Candidate gene identification of existing or induced mutations with pipelines applicable to large genomes

MaizeDek37Encodes a P-type PPR Protein That Affectscis-Splicing of Mitochondrialnad2Intron 1 and Seed Development

(2018) Dawei Dai et al.   GENETICS

MaizeDek37Encodes a P-type PPR Protein That Affectscis-Splicing of Mitochondrialnad2Intron 1 and Seed Development

(2018) Dawei Dai et al.   GENETICS

EMPTY PERICARP11 serves as a factor for splicing of mitochondrial nad1 intron and is required to ensure proper seed development in maize

(2017) Xuemei Ren et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dek35 Encodes a PPR Protein that Affects cis -Splicing of Mitochondrial nad4 Intron 1 and Seed Development in Maize

(2017) Xinze Chen et al.   Molecular Plant

The Mitochondrion-Targeted PENTATRICOPEPTIDE REPEAT78 Protein Is Required for nad5 Mature mRNA Stability and Seed Development in Maize

(2017) Ya-Feng Zhang et al.   Molecular Plant

A Specific Gibberellin 20-Oxidase Dictates the Flowering-Runnering Decision in Diploid Strawberry

(2017) Tracey Tenreira et al.   PLANT CELL

Emp10 encodes a mitochondrial PPR protein that affects the cis -splicing of nad2 intron 1 and seed development in maize

(2017) Manjun Cai et al.   PLANT JOURNAL

A SIMPLE Pipeline for Mapping Point Mutations

(2017) Guy Wachsman et al.   PLANT PHYSIOLOGY

Construction of the third-generation Zea mays haplotype map

(2017) Robert Bukowski et al.   GigaScience

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

(2017) Patrick P Edger et al.   GigaScience

Mitochondrial Function and Maize Kernel Development Requires Dek2, a Pentatricopeptide Repeat Protein Involved in nad1 mRNA Splicing

(2016) Weiwei Qi et al.   GENETICS

EMPTY PERICARP16 is required for mitochondrialnad2intron 4cis-splicing, complex I assembly and seed development in maize

(2016) Zhihui Xiu et al.   PLANT JOURNAL

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

(2016) Jiaqiang Dong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize

(2016) Shangang Jia et al.   G3-Genes Genomes Genetics

Mitochondrial Function and Maize Kernel Development Requires Dek2, a Pentatricopeptide Repeat Protein Involved in nad1 mRNA Splicing

(2016) Weiwei Qi et al.   GENETICS

Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

(2015) Jinliang Yang et al.   PLANT JOURNAL

Positional Cloning in Maize (Zea mays subsp. mays, Poaceae)

(2015) Andrea Gallavotti et al.   Applications in Plant Sciences

Pentatricopeptide Repeat Proteins in Plants

(2014) Alice Barkan et al.   Annual Review of Plant Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Maize glossy13 Gene, Cloned via BSR-Seq and Seq-Walking Encodes a Putative ABC Transporter Required for the Normal Accumulation of Epicuticular Waxes

(2013) Li Li et al.   PLoS One

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Mutation mapping and identification by whole-genome sequencing

(2012) I. Leshchiner et al.   GENOME RESEARCH

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Identification and Characterization of the Missing Pyrimidine Reductase in the Plant Riboflavin Biosynthesis Pathway

(2012) G. Hasnain et al.   PLANT PHYSIOLOGY

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE