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Zea mays subsp. parviglumis

ABSTRACT: teosinte cultivar Ames 21789 response to weeds

PROVIDER: PRJNA543185 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9067010_1.fastq.gz	Fastqsanger.gz
	SRR9067010_2.fastq.gz	Fastqsanger.gz
	SRR9067011_1.fastq.gz	Fastqsanger.gz
	SRR9067011_2.fastq.gz	Fastqsanger.gz
	SRR9067002_1.fastq.gz	Fastqsanger.gz

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Zea mays subsp. parviglumis

Project description:teosinte cultivar Ames 21812 response to weeds

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Zea mays subsp. parviglumis strain:Ames 21789

Project description:Zea mays subsp. parviglumis strain:Ames 21789 Raw sequence reads

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Zea mays subsp. parviglumis strain:Ames 21812

Project description:Zea mays subsp. parviglumis strain:Ames 21812 Raw sequence reads

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Zea mays Transcriptome or Gene expression

Project description:The prolamin-box binding factor-1 (pbf1) gene encodes a transcription factor that controls the expression of seed storage protein (zein) genes in maize. Prior studies show that pbf1 underwent selection during maize domestication, although how it affected trait change during domestication is unknown. To assay how pbf1 affects phenotypic differences between maize and teosinte, we compared isogenic lines (NILs) that differ for a maize vs.and teosinte alleles of pbf1. Kernel weight for the teosinte NIL (162 mg) is slightly and significantly greater than that for the maize NIL (156 mg). RNAseq data for developing kernels show that the teosinte allele of pbf1 is expressed at about twice the level of the maize allele. However, RNA and protein assays showed no difference in zein profiles between the two NILs. The lower expression for the maize pbf1 allele suggests that selection may have favored this change, however, how reduced pbf1 expression alters phenotype remains unknown. One possibility is that pbf1 regulates genes other than zeins and thereby a domestication trait. The observed drop in seed weight associated with the maize allele of pbf1 is counterintuitive, but could represent a negative pleiotropic effect of selection on some other aspect of kernel composition.

2014-10-10 | E-MTAB-4208 | biostudies-arrayexpress

Zea mays

Project description:response of corn to weeds

| PRJNA688473 | ENA

Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis).

Project description:Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evolutionary dynamics of the duplicated defense genes hm1 and hm2 in maize and its wild ancestor Zea mays ssp. parviglumis. Both genes have been shown to confer resistance to the fungal pathogen Cochliobolus carbonum race 1, but the effectiveness of resistance differs between loci. The genes also display different population histories. The hm1 locus has the highest nucleotide diversity of any gene yet sampled in the wild ancestor of maize, and it contains a large number of indel polymorphisms. There is no evidence, however, that high diversity in hm1 is a product of nonneutral evolution. In contrast, hm2 has very low nucleotide diversity in the wild ancestor of maize. The distribution of hm2 polymorphic sites is consistent with nonneutral evolution, as indicated by Tajima's D and other neutrality tests. In addition, one hm2 haplotype is more frequent than expected under the equilibrium neutral model, suggesting hitchhiking selection. Both defense genes retain >80% of the level of genetic variation in maize relative to the wild ancestor, and this level is similar to other maize genes that were not subject to artificial selection during domestication.

| S-EPMC1462307 | biostudies-other

Zea mays subsp. parviglumis cultivar:Ames21814

Project description:Zea mays subsp. parviglumis cultivar:Ames21814 Genome

| PRJNA822523 | ENA

Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis).

Project description:Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genomewide departures from the standard neutral equilibrium (NE) model. Here we investigate the degree to which population structure may account for the excess of rare polymorphisms frequently observed in species-wide samples. On the basis of sequence data from five nuclear and two chloroplast loci, we found significant population genetic structure among seven subpopulations from two geographic regions. Comparisons of estimates of population genetic parameters from species-wide samples and subpopulation-specific samples showed that population genetic subdivision influenced observed patterns of nucleotide polymorphism. In particular, Tajima's D was significantly higher (closer to zero) in subpopulation-specific samples relative to species-wide samples, and therefore more closely corresponded to NE expectations. In spite of these overall patterns, the extent to which levels and patterns of polymorphism within subpopulations differed from species-wide samples and NE expectations depended strongly on the geographic region (Jalisco vs. Balsas) from which subpopulations were sampled. This may be due to the demographic history of subpopulations in those regions. Overall, these results suggest that explicitly accounting for population structure may be important for studies examining the genetic basis of ecologically and agronomically important traits as well as for identifying loci that have been the targets of selection.

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Zea mays subsp. parviglumis cultivar:TIL01

Project description:Zea mays subsp. parviglumis cultivar:TIL01 Genome sequencing and assembly

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Zea mays Transcriptome or Gene expression

Project description:Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement.

2015-01-28 | E-MTAB-4373 | biostudies-arrayexpress

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