ZmMPK6 and ethylene signalling negatively regulate the accumulation of anti‐insect metabolites DIMBOA and DIMBOA‐Glc in maize inbred line A188

Abstract Background The 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. Results Here, 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. Conclusions The 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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Genetic analysis of two new quantitative trait loci for ear weight in maize inbred line Huangzao4

Genetics and Molecular Research ◽

10.4238/vol9-4gmr858 ◽

2010 ◽

Vol 9 (4) ◽

pp. 2140-2147 ◽

Cited By ~ 3

Author(s):

X.-H. Liu ◽

Z.-P. Zheng ◽

Z.-B. Tan ◽

Z. Li ◽

C. He

Keyword(s):

Quantitative Trait Loci ◽

Genetic Analysis ◽

Inbred Line ◽

Quantitative Trait ◽

Maize Inbred Line ◽

Trait Loci

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Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

10.1101/2021.03.15.435372 ◽

2021 ◽

Author(s):

Fei Ge ◽

Jingtao Qu ◽

Peng Liu ◽

Lang Pan ◽

Chaoying Zou ◽

...

Keyword(s):

Single Molecule ◽

Inbred Line ◽

Genome Mapping ◽

Maize Inbred Line ◽

Sequencing Data ◽

Structural Variations ◽

Single Molecule Sequencing ◽

Maize Genetic ◽

Induction Ratio ◽

Phenotypic Variations

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ~30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.

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The race goes on: A fall armyworm-resistant maize inbred line influences insect oral secretion elicitation activity and nullifies herbivore suppression of plant defense

10.1101/2021.05.17.444416 ◽

2021 ◽

Author(s):

Saif ul Malook ◽

Xiao-Feng Liu ◽

Wende Liu ◽

Jinfeng Qi ◽

Shaoqun Zhou

Keyword(s):

Plant Defense ◽

Host Plant ◽

Inbred Line ◽

Defense Mechanisms ◽

Molecular Mechanisms ◽

Fall Armyworm ◽

Defense Responses ◽

Feeding Preference ◽

Maize Inbred Line ◽

Oral Secretion

Fall armyworm (Spodoptera frugiperda) is an invasive lepidopteran pest with strong feeding preference towards maize (Zea mays). Its success on maize is facilitated by a suite of specialized detoxification and manipulation mechanisms that curtail host plant defense responses. In this study, we identified a Chinese maize inbred line Xi502 that was able to mount effective defense in response to fall armyworm attack. Comparative transcriptomics analyses, phytohormonal measurements, and targeted benzoxazinoid quantification consistently demonstrate significant inducible defense responses in Xi502, but not in the susceptible reference inbred line B73. In 24 hours, fall armyworm larvae feeding on B73 showed accelerated maturation-oriented transcriptomic responses and more changes in detoxification gene expression compared to their Xi502-fed sibling. Interestingly, oral secretions collected from larvae fed on B73 and Xi502 leaves demonstrated distinct elicitation activity when applied on either host genotypes, suggesting that variation in both insect oral secretion composition and host plant alleles could influence plant defense response. These results revealed host plant adaptation towards counter-defense mechanisms in a specialist insect herbivore, adding yet another layer to the evolutionary arms race between maize and fall armyworm. This could facilitate future investigation into the molecular mechanisms in this globally important crop-pest interaction system.

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