Estimation Of Recombination Frequencies Research Articles

HaploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors.

Recombination is a key mechanism in breeding for promoting genetic variability. Multiparental populations (MPPs) constitute an excellent platform for precise genotype phasing, identification of genome-wide crossovers (COs), estimation of recombination frequencies, and construction of recombination maps. Here, we introduce haploMAGIC, a pipeline to detect COs in MPPs with single-nucleotide polymorphism (SNP) data by exploiting the pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. haploMAGIC applies filtering to prevent false-positive COs due to genotyping errors (GEs), a common problem in high-throughput SNP analysis of complex plant genomes. Hence, it discards haploblocks not reaching a specified minimum number of informative alleles. A performance analysis using populations simulated with AlphaSimR revealed that haploMAGIC improves upon existing methods of CO detection in terms of recall and precision, most notably when GE rates are high. Furthermore, we constructed recombination maps using haploMAGIC with high-resolution genotype data from 2 large multiparental populations of winter rapeseed (Brassica napus). The results demonstrate the applicability of the pipeline in real-world scenarios and showed good correlations in recombination frequency compared with alternative software. Therefore, we propose haploMAGIC as an accurate tool at CO detection with MPPs that shows robustness against GEs.

F2breed, a New Program for Construction of Genetic Linkage Maps

This paper presents a new program F2breed for Windows and Linux operating systems, which was designed for estimation of recombination frequency between the genetic loci and construction of genetic maps based on the analysis of inheritance in a F2 population. The program implements the approach of the orientation of n points corresponding to n analyzed loci in the (n–1)-dimensional space for relative arrangement of the loci on the genetic map by consideration of various projections of this structure. The program is characterized by a convenient, intuitive interface, is easy to operate, and is suitable for working with small groups of loci (up to 100).

The Predicted Cross Value for Genetic Introgression of Multiple Alleles.

We consider the plant genetic improvement challenge of introgressing multiple alleles from a homozygous donor to a recipient. First, we frame the project as an algorithmic process that can be mathematically formulated. We then introduce a novel metric for selecting breeding parents that we refer to as the predicted cross value (PCV). Unlike estimated breeding values, which represent predictions of general combining ability, the PCV predicts specific combining ability. The PCV takes estimates of recombination frequencies as an input vector and calculates the probability that a pair of parents will produce a gamete with desirable alleles at all specified loci. We compared the PCV approach with existing estimated-breeding-value approaches in two simulation experiments, in which 7 and 20 desirable alleles were to be introgressed from a donor line into a recipient line. Results suggest that the PCV is more efficient and effective for multi-allelic trait introgression. We also discuss how operations research can be used for other crop genetic improvement projects and suggest several future research directions.

Partial preferential chromosome pairing is genotype dependent in tetraploid rose.

It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.

TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences

BackgroundT cells and B cells are essential in the adaptive immunity via expressing T cell receptors and immunoglogulins respectively for recognizing antigens. To recognize a wide variety of antigens, a highly diverse repertoire of receptors is generated via complex recombination of the receptor genes. Reasonably, frequencies of the recombination events have been shown to predict immune diseases and provide insights into the development of immunity. The field is further boosted by high-throughput sequencing and several computational tools have been released to analyze the recombined sequences. However, all current tools assume regular recombination of the receptor genes, which is not always valid in data prepared using a RACE approach. Compared to the traditional multiplex PCR approach, RACE is free of primer bias, therefore can provide accurate estimation of recombination frequencies. To handle the non-regular recombination events, a new computational program is needed.ResultsWe propose TRIg to handle non-regular T cell receptor and immunoglobulin sequences. Unlike all current programs, TRIg does alignments to the whole receptor gene instead of only to the coding regions. This brings new computational challenges, e.g., ambiguous alignments due to multiple hits to repetitive regions. To reduce ambiguity, TRIg applies a heuristic strategy and incorporates gene annotation to identify authentic alignments. On our own and public RACE datasets, TRIg correctly identified non-regularly recombined sequences, which could not be achieved by current programs. TRIg also works well for regularly recombined sequences.ConclusionsTRIg takes into account non-regular recombination of T cell receptor and immunoglobulin genes, therefore is suitable for analyzing RACE data. Such analysis will provide accurate estimation of recombination events, which will benefit various immune studies directly. In addition, TRIg is suitable for studying aberrant recombination in immune diseases. TRIg is freely available at https://github.com/TLlab/trig.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1304-2) contains supplementary material, which is available to authorized users.

