rathore
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India
| |
Collapse
|
2
|
Somegowda VK, Prasad KVSV, Naravula J, Vemula A, Selvanayagam S, Rathore A, Jones CS, Gupta R, Deshpande SP. Genetic Dissection and Quantitative Trait Loci Mapping of Agronomic and Fodder Quality Traits in Sorghum Under Different Water Regimes. Front Plant Sci 2022; 13:810632. [PMID: 35251083 PMCID: PMC8892184 DOI: 10.3389/fpls.2022.810632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/03/2022] [Indexed: 06/01/2023]
Abstract
Livestock provides an additional source of income for marginal cropping farmers, but crop residues that are used as a main source of animal feed are characteristically low in digestibility and protein content. This reduces the potential livestock product yield and quality. The key trait, which influences the quality and the cost of animal feed, is digestibility. In this study, we demonstrate that sorghum breeding can be directed to achieve genetic gains for both fodder biomass and digestibility without any trade-offs. The genotypic variance has shown significant differences for biomass across years (13,035 in 2016 and 3,395 in 2017) while in vitro organic matter digestibility (IVOMD) showed significant genotypic variation in 2016 (0.253) under drought. A range of agronomic and fodder quality traits was found to vary significantly in the population within both the control and drought conditions and across both years of the study. There was significant genotypic variance (σg2) and genotypic × treatment variance (σgxt2) in dry matter production in a recombinant inbred line (RIL) population in both study years, while there was only significant σg2 and σgxt2 in IVOMD under the control conditions. There was no significant correlation identified between biomass and digestibility traits under the control conditions, but there was a positive correlation under drought. However, a negative relation was observed between digestibility and grain yield under the control conditions, while there was no significant correlation under drought population, which was genotyped using the genotyping-by-sequencing (GBS) technique, and 1,141 informative single nucleotide polymorphism (SNP) markers were identified. A linkage map was constructed, and a total of 294 quantitative trait loci (QTLs) were detected, with 534 epistatic interactions, across all of the traits under study. QTL for the agronomic traits fresh and dry weight, together with plant height, mapped on to the linkage group (LG) 7, while QTL for IVOMD mapped on to LG1, 2, and 8. A number of genes previously reported to play a role in nitrogen metabolism and cell wall-related functions were found to be associated with these QTL.
Collapse
Affiliation(s)
- Vinutha K. Somegowda
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Kodukula V. S. V. Prasad
- International Livestock Research Institute (ILRI), International Crops Research Institute for the Semi-arid Tropics Campus, Patancheru, India
| | - Jalaja Naravula
- Department of Biotechnology, Vignan University, Vadlamudi, India
| | - Anilkumar Vemula
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | | | - Abhishek Rathore
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | - Chris S. Jones
- International Livestock Research Institute (ILRI), International Crops Research Institute for the Semi-arid Tropics Campus, Patancheru, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-arid Tropics-HQ, Patancheru, India
| |
Collapse
|
3
|
Bollam S, Romana KK, Rayaprolu L, Vemula A, Das RR, Rathore A, Gandham P, Chander G, Deshpande SP, Gupta R. Nitrogen Use Efficiency in Sorghum: Exploring Native Variability for Traits Under Variable N-Regimes. Front Plant Sci 2021; 12:643192. [PMID: 33968102 PMCID: PMC8097177 DOI: 10.3389/fpls.2021.643192] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Exploring the natural genetic variability and its exploitation for improved Nitrogen Use Efficiency (NUE) in sorghum is one of the primary goals in the modern crop improvement programs. The integrated strategies include high-throughput phenotyping, next generation sequencing (NGS)-based genotyping technologies, and a priori selected candidate gene studies that help understand the detailed physiological and molecular mechanisms underpinning this complex trait. A set of sixty diverse sorghum genotypes was evaluated for different vegetative, reproductive, and yield traits related to NUE in the field (under three N regimes) for two seasons. Significant variations for different yield and related traits under 0 and 50% N confirmed the availability of native genetic variability in sorghum under low N regimes. Sorghum genotypes with distinct genetic background had interestingly similar NUE associated traits. The Genotyping-By-Sequencing based SNPs (>89 K) were used to study the population structure, and phylogenetic groupings identified three distinct groups. The information of grain N and stalk N content of the individuals covered on the phylogenetic groups indicated randomness in the distribution for adaptation under variable N regimes. This study identified promising sorghum genotypes with consistent performance under varying environments, with buffer capacity for yield under low N conditions. We also report better performing genotypes for varied production use-grain, stover, and dual-purpose sorghum having differential adaptation response to NUE traits. Expression profiling of NUE associated genes in shoot and root tissues of contrasting lines (PVK801 and HDW703) grown in varying N conditions revealed interesting outcomes. Root tissues of contrasting lines exhibited differential expression profiles for transporter genes [ammonium transporter (SbAMT), nitrate transporters (SbNRT)]; primary assimilatory (glutamine synthetase (SbGS), glutamate synthase (SbGOGAT[NADH], SbGOGAT[Fd]), assimilatory genes [nitrite reductase (SbNiR[NADH]3)]; and amino acid biosynthesis associated gene [glutamate dehydrogenase (SbGDH)]. Identification and expression profiling of contrasting sorghum genotypes in varying N dosages will provide new information to understand the response of NUE genes toward adaptation to the differential N regimes in sorghum. High NUE genotypes identified from this study could be potential candidates for in-depth molecular analysis and contribute toward the development of N efficient sorghum cultivars.
