Dataset Information

MaizeCUBIC: a comprehensive variation database for a maize synthetic population.

ABSTRACT: MaizeCUBIC is a free database that describes genomic variations, gene expression, phenotypes and quantitative trait locus (QTLs) for a maize CUBIC population (24 founders and 1404 inbred offspring). The database not only includes information for over 14M single nucleotide polymorphism (SNPs) and 43K indels previously identified but also contains 660K structure variations (SVs) and 600M novel sequences newly identified in the present study, which represents a comprehensive high-density variant map for a diverse population. Based on these genomic variations, the database would demonstrate the mosaic structure for each progeny, reflecting a high-resolution reshuffle across parental genomes. A total of 23 agronomic traits measured on parents and progeny in five locations, where are representative of the maize main growing regions in China, were also included in the database. To further explore the genotype-phenotype relationships, two different methods of genome-wide association studies (GWAS) were employed for dissecting the genetic architecture of 23 agronomic traits. Additionally, the Basic Local Alignment Search Tool and primer design tools are developed to promote follow-up analysis and experimental verification. All the original data and corresponding analytical results can be accessed through user-friendly online queries and web interface dynamic visualization, as well as downloadable files. These data and tools provide valuable resources on genetic and genomic studies of maize and other crops.

SUBMITTER: Luo J

PROVIDER: S-EPMC7297647 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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MaizeCUBIC: a comprehensive variation database for a maize synthetic population.

Luo Jingyun J Wei Chengcheng C Liu Haijun H Cheng Shikun S Xiao Yingjie Y Wang Xiaqing X Yan Jianbing J Liu Jianxiao J

Database : the journal of biological databases and curation 20200101

MaizeCUBIC is a free database that describes genomic variations, gene expression, phenotypes and quantitative trait locus (QTLs) for a maize CUBIC population (24 founders and 1404 inbred offspring). The database not only includes information for over 14M single nucleotide polymorphism (SNPs) and 43K indels previously identified but also contains 660K structure variations (SVs) and 600M novel sequences newly identified in the present study, which represents a comprehensive high-density variant ma ...[more]

PMID: 32548639

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Project description:BackgroundMicroarray technology has matured over the past fifteen years into a cost-effective solution with established data analysis protocols for global gene expression profiling. The Agilent-016047 maize 44 K microarray was custom-designed from EST sequences, but only reporter sequences with EST accession numbers are publicly available. The following information is lacking: (a) reporter - gene model match, (b) number of reporters per gene model, (c) potential for cross hybridization, (d) sense/antisense orientation of reporters, (e) position of reporter on B73 genome sequence (for eQTL studies), and (f) functional annotations of genes represented by reporters. To address this, we developed a strategy to annotate the Agilent-016047 maize microarray, and built a publicly accessible annotation database.DescriptionGenomic annotation of the 42,034 reporters on the Agilent-016047 maize microarray was based on BLASTN results of the 60-mer reporter sequences and their corresponding ESTs against the maize B73 RefGen v2 "Working Gene Set" (WGS) predicted transcripts and the genome sequence. The agreement between the EST, WGS transcript and gDNA BLASTN results were used to assign the reporters into six genomic annotation groups. These annotation groups were: (i) "annotation by sense gene model" (23,668 reporters), (ii) "annotation by antisense gene model" (4,330); (iii) "annotation by gDNA" without a WGS transcript hit (1,549); (iv) "annotation by EST", in which case the EST from which the reporter was designed, but not the reporter itself, has a WGS transcript hit (3,390); (v) "ambiguous annotation" (2,608); and (vi) "inconclusive annotation" (6,489). Functional annotations of reporters were obtained by BLASTX and Blast2GO analysis of corresponding WGS transcripts against GenBank.The annotations are available in the Maize Microarray Annotation Database http://MaizeArrayAnnot.bi.up.ac.za/, as well as through a GBrowse annotation file that can be uploaded to the MaizeGDB genome browser as a custom track.The database was used to re-annotate lists of differentially expressed genes reported in case studies of published work using the Agilent-016047 maize microarray. Up to 85% of reporters in each list could be annotated with confidence by a single gene model, however up to 10% of reporters had ambiguous annotations. Overall, more than 57% of reporters gave a measurable signal in tissues as diverse as anthers and leaves.ConclusionsThe Maize Microarray Annotation Database will assist users of the Agilent-016047 maize microarray in (i) refining gene lists for global expression analysis, and (ii) confirming the annotation of candidate genes before functional studies.

Dataset Information

MaizeCUBIC: a comprehensive variation database for a maize synthetic population.

Publications

MaizeCUBIC: a comprehensive variation database for a maize synthetic population.

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