Integrating haplotype-specific linkage maps in tetraploid species using SNP markers.

Key message Linkage mapping can help unravel the complexities of polyploid genomes. Here, we integrate haplotype-specific linkage maps in autotetraploid potato and explore the possibilities for mapping in other polyploid species. High-density linkage mapping in autopolyploid species has become possible in recent years given the increasing number of molecular markers now available through modern genotyping platforms. Such maps along with larger experimental populations are needed before we can obtain sufficient accuracy to make marker-trait association studies useful in practice. Here, we describe a method to create genetic linkage maps for an autotetraploid species with large numbers of markers and apply it to an F1 population of tetraploid potato (Solanum tuberosum L.) of 235 individuals genotyped using a 20K SNP array. SNP intensity values were converted to allele dosages after which we calculated pairwise maximum likelihood estimates of recombination frequencies between all marker segregation types under the assumption of random bivalent pairing. These estimates were used in the clustering of markers into linkage groups and their subsequent ordering into 96 homologue maps. The homologue maps were integrated per chromosome, resulting in a total map length of 1061 cM from 6910 markers covering all 12 potato chromosomes. We examined the questions of marker phasing and binning and propose optimal strategies for both. We also investigated the effect of quadrivalent formation and preferential pairing on recombination frequency estimation and marker phasing, which is of great relevance not only for potato but also for genetic studies in other tetraploid species for which the meiotic pairing behaviour is less well understood.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2768-1) contains supplementary material, which is available to authorized users.

A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1.

BackgroundThe major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates. MHC genes are especially important in regulating immune responses, but even after over 80 years of research on the MHC, much remains to be learned about how it influences adaptive and innate immune responses. In most species, the MHC is highly polymorphic and polygenic. Strong and highly reproducible associations are established for chicken MHC-B haplotypes in a number of infectious diseases. Here, we report (1) the development of a high-density SNP (single nucleotide polymorphism) panel for MHC-B typing that encompasses a 209,296 bp region in which 45 MHC-B genes are located, (2) how this panel was used to define chicken MHC-B haplotypes within a large number of lines/breeds and (3) the detection of recombinants which contributes to the observed diversity.MethodsA SNP panel was developed for the MHC-B region between the BG2 and CD1A1 genes. To construct this panel, each SNP was tested in end-point read assays on more than 7500 DNA samples obtained from inbred and commercially used egg-layer lines that carry known and novel MHC-B haplotypes. One hundred and one SNPs were selected for the panel. Additional breeds and experimentally-derived lines, including lines that carry MHC-B recombinant haplotypes, were then genotyped.ResultsMHC-B haplotypes based on SNP genotyping were consistent with the MHC-B haplotypes that were assigned previously in experimental lines that carry B2, B5, B12, B13, B15, B19, B21, and B24 haplotypes. SNP genotyping resulted in the identification of 122 MHC-B haplotypes including a number of recombinant haplotypes, which indicate that crossing-over events at multiple locations within the region lead to the production of new MHC-B haplotypes. Furthermore, evidence of gene duplication and deletion was found.ConclusionsThe chicken MHC-B region is highly polymorphic across the surveyed 209-kb region that contains 45 genes. Our results expand the number of identified haplotypes and provide insights into the contribution of recombination events to MHC-B diversity including the identification of recombination hotspots and an estimation of recombination frequency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0181-x) contains supplementary material, which is available to authorized users.

The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map.

The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.