Collapse
|
4
|
Rayaprolu L, Selvanayagam S, Daggu DMR, Gupta R, Das RR, Rathore A, Gandham P, Kiranmayee KU, Deshpande SP, Are AK. Genome-Wide Association Study for major Biofuel Traits in Sorghum Using Minicore Collection. Protein Pept Lett 2021; 28:909-928. [PMID: 33588716 DOI: 10.2174/0929866528666210215141243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/26/2020] [Accepted: 01/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Production of biofuels from lignocellulosic crop biomass is an alternative to reduce greenhouse gas emissions. The biofuel production involves collecting biomass, breaking down cell wall components followed by the conversion of sugars to ethanol. The lingo-cellulosic biomass comprises 40-50% cellulose, 20-30% hemicellulose, and 10-25% lignin. Sorghum is a widely adapted energy crop for biofuel production. Biomass with low lignin, high cellulose, and high hemicellulose contents are exploited to attain maximum biofuel production efficiency. Resistance to lodging, pest, disease, and abiotic stresses related to cell wall components is well documented, and quantitative trait loci were identified to understand these traits' genetic correlation. Selection for reduced lignin and increased cellulose content in stover can increase the ethanol yield. The Genome-Wide Association Studies (GWAS) is a complementary approach to evaluating the marker and phenotype associations among large diversity panels. Single nucleotide polymorphisms were scanned to identify loci associated with the traits of interest. In this study, the GWAS was performed on 245 sorghum minicore genotypes to analyze agronomic traits (days to 50%flowering, fresh biomass yield, dry biomass yield) and cell wall components (cellulose, hemicellulose, and lignin). Further, in-silico validation of the candidate genes was performed in a global gene expression data from large-scale RNA sequencing studies in sorghum available in the NCBI GEO database was used. OBJECTIVE The objectives of this study are to evaluate native variations in biofuel related agronomic traits and stalk cell wall components and to identify significant SNPs or loci related to the cell wall components. METHODS In this article, an association mapping panel, comprising of 245 sorghum minicore germplasm accessions, was evaluated during two post rainy seasons of 2013 and 2014, and observations were recorded on the whole plot- for days to 50% flowering, fresh biomass yield (tha-1), and dry biomass yield (tha-1). The biomass of sun-dried plants from both seasons was collected separately, chopped, dried, and ground to powder. The cellulose, hemicellulose, and lignin contents were determined in the powdered. The content of each of these three components in sorghum was expressed in percent of dry matter. The data on agronomic traits and composition analysis was subjected to Analysis of Variance. For the current study, we remapped the raw GBS data with the sorghum assembly version v3.1. A total of 27,589 SNPs were obtained with a minor allele frequency (MAF) >1% and missing data <50%. The GWAS was performed in a single minicore population using FarmCPU, in R software. The syntactic positions of the identified significant SNPs between sorghum and other model crop species viz., maize, switchgrass, and Arabidopsis were represented using CIRCOS software for traits viz., dry biomass yield, cellulose, hemicellulose, and lignin. The transcriptome dataset from where sorghum gene atlas studies of grain, sweet, and bioenergy sorghums are available through NCBI's Gene Expression Omnibus (GEO) under accession number GSE49879, was used to cross-validate the identified SNPs for cellulose, hemicellulose, and lignin through GWAS. RESULTS High broad-sense heritability was exhibited for all the traits in individual seasons along with significant genotype × environment interaction across seasons except lignin. Association mapping with a P < 1×10-4 revealed genomic regions associated with the- (i) agronomic traits (days to 50% flowering, fresh and dry biomass), and (ii) biochemical traits (cellulose, hemicellulose, and lignin) associated with biofuels production, in individual seasons. Twelve significant SNPs for flowering time, 30 fresh biomass yields, and 24 for dry biomass yield, 25 for cellulose, 7 for hemicellulose, and 21 for lignin were identified. CIRCOS plot was constructed to identify and analyze similarities and differences while comparing the sorghum genome with different crops. For cellulose high similarity of >80% was observed for all sorghum gene sequences with the maize homologs. The overall similarity of sorghum homologs with foxtail millet was >65%, for Arabidopsis from 30.6% to 48.6%, and rice from 28.2% to 92.8%. SNPs for hemicellulose displayed maximum similarity to foxtail millet followed by maize. The sequence similarity of lignin SNPs in sorghum was highest with the maize genome followed by Arabidopsis. Both rice and foxtail millet showed >55% similarity to the sorghum genome. CONCLUSION This study reports large variability for agronomic and biofuel traits in the sorghum minicore collection with high heritability. The genetic architecture of cell wall components using the GWAS approach was studied and candidate genes for each component were annotated. These results give a better understanding of the genetic basis of the sorghum cell wall composition. The association analysis identified regions of the genome that could be targeted to enhance the quality of biomass and yield along with the desired composition promoting breeding efficiency for enhanced biofuel yield.
