Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24097884.fastq.gz | Fastqsanger.gz | |||
| SRR25232019.fastq.gz | Fastqsanger.gz | |||
| SRR25232020.fastq.gz | Fastqsanger.gz | |||
| SRR25232021.fastq.gz | Fastqsanger.gz | |||
| SRR25232022.fastq.gz | Fastqsanger.gz |
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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
Project description:In this work, we performed high throughput sequencing of small RNA libraries in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) to investigate the response mediated by miRNAs in these plants under control conditions, submergence, drought and alternated drought-submergence or submergence-drought stress. After Illumina sequencing of 8 small RNA libraries, we obtained from 16,139,354 to 46,522,229 raw reads across the libraries. Bioinformatic analysis identified 88 maize miRNAs and 76 miRNAs from other plants differentially expressed in maize and/or in teosinte in response to at least one of the treatments, and revealed that a larger set of miRNAs were regulated in maize than in teosinte in response to submergence and drought stress.
2020-10-23 | GSE155050 | GEO
Project description:Meiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Cryptic drive is thought to be pervasive and can be unleashed following hybridization with a naïve genome, resulting in sterility and hybrid incompatibility. Using single molecule and single pollen genome sequencing, we describe an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Zea mays ssp. mexicana), that depends on RNA interference (RNAi) in the male germline. Multiple hairpin-derived small RNA from mexicana target a novel domestication gene, Teosinte Drive Responder, that is required for pollen fertility and has undergone selection for immunity to RNAi. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas. A survey of maize landraces and sympatric populations of teosinte mexicana reveals allelic bias at genes required for RNAi on at least 4 chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive likely played a major role in maize domestication, and offers an explanation for the widespread abundance of hairpin-encoded and other endogenous small RNA in the germlines of plants and animals.
2023-07-26 | GSE234924 | GEO