ABSTRACT
In the study of large outbred pedigrees with many founders, individual bi-allelic markers, such as SNP markers, carry little information. After phasing the marker genotypes, multi-allelic loci consisting of groups of closely linked markers can be identified, which are called "haploblocks". Here, we describe PediHaplotyper, an R package capable of assigning consistent alleles to such haploblocks, allowing for missing and incorrect SNP data. These haploblock genotypes are much easier to interpret by the human investigator than the original SNP data and also allow more efficient QTL analyses that require less memory and computation time.
ABSTRACT
UNLABELLED: ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. AVAILABILITY AND IMPLEMENTATION: The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. CONTACT: eric.vandeweg@wur.nl.
Subject(s)
Genotyping Techniques/methods , Polymorphism, Single Nucleotide , Software , Alleles , Animals , HumansABSTRACT
In order to obtain a tuberous root-specific promoter to be used in the transformation of cassava, a 1,728 bp sequence containing the cassava granule-bound starch synthase (GBSSI) promoter was isolated. The sequence proved to contain light- and sugar-responsive cis elements. Part of this sequence (1,167 bp) was cloned into binary vectors to drive expression of the firefly luciferase gene. Cassava cultivar Adira 4 was transformed with this construct or a control construct in which the luciferase gene was cloned behind the 35S promoter. Luciferase activity was measured in leaves, stems, roots and tuberous roots. As expected, the 35S promoter induced luciferase activity in all organs at similar levels, whereas the GBSSI promoter showed very low expression in leaves, stems and roots, but very high expression in tuberous roots. These results show that the cassava GBSSI promoter is an excellent candidate to achieve tuberous root-specific expression in cassava.
Subject(s)
Manihot/enzymology , Promoter Regions, Genetic/genetics , Starch Synthase/genetics , Base Sequence , Cloning, Molecular , Gene Expression Regulation, Plant , Luciferases/genetics , Luciferases/metabolism , Manihot/genetics , Manihot/growth & development , Meristem/enzymology , Meristem/genetics , Meristem/growth & development , Molecular Sequence Data , Organ Specificity , Plant Leaves/enzymology , Plant Leaves/genetics , Plant Leaves/growth & development , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Roots/enzymology , Plant Roots/genetics , Plant Roots/growth & development , Plant Stems/enzymology , Plant Stems/genetics , Plant Stems/growth & development , Plant Tubers/enzymology , Plant Tubers/genetics , Plant Tubers/growth & development , Plants, Genetically Modified , Sequence Analysis, DNA , Starch Synthase/metabolismABSTRACT
Diversity Arrays Technology (DArT) provides a high-throughput whole-genome genotyping platform for the detection and scoring of hundreds of polymorphic loci without any need for prior sequence information. The work presented here details the development and performance of a DArT genotyping array for apple. This is the first paper on DArT in horticultural trees. Genetic mapping of DArT markers in two mapping populations and their integration with other marker types showed that DArT is a powerful high-throughput method for obtaining accurate and reproducible marker data, despite the low cost per data point. This method appears to be suitable for aligning the genetic maps of different segregating populations. The standard complexity reduction method, based on the methylation-sensitive PstI restriction enzyme, resulted in a high frequency of markers, although there was 52-54% redundancy due to the repeated sampling of highly similar sequences. Sequencing of the marker clones showed that they are significantly enriched for low-copy, genic regions. The genome coverage using the standard method was 55-76%. For improved genome coverage, an alternative complexity reduction method was examined, which resulted in less redundancy and additional segregating markers. The DArT markers proved to be of high quality and were very suitable for genetic mapping at low cost for the apple, providing moderate genome coverage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.