Collapse
Affiliation(s)
- Laavanya Rayaprolu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | | | | | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | - Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | - Kns Usha Kiranmayee
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | - Santosh P Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| | - Ashok Kumar Are
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324. India
| |
Collapse
|
5
|
Ruperao P, Thirunavukkarasu N, Gandham P, Selvanayagam S, Govindaraj M, Nebie B, Manyasa E, Gupta R, Das RR, Odeny DA, Gandhi H, Edwards D, Deshpande SP, Rathore A. Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. Front Plant Sci 2021; 12:666342. [PMID: 34140962 PMCID: PMC8204017 DOI: 10.3389/fpls.2021.666342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/28/2021] [Indexed: 05/05/2023]
Abstract
Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
Collapse
Affiliation(s)
- Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | - Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | | | - Baloua Nebie
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, Mali
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Damaris A. Odeny
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Harish Gandhi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- Santosh P. Deshpande
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- *Correspondence: Abhishek Rathore
| |
Collapse
|
6
|
Jensen SE, Charles JR, Muleta K, Bradbury PJ, Casstevens T, Deshpande SP, Gore MA, Gupta R, Ilut DC, Johnson L, Lozano R, Miller Z, Ramu P, Rathore A, Romay MC, Upadhyaya HD, Varshney RK, Morris GP, Pressoir G, Buckler ES, Ramstein GP. A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction. Plant Genome 2020; 13:e20009. [PMID: 33016627 DOI: 10.1002/tpg2.20009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/04/2020] [Indexed: 05/22/2023]
Abstract
Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage-only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57-.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection.
Collapse
Affiliation(s)
- Sarah E Jensen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jean Rigaud Charles
- Chibas and Department of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Terry Casstevens
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Santosh P Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Daniel C Ilut
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Lynn Johnson
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Zachary Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Gael Pressoir
- Chibas and Department of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | | |
Collapse
|
7
|
Kotla A, Phuke R, Hariprasanna K, Mehtre SP, Rathore A, Gorthy S, Srivastava RK, Das R, Bhanu Prakash A, Radhika K, Hash CT, Reddy BV, Patil J, Jabeen F, Shashikanth D, Jaganathan J, Gaddameedi A, Subhasini V, Deshpande SP, Kumar AA. Identification of QTLs and candidate genes for high grain Fe and Zn concentration in sorghum [Sorghum bicolor (L.)Moench]. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.102850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
8
|
Phuke RM, Anuradha K, Radhika K, Jabeen F, Anuradha G, Ramesh T, Hariprasanna K, Mehtre SP, Deshpande SP, Anil G, Das RR, Rathore A, Hash T, Reddy BVS, Kumar AA. Genetic Variability, Genotype × Environment Interaction, Correlation, and GGE Biplot Analysis for Grain Iron and Zinc Concentration and Other Agronomic Traits in RIL Population of Sorghum ( Sorghum bicolor L. Moench). Front Plant Sci 2017; 8:712. [PMID: 28529518 PMCID: PMC5418227 DOI: 10.3389/fpls.2017.00712] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/18/2017] [Indexed: 05/24/2023]
Abstract
The low grain iron and zinc densities are well documented problems in food crops, affecting crop nutritional quality especially in cereals. Sorghum is a major source of energy and micronutrients for majority of population in Africa and central India. Understanding genetic variation, genotype × environment interaction and association between these traits is critical for development of improved cultivars with high iron and zinc. A total of 336 sorghum RILs (Recombinant Inbred Lines) were evaluated for grain iron and zinc concentration along with other agronomic traits for 2 years at three locations. The results showed that large variability exists in RIL population for both micronutrients (Iron = 10.8 to 76.4 mg kg-1 and Zinc = 10.2 to 58.7 mg kg-1, across environments) and agronomic traits. Genotype × environment interaction for both micronutrients (iron and zinc) was highly significant. GGE biplots comparison for grain iron and zinc showed greater variation across environments. The results also showed that G × E was substantial for grain iron and zinc, hence wider testing needed for taking care of G × E interaction to breed micronutrient rich sorghum lines. Iron and zinc concentration showed high significant positive correlation (across environment = 0.79; p < 0.01) indicating possibility of simultaneous effective selection for both the traits. The RIL population showed good variability and high heritabilities (>0.60, in individual environments) for Fe and Zn and other traits studied indicating its suitability to map QTL for iron and zinc.
