Johannes Jansen

Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh).

High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ∼3.7K validated SNPs from the IRSC 8K array. The array has already been used in other studies where ∼15.8K SNP markers were mapped with an average of ∼6.8K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.

Bayesian analysis of complex traits in pedigreed plant populations

A Bayesian approach to analyze complex traits is presented that can help plant eneticists and breeders in exploiting the marker and phenotypic data on pedigreed populations as available from ongoing breeding programs. The statistical model for the quantitative trait may include non-genetic and genetic components. The latter component can be divided into QTL on known marker linkage groups, major genes and a polygenic component. The full probability model, prior assumptions on model variables are presented and criterion for model selection and posterior inferences are given. Simulated data on a known pedigreed population structure of the EU project HiDRAS was used to illustrate the use of the Bayesian approach to analyze complex traits. It was shown that estimates for QTL parameters were more accurate when non-genetic factors were included in the model and when a polygenic component was included when not all linkage groups were analyzed simultaneously. The Bayesian approach has been implemented into the software package FlexQTL and allows plant breeders explore their pedigreed populations for segregating QTL alleles that are relevant in their breeding program.

Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array.

BackgroundA whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNP-based linkage map of an apple rootstock progeny.ResultsOf the 7,867 Malus SNP markers on the array, 1,823 (23.2%) were heterozygous in one of the two parents of the progeny, 1,007 (12.8%) were heterozygous in both parental genotypes, whilst just 2.8% of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S- locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7% of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or mis-assignments of genome sequence contigs during the assembly and anchoring of the genome sequence.ConclusionsWe incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm.

BackgroundMarker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials.ResultsA map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2.ConclusionThis study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes.

Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation

Definition of clear criteria for evaluation of the quality of core collections is a prerequisite for selecting high-quality cores. However, a critical examination of the different methods used in literature, for evaluating the quality of core collections, shows that there are no clear guidelines on the choices of quality evaluation criteria and as a result, inappropriate analyses are sometimes made leading to false conclusions being drawn regarding the quality of core collections and the methods to select such core collections. The choice of criteria for evaluating core collections appears to be based mainly on the fact that those criteria have been used in earlier publications rather than on the actual objectives of the core collection. In this study, we provide insight into different criteria used for evaluating core collections. We also discussed different types of core collections and related each type of core collection to their respective evaluation criteria. Two new criteria based on genetic distance are introduced. The consequences of the different evaluation criteria are illustrated using simulated and experimental data. We strongly recommend the use of the distance-based criteria since they not only allow the simultaneous evaluation of all variables describing the accessions, but they also provide intuitive and interpretable criteria, as compared with the univariate criteria generally used for the evaluation of core collections. Our findings will provide genebank curators and researchers with possibilities to make informed choices when creating, comparing and using core collections.

Genetic distance sampling: a novel sampling method for obtaining core collections using genetic distances with an application to cultivated lettuce

This paper introduces a novel sampling method for obtaining core collections, entitled genetic distance sampling. The method incorporates information about distances between individual accessions into a random sampling procedure. A basic feature of the method is that automatically larger samples are obtained if accessions are further apart and smaller samples if accessions are closer together. Genetic distance sampling can be used in conjunction with predefined stratifications of the accessions. Sample sizes are determined automatically; they depend on the distances between accessions within strata. The method is applied to the collection of cultivated lettuce of the Centre for Genetic Resources, the Netherlands. In this paper, genetic distances between accessions are obtained using AFLP marker data. However, genetic distance sampling can be applied using any measure of genetic distance between accessions. Some properties of genetic distance sampling are discussed.

Dispersal patterns of Lonicera periclymenum determined by genetic analysis

Colonization of Lonicera periclymenum L. (honeysuckle) was studied by RAPD analysis of young ramets in two woodlots planted 20 years ago, and in all ramets in older woodlots within a range of 1 km. Mature ramets that climbed in a particular tree always belonged to one individual. Twenty‐five percent of the mature individuals had reproduced vegetatively to other trees or patches nearby, which indicates that the larger part of reproduction is sexual. Some young plants that were growing at close distances from each other were genetically highly similar and shared high similarities to the same mature plants. They may be the product of one dispersal event. Detection of parents of young individuals by exclusion was not successful, because of the dominant nature of the bands. Average distances from young plants to genetically most similar mature plants were variable, due to the small number of colonization events. However, four ways of analysis of genetic similarity among all individuals indicated that exchange of genetic material by seed and pollen occurs to a large extent over small distances and within woodlots: (i) using the Mantel test, pairs of individuals with highest similarity were found significantly more often in the same woodlot than in different woodlots; (ii) genetic similarities between individuals decreased significantly with geographical distance, but only for distances up to 300 m; (iii) individuals of woodlots in the Western part of the study area were hardly related to individuals in the Eastern part of the study area, a distance of 2–3 km; (iv) ΦST in the study area was 0.186, indicating a limited gene flow between woodlots. These results are consistent with the dispersal distance as estimated from the average distance between colonized woodlots and the nearest occupied old woodlot in earlier research.

Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

Linkage map construction involving a reciprocal translocation

This paper is concerned with a novel statistical–genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to ‘pseudo-linkage’: the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the “pseudo-linkage” using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation.

Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

BackgroundAfter crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency).ResultsDespite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop.ConclusionAs it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.