QTL IciMapping: Integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations

QTL IciMapping is freely available public software capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in biparental populations. Eight functionalities are integrated in this software package: (1) BIN: binning of redundant markers; (2) MAP: construction of linkage maps in biparental populations; (3) CMP: consensus map construction from multiple linkage maps sharing common markers; (4) SDL: mapping of segregation distortion loci; (5) BIP: mapping of additive, dominant, and digenic epistasis genes; (6) MET: QTL-by-environment interaction analysis; (7) CSL: mapping of additive and digenic epistasis genes with chromosome segment substitution lines; and (8) NAM: QTL mapping in NAM populations. Input files can be arranged in plain text, MS Excel 2003, or MS Excel 2007 formats. Output files have the same prefix name as the input but with different extensions. As examples, there are two output files in BIN, one for summarizing the identified bin groups and deleted markers in each bin, and the other for using the MAP functionality. Eight output files are generated by MAP, including summary of the completed linkage maps, Mendelian ratio test of individual markers, estimates of recombination frequencies, LOD scores, and genetic distances, and the input files for using the BIP, SDL, and MET functionalities. More than 30 output files are generated by BIP, including results at all scanning positions, identified QTL, permutation tests, and detection powers for up to six mapping methods. Three supplementary tools have also been developed to display completed genetic linkage maps, to estimate recombination frequency between two loci, and to perform analysis of variance for multi-environmental trials.

Genetic Dissection of Yield and Its Component Traits Using High-Density Composite Map of Wheat Chromosome 3A: Bridging Gaps between QTLs and Underlying Genes

Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield component QTLs, and to map QTLs for biomass-related traits. Many of the previously identified QTLs for yield and its component traits were confirmed and were localized to narrower intervals. Four novel QTLs one each for shoot biomass (Xcfa2262-Xbcd366), total biomass (wPt2740-Xcfa2076), kernels/spike (KPS) (Xwmc664-Xbarc67), and Pseudocercosporella induced lodging (PsIL) were also detected. The major QTLs identified for grain yield (GY), KPS, grain volume weight (GVWT) and spikes per square meter (SPSM) respectively explained 23.2%, 24.2%, 20.5% and 20.2% of the phenotypic variation. Comparison of the genetic map with the integrated physical map allowed estimation of recombination frequency in the regions of interest and suggested that QTLs for grain yield detected in the marker intervals Xcdo549-Xbarc310 and Xpsp3047-Xbarc356 reside in the high-recombination regions, thus should be amenable to map-based cloning. On the other hand, QTLs for KPS and SPSM flanked by markers Xwmc664 and Xwmc489 mapped in the low-recombination region thus are not suitable for map-based cloning. Comparisons with the rice (Oryza sativa L.) genomic DNA sequence identified 11 candidate genes (CGs) for yield and yield related QTLs of which chromosomal location of two (CKX2 and GID2-like) was confirmed using wheat aneuploids. This study provides necessary information to perform high-resolution mapping for map-based cloning and for CG-based cloning of yield QTLs.

Estimation of recombination frequency in bi-parental genetic populations

Summary Linkage analysis plays an important role in genetic studies. In linkage analysis, accurate estimation of recombination frequency is essential. Many bi-parental populations have been used, and determining an appropriate population is of great importance in precise recombination frequency. In this study, we investigated the estimation efficiency of recombination frequency in 12 bi-parental populations. The criteria that we used for comparison were LOD score in testing linkage relationship, deviation between estimated and real recombination frequency, standard error (SE) of estimates and the least theoretical population size (PS) required to observe at least one recombinant and to declare the statistically significant linkage relationship. Theoretical and simulation results indicated that larger PS and smaller recombination frequency resulted in higher LOD score and smaller deviation. Lower LOD score, higher deviation and higher SE for estimating the recombination frequency in the advanced backcrossing and selfing populations are larger than those in backcross and F2 populations, respectively. For advanced backcrossing and selfing populations, larger populations were needed in order to observe at least one recombinant and to declare significant linkage. In comparison, in F2 and F3 populations higher LOD score, lower deviation and SE were observed for co-dominant markers. A much larger population was needed to observe at least one recombinant and to detect loose linkage for dominant and recessive markers. Therefore, advanced backcrossing and selfing populations had lower precision in estimating the recombination frequency. F2 and F3 populations together with co-dominant markers represent the ideal situation for linkage analysis and linkage map construction.

