Mapping Of Markers Research Articles

Time for the zebrafish ENCODE

Genomics research in recent years, especially the human ENCODE project, have made great strides in understanding the genomic and epigenomic structure and organization of humans. These advances promise a new era of precision medicine, through a better understanding of the genomic correlates of human physiology and promise to offer precise and personalized preventive and therapeutic options. The translation of genome-scale maps of genomic and epigenomic markers to clinically relevant information and further to medical practice await functional validation of the genomic features identified through these large-scale efforts. Such studies must essentially be done in model systems where it is possible to model physiological and pathological processes and enquire how they could be modulated by genomic elements and epigenomic signatures. The availability of large number of personal genomes and maps of genomic variations at population scale has created an acute necessity for model systems to model phenotypic and molecular effects of variations, especially in regulatory regions. Efforts to create orthologous maps have been underway in other model systems including Caenorhabditis elegans and Drosophila through the modENCODE programe and in Mus musculus through the mouse ENCODE. We propose that the enormous wealth of disease models and excellent tools to engineer genomes in zebrafish could be effectively capitalized towards making it an effective and widely used model system for precision medicine. This would be possible only through a concerted and systematic effort to create orthologous genomic and epigenomic maps for zebrafish.We discuss how the present understanding and genome-scale methodologies available in this model organism could be effectively used towards realizing this goal.

QTL mapping for important horticultural traits in pepper (Capsicum annuum L.)

Quantitative trait loci (QTLs) for plant height (PHT) and other yield-related traits including number of fruits per plant (NFP), ten fruits weight (TFW), fruit length (FL), fruit width (FW), total fruit weight (ToFW) and pericarp thickness (PT) were mapped in intraspecific advanced recombinant inbred line (RIL) populations of pepper. The RILs were evaluated for 2 years (F8 and F9) for plant height and seven other yield-related traits. Three types of molecular markers; simple sequence repeat (SSR), sequenced characterized amplified region (SCAR) and random amplified polymorphic DNA (RAPD)—were used to generate linkage maps. A total of 10 QTLs for yield-related traits were mapped on four linkage groups (LG). QTLs for plant height were mapped on LG5. The phenotypic contribution of these QTLs ranged from 8 % to 51 % in mean over environments. Out of 10 QTLs detected, nine were stable in both environments except the QTL for fruit length (Qfl.iivr.3.4) on LG3. The five QTLs; Qfw.iivr-2.1, Qtfw.iivr-2.1, Qtofw.iivr-2.1, Qnfp.iivr-2.1 and Qpt.iivr-2.1 were on the same marker interval on LG2 and one QTL, Qtofw.iivr-3.1 were tightly linked on LG3, which suggests that these genomic regions play an important role in enhancing pepper production. The genomic regions of all stable QTLs identified may serve as potential target regions for fine mapping and development of molecular markers for manipulation of yield and morphological traits in pepper.

Mapping and validation of microsatellite markers linked to sugary1 and shrunken2 genes in maize (Zea mays L.)

Sweet corn has emerged as one of the popular choices as fresh and processed vegetables, worldwide. Two genes namely, sugary1 (su1) and shrunken2 (sh2) that cause significant increase in sugar levels of endosperm, have been extensively used in sweet corn cultivar development. In order to identify and validate microsatellite/SSR markers linked to su1 and sh2, F2 mapping populations were generated between wild type and mutant (sugary or shrunken) genotypes. Bulk segregant analysis (BSA) in three mapping populations mapped su1 on short arm of chromosome 4 (bin. 4.05), while sh2 could be located on long arm of chromosome 3 (bin 3.08) using two mapping populations. The analysis identified seven linked SSR markers for su1 and four SSR markers linked to sh2. Across populations, umc2061 was identified as the nearest marker from su1 with genetic distance of 0.3, 0.6 and 1.6 cM, while umc2276 could be located at 1.2 and 1.5 cM from sh2. These two markers can be effectively utilized in marker-assisted selection of sweet corn trait.

Mapping of quantitative trait loci for floral scent compounds in cowpea (Vigna unguiculata L.)

