Genome-wide association analysis of stalk biomass and anatomical traits in maize

Mazaheri, Mona; Heckwolf, Marlies; Vaillancourt, Brieanne; Gage, Joseph L.; Burdo, Brett; Heckwolf, Sven; Barry, Kerrie; Lipzen, Anna; Ribeiro, Cauê; Kono, Thomas J. Y.; Kaeppler, Heidi F.; Spalding, Edgar P.; Hirsch, Candice N.; Buell, C. Robin; León, Natalia de; Kaeppler, Shawn M.

doi:10.1186/s12870-019-1653-x

Cited by 103 publications

(167 citation statements)

References 111 publications

(125 reference statements)

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“…On a chromosomal basis, diversity statistics, including pairwise divergence (p) (Nei & Li, ), Watterson estimator (Watterson, ), and Tajima's D (Tajima, ) were calculated with Tassel 5.0 (Bradbury et al., ) for the WiDiv‐942 (Mazaheri et al., ), ex‐PVP panel, Iodent, and B73 subgroups, with 942, 337, 62, and 66 inbreds, respectively. Pairwise divergence (p) measures the average number of different variants at polymorphic SNPs.…”

Section: Methodsmentioning

confidence: 99%

“…The 329 ex-PVP and eight public inbreds analyzed in this study are a subset of the Wisconsin Diversity Panel (WiDiv-942) containing 942 diverse maize inbreds (Mazaheri et al, 2019). The genotype matrix used in this study consisted of 899,784 biallelic SNPs; the details of the SNPs and methods are described in Mazaheri et al (2019).…”

Section: Germplasmmentioning

confidence: 99%

“…Allele frequency was calculated for the subgroup of ex-PVP inbreds in their corresponding admixture heterotic subgroup across all 899,784 SNPs. To assess allelic variability among B14, B37, B73, Oh43, Iodent, Iodent-Lancaster, Lancaster, and Flint heterotic subgroups, each group was compared with the diverse WiDiv-942 (Mazaheri et al, 2019). Major allele frequency was calculated across the 899,784 SNPs for the inbreds in each of the eight heterotic subgroups.…”

Section: Measures Of Allelic Diversity Among Ex-pvp Inbredsmentioning

confidence: 99%

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Diversity and heterotic patterns in North American proprietary dent maize germplasm

et al. 2020

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Publicly available maize (Zea mays L.) inbred lines with expired Plant Variety Protection certificates (ex‐PVP) constitute the elite germplasm used in hybrids grown by North American farmers during the past half century. A set of 329 ex‐PVP inbreds and eight public reference inbreds was evaluated for genetic diversity using molecular marker and pedigree‐based relationships. The majority of inbreds originated from Dekalb Genetics Corporation, Holden's Foundation Seed, Pioneer Hi‐Bred International, and Syngenta via Novartis and Northrup King. Flowering ranged from 968–1806 growing degree days to anthesis, supporting that these inbreds represent adaptation across the range of North American production environments. Admixture analysis supported eight subgroups (B14, B37, B73, Oh43, Iodent, Iodent‐Lancaster, Lancaster, and Flint), reflecting heterotic patterns and company of origin. Five diallel‐cross experiments identified primary yield heterotic patterns within early‐, intermediate‐, and late‐maturity groups. Parental pedigree information was compiled for 2392 Plant Variety Protection and/or utility patented inbreds through 2017, allowing for multigenerational analysis of progenitors and the eight heterotic subgroups across current proprietary breeding programs. Key progenitors were identified for recently merged companies, Bayer Crop Science and Corteva Agriscience. The results of this study strengthen the value of the ex‐PVP inbreds as a source of elite and relevant germplasm for breeders and researchers to exploit. This study provides information that will be logistically useful to researchers who use ex‐PVP inbreds and adds to our understanding of heterotic grouping within North American proprietary germplasm.