Collapse
Affiliation(s)
- Rahul M. Phuke
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Professor Jayashankar Telangana State Agricultural UniversityHyderbad, India
| | - Kotla Anuradha
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Kommineni Radhika
- Professor Jayashankar Telangana State Agricultural UniversityHyderbad, India
| | - Farzana Jabeen
- Professor Jayashankar Telangana State Agricultural UniversityHyderbad, India
| | - Ghanta Anuradha
- Professor Jayashankar Telangana State Agricultural UniversityHyderbad, India
| | - Thatikunta Ramesh
- Professor Jayashankar Telangana State Agricultural UniversityHyderbad, India
| | | | | | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Gaddameedi Anil
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Roma R. Das
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Tom Hash
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Belum V. S. Reddy
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Are Ashok Kumar
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| |
Collapse
|
9
|
Gogtay NJ, Deshpande SP, Thatte UM. Principles of Regression Analysis. J Assoc Physicians India 2017; 65:48-52. [PMID: 28527164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- N J Gogtay
- Department of Clinical Pharmacology, Seth GS Medical College and KEM Hospital, Mumbai, Maharashtra
| | - S P Deshpande
- Department of Clinical Pharmacology, Seth GS Medical College and KEM Hospital, Mumbai, Maharashtra
| | - U M Thatte
- Department of Clinical Pharmacology, Seth GS Medical College and KEM Hospital, Mumbai, Maharashtra
| |
Collapse
|
10
|
Gorthy S, Narasu L, Gaddameedi A, Sharma HC, Kotla A, Deshpande SP, Are AK. Introgression of Shoot Fly ( Atherigona soccata L. Moench) Resistance QTLs into Elite Post-rainy Season Sorghum Varieties Using Marker Assisted Backcrossing (MABC). Front Plant Sci 2017; 8:1494. [PMID: 28919901 PMCID: PMC5585744 DOI: 10.3389/fpls.2017.01494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/11/2017] [Indexed: 05/19/2023]
Abstract
Shoot fly (Atherigona soccata L. Moench) is a serious pest in sorghum production. Management of shoot fly using insecticides is expensive and environmentally un-safe. Developing host-plant resistance is the best method to manage shoot fly infestation. Number of component traits contribute for imparting shoot fly resistance in sorghum and molecular markers have been reported which were closely linked to QTLs controlling these component traits. In this study, three QTLs associated with shoot fly resistance were introgressed into elite cultivars Parbhani Moti (= SPV1411) and ICSB29004 using marker assisted backcrossing (MABC). Crosses were made between recurrent parents and the QTL donors viz., J2658, J2614, and J2714. The F1s after confirmation for QTL presence were backcrossed to recurrent parents and the resultant lines after two backcrosses were selfed thrice for advancement. The foreground selection was carried out in F1 and BCnF1 generations with 22 polymorphic markers. Forty-three evenly distributed simple sequence repeat markers in the sorghum genome were used in background selection to identify plants with higher recurrent parent genome recovery. By using two backcrosses and four rounds of selfing, six BC2F4 progenies were selected for ICSB29004 × J2658, five BC2F4 progenies were selected for ICSB29004 × J2714 and six BC2F4 progenies were selected for Parbhani Moti × J2614 crosses. Phenotyping of these lines led to the identification of two resistant lines for each QTL region present on chromosome SBI-01, SBI-07 and SBI-10 in ICSB 29004 and Parbhani Moti. All the introgression lines (ILs) showed better shoot fly resistance than the recurrent parents and their agronomic performance was the same or better than the recurrent parents. Further, the ILs had medium plant height, desirable maturity with high yield potential which makes them better candidates for commercialization. In the present study, MABC has successfully improved the shoot fly resistance in sorghum without a yield penalty. This is the first report on the use of MABC for improving shoot fly resistance in post-rainy season sorghum.
