ArticleGenome biology2021
Chromosome-level genome assembly of a regenerable maize inbred line A188.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 83 citations in OpenAlex.
- T-DNA Analyzer: A Long-Read Sequencing Pipeline for Characterizing T-DNA Insertion Sites in Transgenic Crops.International journal of molecular sciences · 2026Article
- Methylome and Transcriptome Analysis Reveals Differences in Callus Development and Plantlet Regeneration Capacity Between TwoPlants (Basel, Switzerland) · 2026Article
- Near-complete genome assembly of a transformation-efficient elite inbred line LH244 and its comparison with B73.Journal of integrative plant biology · 2026Article
- ZmHSCF1 enhances Agrobacterium-mediated transformation frequency in commercial maize inbred lines by promoting embryogenic callus proliferation.Plant communications · 2025Article
- Large DNA and protein language models enhance discovery of deleterious mutations in maize.Genome biology · 2025Article
- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
- Understanding Callus Types in Maize by Genetic Mapping and Transcriptional Profiling.Plants (Basel, Switzerland) · 2025Article
- Enhancing local meiotic crossovers in Arabidopsis and maize through juxtaposition of heterozygous and homozygous regions.Nature plants · 2025Article
- Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.Nature genetics · 2025Article
- Increased maize chromosome number by engineered chromosome fission.Science advances · 2025Article
- Jan and mini-Jan, a model system for potato functional genomics.Plant biotechnology journal · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Centromere drive may propel the evolution of chromosome and genome size in plants.Annals of botany · 2024Article
- Review
- Jan and mini-Jan, a model system for potato functional genomics.bioRxiv : the preprint server for biology · 2024Article
- Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases.NAR genomics and bioinformatics · 2024Article
- Plant pangenomes for crop improvement, biodiversity and evolution.Nature reviews. Genetics · 2024Review
- The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed.The plant genome · 2024Article
- A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics.Molecular horticulture · 2024Article
- Use of remote sensing for linkage mapping and genomic prediction for common rust resistance in maize.Field crops research · 2024Article
Corrections and comments
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Authors and funding
27 authors at 11 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.
resultsHere, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus.
conclusionsThe A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.
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