Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize

Hu, Ying; Ren, Jie; Peng, Zhao; Umana, Arnoldo A.; Le, Ha; Danilova, Tatiana; Fu, Junjie; Wang, Haiyan; Robertson, Alison E.; Hulbert, Scot H.; White, Frank F.; Liu, Sanzhen

doi:10.3389/fpls.2018.00110

Cited by 24 publications

(25 citation statements)

References 69 publications

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“…4 a). One NLR gene cluster on chromosome 10 has 16 genes homologous to the rp1 gene that confers resistance to common rust [ 27 ] and was associated with Goss’s wilt resistance [ 28 ] (Fig. 4 b).…”

Section: Resultsmentioning

confidence: 99%

Chromosome-level genome assembly of a regenerable maize inbred line A188

Lin

Zheng

et al. 2021

Genome Biol

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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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Section: Resultsmentioning

confidence: 99%

Chromosome-level genome assembly of a regenerable maize inbred line A188

Lin

Zheng

et al. 2021

Genome Biol

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“…4a). One NLR gene cluster on chromosome 10 has 16 genes homologous to the rp1 gene that confers resistance to common rust 22 and was associated with Goss's wilt resistance 23 (Fig. 4b).…”

Section: Gene Annotationmentioning

confidence: 99%

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Lin

Zheng

et al. 2020

Preprint

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The highly embryogenic and transformable maize inbred line A188 is an attractive model for analyzing maize gene function. Here we constructed a chromosome-level genome assembly of A188 using long reads and optical maps. Genome comparison of A188 with the reference line B73 identified pervasive structural variation, including a 1.8 Mb duplication on the Gametophyte factor1 locus for unilateral cross-incompatibility and six inversions of 0.7 Mb or greater. Increased copy number of the gene, carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression together with low expression of yellow endosperm 1 (y1) condition reduced carotenoid accumulation, which accounts for the white seed phenotype of A188 that contrasts with the yellow seed of B73 that has high expression of y1 and low expression of the single-copy ccd1. Further, transcriptome and epigenome analyses with the A188 reference genome revealed enhanced expression of defense pathways and altered DNA methylation patterns of embryonic callus.

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“…Subsequent studies identified regions, and even genes, that confer resistance to the three most significant fungal foliar diseases – southern corn leaf blight (SCLB), northern corn leaf blight (NCLB), and gray leaf spot (GLS) ( Lopez-Zuniga et al 2019 ; Zwonitzer et al 2010 ; Belcher et al 2012 ; Yang et al 2017b ). Relatively few regions have been identified that confer resistance to both a fungal and a bacterial pathogen in maize ( Chung et al 2010 ; Chung et al 2011 ; Qiu et al 2020 ; Jamann et al 2014 ; Jamann et al 2016 ; Hu et al 2018 ). In this study, we focused on two bacterial diseases bacterial leaf streak (BLS) and Goss’s bacterial wilt and blight (GW), as well as three fungal diseases: SCLB, NCLB, and GLS.…”

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confidence: 99%

Identification of Loci That Confer Resistance to Bacterial and Fungal Diseases of Maize

Qiu

Cooper

Kaiser

et al. 2020

G3 Genes|Genomes|Genetics

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Crops are hosts to numerous plant pathogenic microorganisms. Maize has several major disease issues; thus, breeding multiple disease resistant (MDR) varieties is critical. While the genetic basis of resistance to multiple fungal pathogens has been studied in maize, less is known about the relationship between fungal and bacterial resistance. In this study, we evaluated a disease resistance introgression line (DRIL) population for the foliar disease Goss's bacterial wilt and blight (GW) and conducted quantitative trait locus (QTL) mapping. We identified a total of ten QTL across multiple environments. We then combined our GW data with data on four additional foliar diseases (northern corn leaf blight, southern corn leaf blight, gray leaf spot, and bacterial leaf streak) and conducted multivariate analysis to identify regions conferring resistance to multiple diseases. We identified 20 chromosomal bins with putative multiple disease effects. We examined the five chromosomal regions (bin 1.05, 3.04, 4.06, 8.03, and 9.02) with the strongest statistical support. By examining how each haplotype effected each disease, we identified several regions associated with increased resistance to multiple diseases and three regions associated with opposite effects for bacterial and fungal diseases. In summary, we identified several promising candidate regions for multiple disease resistance in maize and specific DRILs to expedite interrogation.

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Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize

Cited by 24 publications

References 69 publications

Chromosome-level genome assembly of a regenerable maize inbred line A188

Chromosome-level genome assembly of a regenerable maize inbred line A188

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

Identification of Loci That Confer Resistance to Bacterial and Fungal Diseases of Maize

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