EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome

In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (π) ranged from 0 to 40.0 × 10⁻³ (average 3.1 × 10⁻³) and 0.52 × 10⁻³ to 39.51 × 10^–3 (average 4.37 × 10⁻³) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Both R. Kota and R.K. Varshney contributed equally to this work.     

Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers

The extent of linkage disequilibrium (LD) is an important factor in designing association mapping experiments. Unlike other plant species that have been analyzed so far for the extent of LD, cultivated potato (Solanum tuberosum L.), an outcrossing species, is a highly heterozygous autotetraploid. The favored genotypes of modern cultivars are maintained by vegetative propagation through tubers. As a first step in the LD analysis, we surveyed both coding and noncoding regions of 66 DNA fragments from 47 accessions for single nucleotide polymorphism (SNP). In the process, we combined information from the potato SNP database with experimental SNP detection. The total length of all analyzed fragments was >25 kb, and the number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (=11.5x10(-3)) and diversity (pi=14.6x10(-3)) was high compared to the other plant species. The overall Tajima's D value (0.5) was not significant, but indicates a deficit of low-frequency alleles relative to expectation. To eliminate the possibility that an elevated D value occurs due to population subdivision, we assessed the population structure with probabilistic statistics. The analysis did not reveal any significant subdivision, indicating a relatively homogenous population structure. However, the analysis of individual fragments revealed the presence of subgroups in the fragment closely linked to the R1 resistance gene. Data pooled from all fragments show relatively fast decay of LD in the short range (r2=0.208 at 1 kb) but slow decay afterward (r2=0.137 at approximately 70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of approximately 10 cM. We speculate that two conflicting factors play a vital role in shaping LD in potato: the outcrossing mating type and the very limited number of meiotic generations.     

Development of polymorphic microsatellite and single nucleotide polymorphism markers for Cercospora beticola (Mycosphaerellaceae)

The plant pathogenic fungus, Cercospora beticola, causes the most important foliage disease of sugar beet. A previous study has shown that isolates of opposite mating types are present in equal proportions in natural populations; therefore, the aim of this study was to develop highly reproducible polymorphic markers for analysing populations of C. beticola. Five microsatellite and four single nucleotide polymorphism (SNP) markers were developed that allow rapid screening of genetic diversity in C. beticola. Six populations were screened with these markers and all were found to be in gametic equilibrium, indicating random mating in C. beticola.     

Construction of a rat genetic map by using randomly amplified microsatellite polymorphism (RAMP) markers

Many rat strains have been employed in the genetic study of quantitative traits such as blood pressure. In such genetic studies, it is essential to prepare rat genetic maps fine enough to identify the genes regulating quantitative traits. However, it is not an easy task to isolate a sufficient number of genetic markers polymorphic between a particular pair of rat strains. In this study, we applied the randomly amplified microsatellite polymorphism (RAMP) method, a simple method to identify co-dominant markers (Wu et al. Nucleic Acids Res 22, 3257, 1994), to isolate markers polymorphic between the stroke-prone spontaneously hypertensive rat and the Wistar-Kyoto rat, a genetically hypertensive strain and its normotensive control strain, which share a common genetic background. We successfully identified 111 RAMP markers distributed throughout the rat genome after screening 3046 sets of primers. We also showed that we could isolate ordinary simple-sequence-length-polymorphism markers by cloning RAMP markers. The RAMP method is a simple and efficient way to identify co-dominant genetic markers on mammalian genomes. Received: 10 October 1997 / Accepted: 16 March 1998     

Effect of genotyping error in model-free linkage analysis using microsatellite or single-nucleotide polymorphism marker maps

