The findmap.f90 program aligns sequence reads to reference map, calls previous variants, and identifies new variants.
Data from: Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly
Population structure and genetic diversity of 417 USDA sweetpotato (Ipomoea batatas) accessions originating from 8 broad geographical regions (Africa, Australia, Caribbean, Central America, Far East, North America, Pacific Islands, and South America) were determined using single nucleotide polymorphisms (SNPs) identified with a genotyping-by-sequencing (GBS) protocol, GBSpoly, optimized for highly heterozygous and polyploid species.
Data from: Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize
This study supports the notion that genotyping-by-sequencing (GBS) can be tailored to particular aims, and using Zea mays results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. A GBS procedure was established that produces high call rates per marker (>85%) with accuracy exceeding 99.4%.
TIFF and JPEG files for the photographs used in constructing figures and supplemental figures in the manuscript, "ELIGULUM-A regulates lateral branch and leaf development," submitted to Plant Physiology. The images document a mutation that alters most of the structures of the plant and how the ELIGULUM-A gene interacts with different developmental pathways. The Figure Legend files describe the images individually.
As part of our project, “Developing Association Mapping in Polyploid Perennial Biofuel Grasses” (DOE-USDA Plant Feedstock Genomics for Bioenergy Program grant DE-A102-07ER64454)*, two SNP discovery initiatives were carried out. The earlier one (2009) was an approach based on EST sequences. The latest initiative (2011-12) adopted a more powerful approach, based on GBS (Genotyping by Sequencing). We believe that the SNP markers identified in these studies will greatly enhance breeding efforts that target the improvement of key biofuel traits and the development of new switchgrass cultivars.