Collapse
Affiliation(s)
- Sunita Gorthy
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
- Department of Biotechnology, Jawaharlal Nehru Technological UniversityHyderabad, India
| | - Lakshmi Narasu
- Department of Biotechnology, Jawaharlal Nehru Technological UniversityHyderabad, India
| | - Anil Gaddameedi
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | - Hari C. Sharma
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | - Anuradha Kotla
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | | | - Ashok K. Are
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
- *Correspondence: Ashok K. Are,
| |
Collapse
|
11
|
Deshpande SP, Gogtay NJ, Thatte UM. Which Test Where? J Assoc Physicians India 2016; 64:64-66. [PMID: 27805335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- S P Deshpande
- Dept. of Clinical Pharmacology, Seth GS Medical College, Mumbai, Maharashtra
| | - N J Gogtay
- Dept. of Clinical Pharmacology, Seth GS Medical College, Mumbai, Maharashtra
| | - U M Thatte
- Dept. of Clinical Pharmacology, Seth GS Medical College, Mumbai, Maharashtra
| |
Collapse
|
12
|
Gogtay NJ, Deshpande SP, Thatte UM. Normal Distribution, "p" Value and Confidence Intervals. J Assoc Physicians India 2016; 64:74-76. [PMID: 27762113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- N J Gogtay
- Dept. of Clinical Pharmacology, Seth GS Medical College, Parel, Mumbai 400 012
| | - S P Deshpande
- Dept. of Clinical Pharmacology, Seth GS Medical College, Parel, Mumbai 400 012
| | - U M Thatte
- Dept. of Clinical Pharmacology, Seth GS Medical College, Parel, Mumbai 400 012
| |
Collapse
|
13
|
Upadhyaya HD, Vetriventhan M, Deshpande SP, Sivasubramani S, Wallace JG, Buckler ES, Hash CT, Ramu P. Population Genetics and Structure of a Global Foxtail Millet Germplasm Collection. Plant Genome 2015; 8:eplantgenome2015.07.0054. [PMID: 33228275 DOI: 10.3835/plantgenome2015.07.0054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/24/2015] [Indexed: 05/25/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is one among the most ancient crops of dryland agriculture. It is the second most important crop among millets grown for grains or forage. Foxtail millet germplasm resources provide reservoirs of novel alleles and genes for crop improvement that have remained mostly unexplored. We genotyped a set of 190 foxtail millet germplasm accessions (including 155 accessions of the foxtail millet core collection) using genotyping-by-sequencing (GBS) for rapid single nucleotide polymorphisms (SNP) characterization to study population genetics and structure, which enable allele mining through association mapping approaches. After filtering a total 350,000 raw SNPs identified across 190 germplasm accessions for minor allele frequency (MAF), coverage for samples and coverage for sites, we retained 181 accessions with 17,714 high-quality SNPs with ≥5% MAF. Genetic structure analyses revealed that foxtail millet germplasm accessions are structured along both on the basis of races and geographic origin, and the maximum proportion of variation was due to among individuals within populations. Accessions of race indica were less diverse and are highly differentiated from those of maxima and moharia. Genome-wide linkage disequilibrium (LD) analysis showed on an average LD extends up to ∼150 kbp and varied with individual chromosomes. The utility of the data for performing genome-wide association studies (GWASs) was tested with plant pigmentation and days to flowering and identified significant marker-trait associations. This SNP data provides a foundation for exploration of foxtail millet diversity and for mining novel alleles and mapping genes for economically important traits.
Collapse
Affiliation(s)
- Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
- Dep. of Agronomy, Kansas State Univ., Manhattan, KS, 66506, USA
- Institute of Agriculture, Univ. of Western Australia, Crawley, WA, 6009, Australia
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Santosh P Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Selvanayagam Sivasubramani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Telangana, India
| | - Jason G Wallace
- Institute for Genomic Diversity, Cornell Univ., Ithaca, NY, 14853
| | - Edward S Buckler
- USDA-ARS, Ithaca, NY, 14853
- Institute for Genomic Diversity, Cornell Univ., Ithaca, NY, 14853
| | - C Tom Hash
- ICRISAT Sahelian Center (ISC), BP, 12404, Niamey, Niger
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell Univ., Ithaca, NY, 14853
| |
Collapse
|
14
|
Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci U S A 2013; 110:453-8. [PMID: 23267105 PMCID: PMC3545811 DOI: 10.1073/pnas.1215985110] [Citation(s) in RCA: 459] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ~265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.