Errors while genotyping are inevitable and can reduce the power to detect linkage. However, does genotyping error have the same impact on linkage results for single-nucleotide polymorphism (SNP) and microsatellite (MS) marker maps? To evaluate this question we detected genotyping errors that are consistent with Mendelian inheritance using large changes in multipoint identity-by-descent sharing in neighboring markers. Only a small fraction of Mendelian consistent errors were detectable (e.g., 18% of MS and 2.4% of SNP genotyping errors). More SNP genotyping errors are Mendelian consistent compared to MS genotyping errors, so genotyping error may have a greater impact on linkage results using SNP marker maps. We also evaluated the effect of genotyping error on the power and type I error rate using simulated nuclear families with missing parents under 0, 0.14, and 2.8% genotyping error rates. In the presence of genotyping error, we found that the power to detect a true linkage signal was greater for SNP (75%) than MS (67%) marker maps, although there were also slightly more false-positive signals using SNP marker maps (5 compared with 3 for MS). Finally, we evaluated the usefulness of accounting for genotyping error in the SNP data using a likelihood-based approach, which restores some of the power that is lost when genotyping error is introduced.     

Construction of genetic linkage maps in maize and tomato using restriction fragment length polymorphisms

Summary Genetic linkage maps were constructed for both maize and tomato, utilizing restriction fragment length polymorphisms (RFLPs) as the source of genetic markers. In order to detect these RFLPs, unique DNA sequence clones were prepared from either maize or tomato tissue and hybridized to Southern blots containing restriction enzyme-digested genomic DNA from different homozygous lines. A subsequent comparison of the RFLP inheritance patterns in F2 populations from tomato and maize permitted arrangement of the loci detected by these clones into genetic linkage groups for both species.     

Construction of a genetic linkage map in Fenneropenaeus chinensis using SNP markers

Genetic linkage maps of Fenneropenaeus chinensis were constructed using a “double pseudo-testcross” strategy with 200 single nucleotide polymorphisms (SNPs) markers. This study represents the first SNP genetic linkage map for F. chinensis. The parents and F ₁ progeny of 100 individuals were used as mapping populations. 21 genetic linkage groups in the male and female maps were identified. The male linkage map was composed of 115 loci and spanned 879.7 cM, with an average intermarker spacing of 9.4 cM, while the female map was composed of 119 loci and spanned 876.2 cM, with an average intermarker spacing of 8.9 cM. The estimated coverage of the linkage maps was 51.94% for the male and 53.77% for the female, based on two estimates of genome length. The integrated map contains 180 markers distributed in 16 linkage groups, and spans 899.3 cM with an average marker interval of 5.2 cM. This SNP genetic map lays the foundation for future shrimp genomics and genetic breeding studies, especially the discovery of gene or regions for economically important traits in Chinese shrimp.     

Construction of a genetic linkage map for roses using RAPD and AFLP markers

A segregating population of diploid rose hybrids (2n = 2x = 14) was used to construct the first linkage maps of the rose genome. A total of 305 RAPD and AFLP markers were analysed in a population of 60 F₁ plants based on a so-called ”double-pseudotestcross” design. Of these markers 278 could be located on the 14 linkage groups of the two maps, covering total map lengths of 326 and 370 cM, respectively. The average distances between markers in the maps for 93/1–117 and 93/1–119 is 2.4 and 2.6 cM, respectively. In addition to the molecular markers, genes controlling two phenotypic characters, petal number (double versus single flowers) and flower colour (pink versus white), were mapped on linkage groups 3 and 2, respectively. The markers closest to the gene for double flowers, Blfo, and to the gene for pink flower colour, Blfa, cosegregated without recombinants. The maps provide a tool for further genetic analyses of horticulturally important genes as, for example, resistance genes and a starting point for marker-assisted breeding in roses. Received: 22 September 1998 / Accepted: 12 March 1999     

Construction of a genetic linkage map in celery using DNA-based markers.

A F2 population of two celery cultivated types (Apium graveolens L. var. rapaceum and A. graveolens L. var. secalinum) was used to construct a linkage map consisting of 29 RFLP (restriction fragment length polymorphism), 100 RAPD (random amplified polymorphic DNA), four isozyme, one disease resistance, and one growth habit markers. The map contains 11 major groups and 9 small groups and has a total length of 803 cM with an average distance of 6.4 cM between two adjacent loci. Ten percent of the RAPDs segregated as codominant markers and their allelic homologies were tested by Southern hybridization. One-quarter of the dominant RAPDs were linked in repulsion phase, whereas the majority of them were linked to either codominant or dominant markers in coupling phase. About 10% of the markers showed significant segregation distortion. The detectable level of duplications in the celery genome was relatively low.     