AbstractFloral scent is a very important trait in plant evolution. Currently, little is known about the inheritance of floral scent in cowpea (Vigna unguiculata L.) or changes that might have occurred during its domestication. Therefore, we analysed scent volatiles and molecular markers in a population of 159 F7 recombinant inbred lines derived from a cross of a domesticated blackeye cowpea cultivar, ‘524B’ and a wild accession ‘219‐01’. Using gas chromatography‐mass spectrometry (GC–MS) 23 volatile compounds were identified that fall into five general functional categories. Twenty‐two of the compounds displayed quantitative variation in the progeny, and a total of 63 QTLs influencing the amounts of these volatiles were mapped onto the cowpea genetic marker map. Although QTLs for volatile compounds putatively involved in cowpea flower scent were found on 9 of the 11 cowpea chromosomes, they were not evenly distributed with QTLs mainly clustered on LGs 1, LGs 2 and LG 4. Our results serve as a starting point for both more detailed analyses of complex scent biosynthetic pathways and the development of markers for marker‐assisted breeding of scented rose varieties.

Recent Developments in Cardiovascular Genetics

Recent Developments in Cardiovascular Genetics

A whole-genome DNA marker map for cotton based on the D-genome sequence of Gossypium raimondii L.

We constructed a very-high-density, whole-genome marker map (WGMM) for cotton by using 18,597 DNA markers corresponding to 48,958 loci that were aligned to both a consensus genetic map and a reference genome sequence. The WGMM has a density of one locus per 15.6 kb, or an average of 1.3 loci per gene. The WGMM was anchored by the use of colinear markers to a detailed genetic map, providing recombinational information. Mapped markers occurred at relatively greater physical densities in distal chromosomal regions and lower physical densities in the central regions, with all 1 Mb bins having at least nine markers. Hotspots for quantitative trait loci and resistance gene analog clusters were aligned to the map and DNA markers identified for targeting of these regions of high practical importance. Based on the cotton D genome reference sequence, the locations of chromosome structural rearrangements plotted on the map facilitate its translation to other Gossypium genome types. The WGMM is a versatile genetic map for marker assisted breeding, fine mapping and cloning of genes and quantitative trait loci, developing new genetic markers and maps, genome-wide association mapping, and genome evolution studies.

Genome-wide association study implicates a novel RNA gene, the lincRNA AC068718.1, as a risk factor for post-traumatic stress disorder in women

Posttraumatic stress disorder (PTSD) is a common and debilitating mental disorder with a particularly high burden for women. Emerging evidence suggests PTSD may be more heritable among women and evidence from animal models and human correlational studies suggest connections between sex-linked biology and PTSD vulnerability, which may extend to the disorder's genetic architecture. We conducted a genome-wide association study (GWAS) of PTSD in a primarily African American sample of women from the Detroit Neighborhood Health Study (DNHS) and tested for replication in an independent cohort of primarily European American women from the Nurses Health Study II (NHSII). We genotyped 413 DNHS women - 94 PTSD cases and 319 controls exposed to at least one traumatic event - on the Illumina HumanOmniExpress BeadChip for >700,000 markers and tested 578 PTSD cases and 1963 controls from NHSII for replication. We performed a network-based analysis integrating data from GWAS-derived independent regions of association and the Reactome database of functional interactions. We found genome-wide significant association for one marker mapping to a novel RNA gene, lincRNA AC068718.1, for which we found suggestive evidence of replication in NHSII. Our network-based analysis indicates that our top GWAS results were enriched for pathways related to telomere maintenance and immune function. Our findings implicate a novel RNA gene, lincRNA AC068718.1, as risk factor for PTSD in women and add to emerging evidence that non-coding RNA genes may play a crucial role in shaping the landscape of gene regulation with putative pathological effects that lead to phenotypic differences.