Collapse
Affiliation(s)
- Geoffrey P Morris
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Vadez V, Deshpande SP, Kholova J, Hammer GL, Borrell AK, Talwar HS, Hash CT. Stay-green quantitative trait loci's effects on water extraction, transpiration efficiency and seed yield depend on recipient parent background. Funct Plant Biol 2011; 38:553-566. [PMID: 32480908 DOI: 10.1071/fp11073] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/31/2011] [Indexed: 05/19/2023]
Abstract
A stay-green phenotype enhances the adaptation of sorghum (Sorghum bicolor (L.) Moench) to terminal drought, although the mechanisms leading to its expression remain unclear. Differences in tillering and leaf area at anthesis, transpiration efficiency (TE), water extraction, harvest index (HI) and yield under terminal drought and fully irrigated conditions were assessed in 29 introgression lines (IL) targeting stay-green quantitative trait loci (QTLs) Stg1, Stg2, Stg3, Stg4, StgA and StgB in an S35 background, and 16 IL targeting Stg1, Stg3, Stg4 and StgB in an R16 background. TE was increased by StgB in the R16 background, whereas there was no effect in the S35 background. Water extraction was increased by Stg1 in the S35 background but not in R16. StgB modified the proportion of water extracted before and after anthesis in the S35 background. While tillering and leaf area at anthesis were decreased by Stg1 and Stg3 in S35, there was no effect in R16. Yield data under fully irrigated conditions showed higher tiller grain yield in Stg1, Stg2 and Stg3 ILs. Although yield differences were mostly explained by HI variation, the yield variation unexplained by HI was closely related to TE in S35 (R2=0.29) and R16 (R2=0.72), and was closely related to total water extracted in S35 (R2=0.41) but not in R16. These data indicate the potential for several stay-green QTLs to affect traits related to plant water use. However, these effects depend on the interaction between the genetic background and individual QTLs.
Collapse
Affiliation(s)
- Vincent Vadez
- International Crops Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502324, Andhra Pradesh, India
| | - Santosh P Deshpande
- International Crops Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502324, Andhra Pradesh, India
| | - Jana Kholova
- International Crops Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502324, Andhra Pradesh, India
| | - Graeme L Hammer
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Station, Warwick, Qld 4370, Australia
| | - Andrew K Borrell
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Station, Warwick, Qld 4370, Australia
| | - Harvinder S Talwar
- Directorate of Sorghum Research Directorate of Sorghum Research (DSR), Rajendranagar Hyderabad 500030, Andhra Pradesh, India
| | - C Thomas Hash
- International Crops Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502324, Andhra Pradesh, India
| |
Collapse
|
16
|
David M, Ramesh H, Deshpande SP, Chebbi SG, Krishnamurthy G. Respiratory distress and behavioral changes induced by sodium cyanide in the fresh water TELEOST, Cyprinus carpio (Linnaeus). J Basic Clin Physiol Pharmacol 2009; 20:55-65. [PMID: 19601395 DOI: 10.1515/jbcpp.2009.20.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
An acute toxicity (LC50) test using a static renewal bioassay method was conducted to determine the toxicity of sodium cyanide in freshwater exotic carp, Cyprinus carpio exposed for 96 h to different concentrations of sodium cyanide. The acute toxicity value was found to be 1 mg/L; one third of the LC50 (0.33 mg/L) was selected as the sublethal concentration for subacute studies. Behavioral patterns were observed in lethal (1, 2, 3, and 4 d) and sublethal concentrations (1, 5, 10, and 15 d). Cyprinus carpio in toxic media exhibited irregular, erratic, and darting swimming movements, hyperexcitability, loss of equilibrium, and sinking to the bottom, which might be due to inhibition of cytochrome c oxidase activity and decreased blood pH. The combination of cytotoxic hypoxia with lactate acidosis depresses the central nervous system and myocardium, the most sensitive critical sites for anoxia, resulting in respiratory arrest and death. A decrease in oxygen consumption (-28.36 to -78.28%; -14.22 to -47.25%) was observed at both lethal and sublethal concentrations of sodium cyanide respectively. Fish at the sublethal concentration were found under stress, but that was not fatal.
Collapse
Affiliation(s)
- M David
- Karnatak University's Research Laboratory, Toxicology Division, Department of Zoology, Karnatak Science College and J.S.S. College, Dharwad-580 001, Karnataka, India.
