Design and validation of microarray for chickpea (Cicer arietinum) based on the analysis of transcriptome data
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ABSTRACT:
ORGANISM(S): Cicer arietinum
PROVIDER: GSE78987 | GEO | 2017/01/07
SECONDARY ACCESSION(S): PRJNA314577
REPOSITORIES: GEO
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Project description:Microarrays have increasingly become a powerful tool for high throughput gene-expression studies and discovery of novel biomarker genes. Developed for a large number of organisms, including plants, microarrays are commonly performed for species that have sequenced data, for performing gene expression analysis, miRNA profiling, comparative genomic hybridization (CGH), ChIP-on-chip and SNP analysis. Genomic resources are still very limited for chickpea, a very important food legume crop. Here, we report the design and comprehensive validation of Next Generation Sequencing transcriptome data for chickpea through microarray technology to develop a high-throughput resource for studying the expression of all the transcripts in different biological samples to help functional genomics and breeding programs. This microarray design was developed and validated jointly by Genotypic Technology Private Limited and National Institute of Plant Genome Research. First, we designed 400k probes using reads covering 35k assembled contigs and 100k singletons chickpea transcripts. The 400k chip was hybridized with DNA and RNA samples of chickpea and microarray analysis was carried out. A total of 73,922 probes were found to be specific to chickpea transcripts. Best probes were filtered from the analyzed data and a total of 61,659 probes were selected to develop the final microarray design in 60k gene-expression microarray format. The probes represented 51,444 unique transcripts. The probes were annotated based on their corresponding chickpea transcript and similarity with other plants species. Microarray results were concordant with previous results from the NGS studies. The design of custom oligonucleotide probes for microarrays have varied functional genomic applications and this approach represents a valuable resource for chickpea.
2017-01-05 | GSE76972 | GEO
Project description:Microarrays have increasingly become a powerful tool for high throughput gene-expression studies and discovery of novel biomarker genes. Developed for a large number of organisms, including plants, microarrays are commonly performed for species that have sequenced data, for performing gene expression analysis, miRNA profiling, comparative genomic hybridization (CGH), ChIP-on-chip and SNP analysis. Genomic resources are still very limited for chickpea, a very important food legume crop. Here, we report the design and comprehensive validation of Next Generation Sequencing transcriptome data for chickpea through microarray technology to develop a high-throughput resource for studying the expression of all the transcripts in different biological samples to help functional genomics and breeding programs. This microarray design was developed and validated jointly by Genotypic Technology Private Limited and National Institute of Plant Genome Research. First, we designed 400k probes using reads covering 35k assembled contigs and 100k singletons chickpea transcripts. The 400k chip was hybridized with DNA and RNA samples of chickpea and microarray analysis was carried out. A total of 73,922 probes were found to be specific to chickpea transcripts. Best probes were filtered from the analyzed data and a total of 61,659 probes were selected to develop the final microarray design in 60k gene-expression microarray format. The probes represented 51,444 unique transcripts. The probes were annotated based on their corresponding chickpea transcript and similarity with other plants species. Microarray results were concordant with previous results from the NGS studies. The design of custom oligonucleotide probes for microarrays have varied functional genomic applications and this approach represents a valuable resource for chickpea.
2017-01-07 | GSE78985 | GEO
Project description:Microarrays have increasingly become a powerful tool for high throughput gene-expression studies and discovery of novel biomarker genes. Developed for a large number of organisms, including plants, microarrays are commonly performed for species that have sequenced data, for performing gene expression analysis, miRNA profiling, comparative genomic hybridization (CGH), ChIP-on-chip and SNP analysis. Genomic resources are still very limited for chickpea, a very important food legume crop. Here, we report the design and comprehensive validation of Next Generation Sequencing transcriptome data for chickpea through microarray technology to develop a high-throughput resource for studying the expression of all the transcripts in different biological samples to help functional genomics and breeding programs. This microarray design was developed and validated jointly by Genotypic Technology Private Limited and National Institute of Plant Genome Research. First, we designed 400k probes using reads covering 35k assembled contigs and 100k singletons chickpea transcripts. The 400k chip was hybridized with DNA and RNA samples of chickpea and microarray analysis was carried out. A total of 73,922 probes were found to be specific to chickpea transcripts. Best probes were filtered from the analyzed data and a total of 61,659 probes were selected to develop the final microarray design in 60k gene-expression microarray format. The probes represented 51,444 unique transcripts. The probes were annotated based on their corresponding chickpea transcript and similarity with other plants species. Microarray results were concordant with previous results from the NGS studies. The design of custom oligonucleotide probes for microarrays have varied functional genomic applications and this approach represents a valuable resource for chickpea.
2017-01-07 | GSE78986 | GEO
Project description:Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.
| S-EPMC4267183 | biostudies-literature
Project description:A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.
| S-EPMC4922567 | biostudies-literature
Project description:Design and validation of microarray for chickpea (Cicer arietinum) based on the analysis of transcriptome data
| PRJNA314577 | ENA
Project description:BackgroundChickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea.ResultsWe present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL.ConclusionThe physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.
| S-EPMC2996997 | biostudies-literature
Project description:The total RNA were extracted from pooled tissues of leaves and flowers from several plants of chickpea (Cicer arietinum) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Then small RNAs ranging in 18–30 nucleotides were size fractionated electrophoretically, isolated from the gel, ligated with the 5′ and 3′ RNA adapters. The ligated product was reverse transcribed and subsequently amplified using 10–12 PCR cycles. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to predict microRNAs and phased small interfering RNAs from chickpea. Identification of microRNAs and phased small inferfering RNAs in chickpea (Cicer arietinum) by analyzing small RNA sequencing profiles of leaves and flowers using Illumina GAII.
2015-05-08 | E-GEOD-62216 | biostudies-arrayexpress
Project description:The total RNA were extracted from pooled tissues of leaves and flowers from several plants of chickpea (Cicer arietinum) using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Then small RNAs ranging in 18–30 nucleotides were size fractionated electrophoretically, isolated from the gel, ligated with the 5′ and 3′ RNA adapters. The ligated product was reverse transcribed and subsequently amplified using 10–12 PCR cycles. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to predict microRNAs and phased small interfering RNAs from chickpea.
2015-05-08 | GSE62216 | GEO
Project description:The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers' fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016-2017 and 2018-2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017-2018, 2018-2019, and 2019-2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers.
| S-EPMC8703834 | biostudies-literature