On the bias of recombination fractions, Kosambi's and Haldane's distances based on frequencies of gametes

The estimation of recombination frequencies is a crucial step in genetic mapping. For the construction of linkage maps, nonadditive recombination fractions must be transformed into additive map distances. Two of the most commonly used transformations are Kosambi's and Haldane's mapping functions. This paper reports on the calculation of the bias associated with estimation of recombination fractions, Kosambi's distances, and Haldane's distances. I calculated absolute and relative biases numerically for a wide range of recombination fractions and sample sizes. I assumed that the ratio of recombinant gametes to the total number of gametes can be adequately represented by a binomial function. I found that the bias in recombination fraction estimates is negative, i.e., the estimator is an underestimate. However, significant values were only obtained when recombination fractions were large and sample sizes were small. The relevant estimates of recombination fractions were, therefore, nearly unbiased. Haldane's and Kosambi's distances were found to be strongly biased, with positive bias for the most interesting values of recombination fractions and sample sizes. The bias of Kosambi's distance was considerably smaller than the bias of Haldane's distance.

Analysis of linkage and linkage disequilibrium for eight X-STR markers

X-chromosomal short tandem repeats (X-STR) have proven to be informative and useful in complex relationship testing. The main feature of X-STR markers, compared to autosomal forensic markers, is that all loci are located on the same chromosome. Thus, linkage and linkage disequilibrium may occur. The aim of this work was to study population genetic parameters of eight X-STR markers, located in four linkage groups. We present haplotype frequencies, based on 718 Swedish males, for the four linkage groups included in the Argus X-8 kit. Forensic efficiency parameters have been calculated as well as the allelic association between the tested markers for detection of linkage disequilibrium. To study the occurrences of recombination between the loci, both Swedish and Somali families were typed. A mathematical model for the estimation of recombination frequencies is presented and applied on the family samples. Our study showed that the tested markers all have highly informative forensic values and that there is a significant degree of linkage disequilibrium between the STR markers within the four linkage groups. Furthermore, based on the tested families, we also demonstrated that two of the linkage groups are partially linked. A consequence of these findings is that both linkage and linkage disequilibrium should be accounted for when producing likelihood ratios in relationship testing with X-STR markers.

Estimativa de freqüência de recombinação no mapeamento genético de famílias de irmãos completos

O objetivo deste trabalho foi obter as estimativas de freqüência de recombinação, por meio de simulação, para diferentes situações do mapeamento genético de famílias de irmãos completos. Foi simulado um genoma constituído de três grupos de ligação, em que cada um apresentava 11 marcas moleculares multialélicas, codominantes, distribuídas a cada 10 cM. A partir desse genoma, foram simulados dois cenários: um com genitores completamente informativos e outro com genitores formados aleatoriamente. Após a obtenção de todas as estimativas das freqüências de recombinação, concluiu-se que, para locos completamente informativos, pode-se calcular a freqüência de recombinação entre pares de locos, a partir da freqüência gamética de cada genitor ou a partir da freqüência genotípica da progênie. Para locos parcialmente informativos, a obtenção da freqüência de recombinação a partir da freqüência genotípica conjunta é mais apropriada.

Precision of Recombination Frequency Estimates After Random Intermating With Finite Population Sizes

Random intermating of F2 populations has been suggested for obtaining precise estimates of recombination frequencies between tightly linked loci. In a simulation study, sampling effects due to small population sizes in the intermating generations were found to abolish the advantages of random intermating that were reported in previous theoretical studies considering an infinite population size. We propose a mating scheme for intermating with planned crosses that yields more precise estimates than those under random intermating.

The development of a genetic linkage map of blackcurrant (Ribes nigrum L.) and the identification of regions associated with key fruit quality and agronomic traits

The first genetic linkage map of blackcurrant (Ribes nigrum L.) was constructed using AFLP, SSR (genomic and EST-derived) and SNP markers, in a mapping population derived from two diverse breeding clones of blackcurrant from the SCRI breeding programme. Cluster analysis of the population revealed that the individuals within the population formed two distinct sub-populations, with segregation ratios consistent with one sub-population having the two intended parents, and the other being selfed segregants. The latter sub-population improves the map by providing a more informative estimate of recombination frequency than the crossed sub-population for some marker configurations, and also revealed the presence of two unlinked loci affecting viability. Several important phenological, agronomic and fruit quality traits were evaluated in the mapping population, and QTLs affecting these are located on the linkage map. This provides a framework for the development of marker-assisted breeding strategies for blackcurrant, to improve breeding efficiency and time to cultivar.