| | | | | | | | | |
Collapse
|
17
|
Deshpande SP, Lee S, Zheng M, Song B, Knipe D, Kapp JA, Rouse BT. Herpes simplex virus-induced keratitis: evaluation of the role of molecular mimicry in lesion pathogenesis. J Virol 2001; 75:3077-88. [PMID: 11238834 PMCID: PMC114101 DOI: 10.1128/jvi.75.7.3077-3088.2001] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2000] [Accepted: 12/24/2000] [Indexed: 01/19/2023] Open
Abstract
Viruses are suspected but usually unproven triggering factors in autoimmunity. One favored mechanism to explain the role of viruses in the genesis of autoimmunity is molecular mimicry. An immunoinflammatory blinding lesion called herpetic stromal keratitis (HSK) that follows ocular infection with herpes simplex virus (HSV) is suggested to result from a CD4(+) T-cell response to a UL6 peptide of HSV that cross-reacts with a corneal autopeptide shared with the immunoglobulin G2a(b) (IgG2a(b)) isotype. The present report reevaluates the molecular mimicry hypothesis to explain HSK pathogenesis. Our results failed to reveal cross-reactivity between the UL6 and IgG2a(b) peptides or between peptide reactive T cells and HSV antigens. More importantly, animals infected with HSV failed to develop responses that reacted with either peptide, and infection with a recombinant vaccinia UL6 vector failed to cause HSK, in spite of generating UL6 reactivity. Other lines of evidence also failed to support the molecular mimicry hypothesis, such as the failure to affect HSK severity upon tolerization of susceptible BALB/c and B-cell-deficient mice with IgG2a(b) or UL6 peptides. An additional study system revealed that HSK could be induced in mouse strains, such as the OT2 x RAG1(-/-) mice (T cell receptor transgenic recognizing OVA(323-339)) that were unable to produce CD4(+) T-cell responses to any detectable HSV antigens. Our results cast doubt on the molecular mimicry hypothesis as an explanation for the pathogenesis of HSK and indicate that if autoimmunity is involved its likely proceeds via a bystander activation mechanism.
Collapse
Affiliation(s)
- S P Deshpande
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
This study examines union certification elections in hospitals from October 1994 to September 1997. Results indicate that union win rates were significantly higher in single-union elections and larger bargaining units. On the other hand, union win rates were significantly lower in church-related hospitals and hospitals that belonged to a health care system or had higher payroll costs. Unions also appeared to win elections at a higher rate in this period than in the past.
Collapse
Affiliation(s)
- S P Deshpande
- Department of Management, Haworth College of Business, Western Michigan University, Kalamazoo, Michigan, USA
| |
Collapse
|
19
|
Abstract
This review discusses the possible causes for the lack of an effective antiherpes vaccine. Future prospects of vaccines based on the current knowledge of immune responses to herpes viruses are discussed. It is argued that vaccines capable of expanding CD8 T-cell memory responses should be the focus of future anti-herpes simplex virus research.
Collapse
Affiliation(s)
- S P Deshpande
- Department of Microbiology, University of Tennessee, Knoxville 37996-0845, USA
| | | | | |
Collapse
|
20
|
Abstract
mu-immunoglobulin chain gene targeted B-cell-deficient mice of susceptible BALB/c strain and resistant C57B1/6 strain are up to 100- to 1000-fold more susceptible to cutaneous infection by herpes simplex virus (HSV) than the respective control wild type mice. The effect of the lack of B cells on immunity to HSV infections was analyzed and B cells were found to play a dual role in affecting both innate and acquired immune responses. Natural antibodies (IgM isotype), reactive with HSV have an anti-viral effect in the innate control of primary cutaneous HSV infection. B cells can also function as antigen-presenting cells for the stimulation of HSV-specific CD4+ T-cell responses. Consequently, CD4+ T cells and interferon-gamma responses were found to be significantly impaired in HSV-infected B-cell-deficient mice compared to that seen in control mice. No significant differences were found in natural-killer-cell- or HSV-specific CD8+ T-cell activity between control and B-cell-deficient mice. Our results imply a role for B cell in mediating innate and CD4+ T-cell-specific immunity in determining susceptibility to primary HSV infections.
Collapse
Affiliation(s)
- S P Deshpande
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | | |
Collapse
|
21
|
Abstract
The role of B cells and humoral immunity in herpes simplex virus (HSV) ocular infections was studied in immunoglobulin mu chain gene-targeted B-cell-deficient mice (muK/O). At doses of virus well tolerated by immunocompetent mice, heightened susceptibility of muK/O mice to herpetic encephalitis as well as to herpetic stromal keratitis (HSK) was observed. An explanation was sought for the increased severity of HSK in the muK/O mice. First, the lack of antibody responses in muK/O mice resulted in longer viral persistence and dissemination to the corneal stroma, the site of inflammation. Prolonged virus expression in the corneal stroma was suggested to cause bystander activation of Th1-type CD4(+) T cells, further contributing to the severity of HSK lesion expression in muK/O mice. Second, muK/O mice generated minimal Th2 cytokine responses compared to wild-type mice. Such responses might serve to downregulate the severity of Th1-mediated HSK lesions.