The linkage information content value of polymorphism genetic markers in model-free linkage analysis

Guo and Elston [Hum Hered 1999;49:112-118] developed a linkage information content (LIC) value to measure the informativeness of a marker for identity-by-descent (IBD) sharing status of relative pairs. LIC values were derived for five types of relative pairs: full sib, half sib, grandparent-grandchild, first cousin and avuncular. In this paper, we give corrected LIC values for full sib, grandparent-grandchild, first cousin and avuncular pairs, and indicate the availability of a computer program to calculate them.     

Construction of a genetic linkage map in tetraploid species using molecular markers

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.     

QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers

Avian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long-distance migrants typically have longer wings than short-distance migrants and sedentary species, and long-winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large-scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within-population variation of relative wing length (h(2) = 0.74 ± 0.05) is associated with standing genetic variation in at least six genomic regions (one genome-wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co-locate with Wnt growth factors and closely interacting genes (Wnt3a, Wnt5a, Wnt6, Wnt7a, Wnt9a, RhoU and RhoV). Our findings therefore suggest that standing genetic variation in the Wnt genes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.     

Alignment of two genetic linkage maps on porcine chromosome 13

A set of four microsatellite markers from the USDA genetic linkage map of porcine chromosome 13 were mapped in the European Pig Gene Mapping Project (PiGMaP) reference pedigrees. A two-point linkage analysis was performed between these markers and a set of markers known to map to chromosome 13. Pairs of markers that had a lod score greater than three were used to construct a multi-point linkage map, permitting alignment of the United States Department of Agriculture (USDA) map to the PiGMaP.     

Characterization of 19 single nucleotide polymorphism markers for coho salmon

We report 39 single nucleotide polymorphisms (SNPs) observed in 23 nuclear DNA sequences in coho salmon Oncorhynchus kisutch. High‐throughput genotyping assays based on the 5′‐nuclease reaction were developed for 17 of these nuclear SNPs and for two previously published mitochondrial DNA SNPs. Minor allele frequency differences (Δq) among collections were between 5.2% and 51.2%, resulting in per locus F_ST estimates of 0.00–0.24 with an average of 0.09.     

Characterization of eight single nucleotide polymorphism markers in Aedes aegypti

Sequencing of part of seven genes from Aedes aegypti collected in 16 Brazilian cities revealed the existence of 53 single nucleotide polymorphisms (SNPs), representing one SNP every 52 base pairs. From these 53 SNPs, we selected eight that are independent and highly polymorphic. We describe the use of these markers for differentiation of Brazilian populations of A. aegypti. These are the first SNPs developed for delineating population structure in A. aegypti, and will be a useful complement to epidemiological studies.     

HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers

We present two Web interfaces that generate genetic maps for given sets of human or mouse microsatellite markers. The genetic maps are generated from available databases using linear interpolation of physical map distances to infer genetic map positions for missing markers in these databases.     

Joining genetic linkage maps using a joint likelihood function

We present an efficient method to join genetic maps derived from different crosses, which is especially appropriate for dominant markers. In contrast to the JoinMap algorithm, which estimates information about recombination in a given cross from the LOD values and then combines estimates among crosses assuming a binomial sampling distribution, we construct a joint likelihood function that combines information across all crosses, to obtain a joint estimate of recombination. Simulations indicate that the difference between these two approaches is small when codominant markers are used, but that the joint likelihood approach shows substantially improved estimates when dominant or a mixture of dominant and codominant markers are used. This is because the joint likelihood implicitly finds the optimal weights among different classes of data, while the former method does not accurately predict the information from crosses involving dominant markers. Application of our method is illustrated by the construction of a linkage map for Linanthus using both backcrosses and the F₂ of a cross between Linanthus jepsonii and L. bicolor, assayed with amplified fragment length polymorphisms (AFLP).