The misuse of the three-point cross for estimating chiasma interference

The building of genetic maps in diploid organisms by crosses between different genotypes and estimation of recombination frequencies from the obtained segregation data has been successfully used since a very young step in the birth of genetics. The three-point cross methodology has facilitated this task and has demonstrated at the same time that genetic distances are not additive, as some recombinant products are not recognised in the progeny. Three-point cross also allows to examine if chiasma interference exists and its evaluation. Here I show that the classical method of this estimation is erroneous and inevitably determines the apparition of a spurious, positive interference, which has been claimed to be an almost general phenomenon. Interference can only be estimated from a precise knowledge of the number of crossing over events occurring in meiocytes.

Microsatellite analysis of gynogenetic families in the Pacific oyster, Crassostrea gigas

Five families of gynogenetic diploid Pacific oyster ( Crassostrea gigas) were induced by inhibiting the second polar body in meiotic cell division of eggs fertilized with UV-irradiated sperm. Segregation patterns of eight microsatellite loci were investigated in the gynogenetic diploid offspring; the proportion of heterozygous progeny was used to estimate microsatellite–centromere (M–C) distances. Mendelian inheritance was confirmed for the eight loci by examining the genotypic segregation in the control crosses. Three of the eight microsatellite loci showed the existence of null alleles in four control crosses. All gynogenetic offspring only possessed the alleles of the mother, indicating 100% success level for the five families. The M–C recombination frequency estimates ranged from 0.62 to 0.77 (0.72 mean), comparable to those in the oyster based on allozyme markers and suggesting that meiotic gynogenesis does not appear to be a very efficient inbreeding method in the oyster. Recombination frequencies observed were often higher than the theoretical maximum of 0.67, indicating the existence of positive interference after a single chiasma formation in some chromosomes. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution toward assembly of genetic maps in C. gigas.

Tetrad Analysis with Translocation Heterozygotes in Cranberry (Vaccinium Macrocarpon Ait.): Interstitial Chiasma and Directed Segregation of Centromeres

Tetrad analysis of translocation heterozygotes was used in cranberry (Vaccinium macrocarpon Ait.) to study the co-orientation of centromeres during meiosis 1 and its relationship with the frequency of interstitial chiasma. Pollen tetrads from one reciprocal and three cyclical translocation heterozygotes were analyzed and their frequency distribution, as manifest in pollen stainability, was determined. Pollen tetrads were characterized as having four, two, one or zero stained pollen grains. The occurrence of each type was the result of the type of centromere segregation and the presence of crossing over in the interstitial region(s). Based on this information, the predominance of alternate segregation was found to be correlated with a reduction of the crossing over in the interstitial region. Significant differences were found in the tetrad frequency distribution for pollen stainability between years, and for cultivars carrying the same translocation. This variation was correlated with significant differences in the frequency of crossing over between years and among cultivars, which indicates that the estimation of recombination frequencies was influenced by both environment and genotype. The occurrence of translations in cultivars selected from wild populations indicates the possible advantage of maintaining heterozygosity or a block of genes as a linkat through this chromosome aberration in a self-pollinated crop like cranberry.

Linkage analysis using direct and indirect counting and relative efficiencies for codominant and dominant loci1

A method based on direct and indirect counting is developed for rapid and accurate linkage analysis for codominant and dominant loci. Methods for estimating gender-specific recombination frequencies are available for cases where at least one of the two loci is multiallelic and for biallelic loci with mixed parental linkage phases where at least one locus is codominant. Most of the estimates of gender-average and gender-specific recombination frequencies required iterative solutions. The new method makes use of the full data set, yields exact estimates of the recombination frequencies when the observed and expected genotypic frequencies are equal, and are computationally efficient. Relative efficiency of various data types is affected by the inheritance mode and by parental linkage phases of biallelic loci, but unaffected by the locus polymorphism when using the full data set for linkage analysis. The ability to determine parental linkage phases is affected by the locus polymorphism as well as inheritance mode. Intercross (or F-2 design) is more efficient for mapping codominant loci, whereas backcross is more efficient if dominance is involved. Mixed parental linkage phases of biallelic loci are less efficient than coupling or repulsion linkage phases. Ignoring noninformative offspring results in biased estimates of recombination frequency for biallelic loci only and reduced LOD scores for all cases.