Collapse
Affiliation(s)
- S P Deshpande
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845, USA
| | | | | | | |
Collapse
|
22
|
Gangappa S, Deshpande SP, Rouse BT. Bystander activation of CD4+ T cells accounts for herpetic ocular lesions. Invest Ophthalmol Vis Sci 2000; 41:453-9. [PMID: 10670475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
PURPOSE Stromal keratitis is an immunopathologic consequence of herpes simplex virus (HSV) infection of the cornea. The lesion is immunopathologic, but the identities of molecules that drive the reaction remain unresolved. To exclude viral antigen recognition as a necessary step in the disease process, ocular HSV infection was followed in Tg-RAG mice (OVA-TCR transgenic mice crossed to RAG2-deficient mice) whose limited T-cell repertoire did not include immune responsiveness to HSV. METHODS Mice with T-cell specificity to OVA peptide (Tg-RAG mice) as well as control DO11.10 and BALB/c mice were infected with HSV on the scarified cornea and subjected to clinical, histologic, and immunologic analysis. To evaluate involvement of OVA-specific CD4+ T cells in lesion development in Tg-RAG mice, monoclonal antibody to CD4+ T cells was used for in vivo CD4+ T-cell depletion. RESULTS Tg-RAG mice were capable of eliciting ocular lesions in the absence of detectable reactivity to viral antigens. Lesion manifestation in Tg-RAG mice was CD4+ T-cell dependent and the cellular infiltrates and their inflammatory products in the HSV-infected cornea were comparable to similarly infected BALB/c and DO11.10 mice. CONCLUSIONS The authors conclude that mechanisms other than viral antigen recognition, and hence molecular mimicry, are at play and are sufficient to cause HSV-induced stromal keratitis. The data imply a significant role for non-virus-specific CD4+ T cells that could become activated by an inflammatory milieu consisting of enhanced accessory molecules and proinflammatory cytokines in the cornea.
Collapse
Affiliation(s)
- S Gangappa
- Department of Microbiology, College of Veterinary Medicine, The University of Tennessee, Knoxville 37996-0845, USA
| | | | | |
Collapse
|
23
|
Abstract
Herpetic stromal keratitis (HSK) is an immunopathological lesion involving herpes simplex virus (HSV) infection and CD4(+) T cells of the Th1 phenotype, but the nature of the target antigens which drive HSK remains uncertain. In the present report we show that ovalbumin TCR-transgenic mice backcrossed to SCID mice unable to recognize HSV show clinical signs of HSK but die of viral encephalitis before the lesions become severe. However, passive transfer of anti-HSV serum at 24 h clears virus and affords protection from both HSK lesions and death. Adoptive transfer of CD8(+) T cells at 72 h usually conferred protection but animals developed severe corneal pathology by 3 weeks post infection. At this time viral antigens were not demonstrable in the cornea and the T cells in the inflammatory lesions were CD4(+)KJ1-26.1 idiotype positive, i. e. OVA peptide specific. These results indicate bystander activation of CD4(+) T cells in a virus-induced inflammatory milieu. This mechanism of immunoinflammation may represent an important component of any lesion which involves CD4(+) T cells.
Collapse
Affiliation(s)
- S Gangappa
- Department of Microbiology, College of Veterinary Medicine, The University of Tennessee, Knoxville, USA
| | | | | |
Collapse
|
24
|
Deshpande SP. An alternative approach to a posteriorly dislocated intraocular lens. Indian J Ophthalmol 1999; 47:205. [PMID: 10858782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
|
25
|
Deshpande SP, Schoderbek PP. Pay allocations by hospital administrators: an empirical analysis. Hosp Health Serv Adm 1999; 37:321-32. [PMID: 10120492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
This study uses a policy-capturing approach to examine 816 pay-increase decisions made by 17 hospital administrators. Subjects were asked to respond to packages consisting of hypothetical employees who varied in performance levels, specialized skills or expertise, difficulty in replacing, potential turnover, and current salary. Results indicated that all five factors were significant and in the direction expected for most of the raters. None of the hypothesized interaction effects were significant for any of the raters. Results also showed that subjects' explicit rankings of the importance of the factors did not correspond highly with the rankings of their regression weights. The implications of this study for both research and practice are discussed.
Collapse
Affiliation(s)
- S P Deshpande
- Haworth College of Business, Western Michigan University, Kalamazoo
| | | |
Collapse
|
26
|
Joseph J, Deshpande SP. The impact of ethical climate on job satisfaction of nurses. Health Care Manage Rev 1997; 22:76-81. [PMID: 9058089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This article examines the impact of ethical climate types (shared perception of how ethical issues should be addressed and what is ethically correct behavior) on various facets of job satisfaction of nurses in a large nonprofit private hospital. The results of the study indicate that hospitals may be able to enhance job satisfaction of nurses by influencing the organization's ethical climate.
Collapse
Affiliation(s)
- J Joseph
- University of Alaska at Fairbanks, USA
| | | |
Collapse
|
27
|
Maria DL, Deshpande SP, Kamble BS. Keratomycosis(a case report due to mucormycosis). Indian J Ophthalmol 1979; 27:55-6. [PMID: 511293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|