Ontology highlight
ABSTRACT:
PROVIDER: PRJNA795689 | ENA |
REPOSITORIES: ENA
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Project description:Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. This procedure, however, requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples using the same RNA-Seq data. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. We previously generated a large collection of glossy mutants using the Mu transposon system. By subjected a reference allele to BSR-Seq, we were able to map the gl3 locus to a ~2.3Mb interval that is consistent with the results of prior mapping experiments. The single gene located in the 2.3Mb mapping interval that contained a Mu insertion and whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independently Mu transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.
2012-12-03 | E-MTAB-4234 | biostudies-arrayexpress
Project description:Small peptides (sPeptides), a class of biological molecules of less than 100 amio acids encoded by small open reading frames (sORFs), play important roles in multiple biological process. Here, we conducted a comprehensive study using mRNA-seq, Ribo-seq, and Mass Spectrometry (MS) on six tissues (each with at least two replicates) of maize, set up a bioinformatic pipeline, and performed a genome-wide scan of sORFs and sPeptides in maize. Our study sets up a guildline for the genome-wide scan of sORFs and sPeptides in plants by integrating Ribo-seq, and MS data, provides a more comprehensive resource of functional sPeptides in maize, and sheds light on the complex biological system of plants in a new perspective.
2021-05-30 | PXD025997 | Pride