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

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.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-016-0539-y) contains supplementary material, which is available to authorized users.

The development and testing in the field of genetically modified -so called- orphan crops like cassava in tropical countries is still in its infancy, despite the fact that cassava is not only used for food and feed but is also an important industrial crop. As traditional breeding of cassava is difficult (allodiploid, vegetatively propagated, outbreeding species) it is an ideal crop for improvement through genetic modification. We here report on the results of production and field testing of genetically modified low-amylose transformants of commercial cassava variety Adira4 in Indonesia. Twenty four transformants were produced and selected in the Netherlands based on phenotypic and molecular analyses. Nodal cuttings of these plants were sent to Indonesia where they were grown under biosafety conditions. After two screenhouse tests 15 transformants remained for a field trial. The tuberous root yield of 10 transformants was not significantly different from the control. Starch from transformants in which amylose was very low or absent showed all physical and rheological properties as expected from amylose-free cassava starch. The improved functionality of the starch was shown for an adipate acetate starch which was made into a tomato sauce. This is the first account of a field trial with transgenic cassava which shows that by using genetic modification it is possible to obtain low-amylose cassava plants with commercial potential with good root yield and starch quality.Electronic supplementary materialThe online version of this article (doi:10.1007/s11248-011-9507-9) contains supplementary material, which is available to authorized users.

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 materialThe online version of this article (doi:10.1007/s11032-011-9579-5) contains supplementary material, which is available to authorized users.

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.

The Netherlands’ field genebank collection of European wild apple (Malus sylvestris), consisting of 115 accessions, was studied in order to determine whether duplicates and mistakes had been introduced, and to develop a strategy to optimize the planting design of the collection as a seed orchard. We used the apple 20K Infinium single nucleotide polymorphism (SNP) array, developed in M. domestica, for the first time for genotyping in M. sylvestris. We could readily detect the clonal copies and unexpected duplicates. Thirty-two M. sylvestris accessions (29%) showed a close genetic relationship (parent-child, full-sib, or half-sib) to another accession, which reflects the small effective population size of the in situ populations. Traces of introgression from M. domestica were only found in 7 individuals. This indicates that pollination preferentially took place among the M. sylvestris trees. We conclude that the collection can be considered as mainly pure M. sylvestris accessions. The results imply that it should be managed as one unit when used for seed production. A bias in allele frequencies in the seeds may be prevented by not harvesting all accessions with a close genetic relationship to the others in the seed orchard. We discuss the value of using the SNP array to elaborate the M. sylvestris genetic resources more in depth, including for phasing the markers in a subset of the accessions, as a first step towards genetic resources management at the level of haplotypes.

Twenty carnation genotypes of diverse origin were planted in September and were kept under an 8 h day and a light intensity of 15 W/m 2 visible radiation in a phytotron from 30 November to 24 February . Long photoperiods (24 h ; LD) were applied in December-January for 25 days . In addition to flowering dates of individual shoots, records were kept on shoot development (number of visible leaf pairs) on four dates : (1) six weeks after pinching, (2) at the beginning of the LD treatment in December, (3) when plants were transferred from the phytotron to the glasshouse in February and (4) at the time of flowering of individual shoots . The genetic variation in number of visible leaf pairs on each of these dates, in relation to shoot position and rate of unfolding of leaf pairs, was analysed .On the basis of these analyses, the between and within-genotype variation in time of flowering, yield distribution and LD response could be, at least partly, related to variation in the above-mentioned parameters . It was established that relevant genetic variation exists in (1) the initial development of the axillary bud from which a primary shoot is produced after pinching ; (2) the rate of leaf unfolding ; (3) the minimum number of leaf pairs required for flower initiation and (4) the within-plant variation in the above three characters in relation to shoot position .

Improvement of dry matter production in the vegetative phase is a breeding objective in many crops, especially where whole plants or parts of plants in the vegetative phase constitute the commercial product . Dry matter production is a complex process and plant dry weight, as measured at a given date, is a complex character, of which initial weight of planting material and mean relative growth rate over the period of growth are the major components .The primary objective of the present paper is to demonstrate how a method of component analysis proposed by Spamaaij and Bos can be used to facilitate breeding for a high rate of vegetative growth . The procedure is illustrated by data from a study of variation in forcing ability among 13 carnation cultivars . It involves a detailed analysis of mean relative growth rate over the period of vegetative growth, including components derived from observations on net rate of photosynthesis and dark respiration .It is shown how component analysis can be used (a) to quantify the relative contribution of initial plant weight and of mean relative growth rate and its components to the genetic variation in plant dry weight, thus allowing a judicious choice of selection criteria for breeding parents, and (b) to predict mean plant dry weight of F, hybrids obtained by crossing these parent genotypes, thus facilitating the choice of crosses to be made .