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Section: Methodsmentioning

confidence: 99%

Section: Germplasmmentioning

confidence: 99%

Section: Measures Of Allelic Diversity Among Ex-pvp Inbredsmentioning

confidence: 99%

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Diversity and heterotic patterns in North American proprietary dent maize germplasm

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“…Based on their location in the tree and known pedigree information, the inbred line Mo8W was removed from the SNP and fragments per kb of exon model per million mapped reads (FPKM) matrix files. An additional 16 inbred lines were also removed from the SNP and FPKM files, resulting in a final set of 942 inbreds, referred to as the WiDiv‐942 (Mazaheri et al, 2019), which were analyzed in this study.…”

Section: Methodsmentioning

confidence: 99%

Multiple Maize Reference Genomes Impact the Identification of Variants by Genome‐Wide Association Study in a Diverse Inbred Panel

Gage

Vaillancourt²,

Hamilton³

et al. 2019

The Plant Genome

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Core Ideas We present the draft de novo genome assembly of the ‘Oh43’‐type maize inbred ‘PHJ89’. Expression and single nucleotide polymorphism data were generated separately from three different references. Genome‐wide association studies’ candidate gene predictions vary depending on the reference used. Use of a single reference genome for genome‐wide association studies (GWAS) limits the gene space represented to that of a single accession. This limitation can complicate identification and characterization of genes located within presence–absence variations (PAVs). In this study, we present the draft de novo genome assembly of ‘PHJ89’, an ‘Oh43’‐type inbred line of maize (Zea mays L.). From three separate reference genome assemblies (‘B73’, ‘PH207’, and PHJ89) that represent the predominant germplasm groups of maize, we generated three separate whole‐seedling gene expression profiles and single nucleotide polymorphism (SNP) matrices from a panel of 942 diverse inbred lines. We identified 34,447 (B73), 39,672 (PH207), and 37,436 (PHJ89) transcripts that are not present in the respective reference genome assemblies. Genome‐wide association studies were conducted in the 942 inbred panel with both the SNP and expression data values to map Sugarcane mosaic virus (SCMV) resistance. Highlighting the impact of alternative reference genomes in gene discovery, the GWAS results for SCMV resistance with expression values as a surrogate measure of PAV resulted in robust detection of the physical location of a known resistance gene when the B73 reference that contains the gene was used, but not the PH207 reference. This study provides the valuable resource of the Oh43‐type PHJ89 genome assembly as well as SNP and expression data for 942 individuals generated from three different reference genomes.

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“…SNP genotype calls for 29 of the genotypes with resequencing data were obtained from (Mazaheri et al, 2019). For the five inbreds (DKFAPW, H99, NKS8326, W64A, Ny821) without re-sequencing data, SNPs were called by pooling all RNA-Seq reads from the corresponding inbred and mapping to the reference genome as previously described for the resequencing data (Mazaheri et al, 2019).…”

Section: Characterization Of Allele Expression Patterns In the Hybridsmentioning

confidence: 99%

Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids

Zhou

Coletta

et al. 2019

Preprint

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Maize exhibits tremendous gene expression variation between different lines.Complementation of diverse gene expression patterns in hybrids could play an important role in the manifestation of heterosis. In this study, we used transcriptome data of five different tissues from 33 maize inbreds and 89 hybrids (430 samples in total)to survey the global gene expression landscape of F 1 -hybrids relative to their inbred parents. Analysis of this data set revealed that single parent expression (SPE), which is defined as gene expression in only one of the two parents, while commonly observed, is highly genotype-and tissue-specific. Genes that have SPE in at least one pair of inbreds also tend to be tissue-specific. Genes with SPE caused by genomic presence/absence variation (PAV SPE) are much more frequently expressed in hybrids than genes that are present in the genome of both inbreds, but expressed in only a single-parent (non-PAV SPE) (74.7% vs. 59.7%). For non-PAV SPE genes, allele specific expression was used to investigate whether parental alleles not expressed in the inbred line ("silent allele") can be actively transcribed in the hybrid. We found that expression of the silent allele in the hybrid is relatively rare (~6.3% of non-PAV SPE genes), but is observed in almost all hybrids and tissues. Non-PAV SPE genes with expression of the silent allele in the hybrid are more likely to exhibit above high-parent expression level in the hybrid than those that do not express the silent allele. Finally, both PAV SPE and non-PAV SPE genes are highly enriched for being classified as non-syntenic, but depleted for curated genes with experimentally determined functions. This study provides a more comprehensive understanding of the potential role of non-PAV SPE and PAV SPE genes in heterosis.

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Genome-wide association analysis of stalk biomass and anatomical traits in maize

Cited by 103 publications

References 111 publications

Diversity and heterotic patterns in North American proprietary dent maize germplasm

Diversity and heterotic patterns in North American proprietary dent maize germplasm

Multiple Maize Reference Genomes Impact the Identification of Variants by Genome‐Wide Association Study in a Diverse Inbred Panel

Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids

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