Valproic acid promotes neuronal differentiation by induction of neuroprogenitors in human bone-marrow mesenchymal stromal cells

Recent studies have shown that the inhibition of histone deacetylases (HDACs) induces the differentiation of diverse cancer and stem cells, which suggests HDAC inhibitors may be good candidates for the induction of stem cell differentiation. In this study, we investigated the effects of a HDAC inhibitor, valproic acid (VPA), for the neuronal differentiation of human bone marrow-mesenchymal stromal cells (hBM-MSCs). VPA-treated MSCs had significant increases in their expression of the neuro-progenitor marker Nestin, Musashi, CD133, and GFAP, as measured by real-time PCR and immunoblot analysis. When VPA-pretreated MSCs were differentiated with neuronal induction media (VPA-dMSCs), they exhibited a cell body and dendritic morphology similar to neurons. The number and neurite length of these VPA-dMSCs significantly increased compared to differentiated MSCs (dMSCs). The VPA-dMSCs and dMSCs had significantly increased transcripts of neuronal-specific marker genes, including Nestin, Musashi, CD133, GFAP, NeuN, MAP-2, NF-M, KCNH1, and KCNH5. The cells also showed a higher expression of the neuronal marker proteins Nestin and NF-M from immunocytochemical staining and immunoblot analysis. This study has shown that VPA pretreatment of hBM-MSCs, following their incubation with neuronal induction media, effectively stimulates neuronal cell differentiation to BM-MSCs.

Genomic Selection: Status in Different Species and Challenges for Breeding

Technical advances and development in the market for genomic tools have facilitated access to whole-genome data across species. Building-up on the acquired knowledge of the genome sequences, large-scale genotyping has been optimized for broad use, so genotype information can be routinely used to predict genetic merit. Genomic selection (GS) refers to the use of aggregates of estimated marker effects as predictors which allow improved individual differentiation at young age. Realizable benefits of GS are influenced by several factors and vary in quantity and quality between species. General characteristics and challenges of GS in implementation and routine application are described, followed by an overview over the current status of its use, prospects and challenges in important animal species. Genetic gain for a particular trait can be enhanced by shortening of the generation interval, increased selection accuracy and increased selection intensity, with species- and breed-specific relevance of the determinants. Reliable predictions based on genetic marker effects require assembly of a reference for linking of phenotype and genotype data to allow estimation and regular re-estimation. Experiences from dairy breeding have shown that international collaboration can set the course for fast and successful implementation of innovative selection tools, so genomics may significantly impact the structures of future breeding and breeding programmes. Traits of great and increasing importance, which were difficult to improve in the conventional systems, could be emphasized, if continuous availability of high-quality phenotype data can be assured. Equally elaborate strategies for genotyping and phenotyping will allow tailored approaches to balance efficient animal production, sustainability, animal health and welfare in future.

Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures inPiedmontese andItalianBrown cattle breeds

Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50years, cattle breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst ) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two cattle breeds with different production aptitudes (dairy and beef). Fst was calculated for 42514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in cattle studies were detected.

A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis

BackgroundRyegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses.ResultsA F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor.ConclusionsDArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

DNA markers for resistance to common bunt in ‘McKenzie’ wheat

Common bunt, caused by Tilletia tritici (Bjerk.) G. Wint. in Rabenh. and T. laevis Kϋhn in Rabenh., is an economically important disease of wheat (Triticum aestivum L.) worldwide. The hexaploid wheat cultivar ‘McKenzie’ possesses effective resistance against known races of common bunt in western Canada. Understanding the nature of this resistance through DNA marker mapping will be useful for breeding. Disease reaction to T. tritici race T19 and T. laevis race L16 from field tests was analysed with simple sequence repeat markers for 174 doubled haploid lines using interval mapping. Markers Xgwm573 and Xwmc17, located on wheat chromosome 7B, were strongly associated with the resistance. The quantitative trait locus was designated QCbt.spa-7B.1. The markers were validated on two other populations in which ‘McKenzie’ was in the parentage. The markers will be useful in breeding as a tool for selecting for common bunt resistance from ‘McKenzie’ and will assist in identifying the resistance among potential new sources.

Mapping of QTL for seed dormancy in a winter oilseed rape doubled haploid population

Following winter oilseed rape cultivation, considerable numbers of volunteer oilseed rape plants may occur in subsequent years in following crops. The appearance of volunteer oilseed rape plants is based on the capability of the seeds to become secondary dormant and to survive in this stage for many years in the soil. Genetic reduction of secondary seed dormancy in oilseed rape could provide a means to reduce the frequency of volunteer plants and especially the dispersal of transgenic oilseed rape. The objective of the present study was to analyse the inheritance of primary and secondary seed dormancy in a winter oilseed rape doubled haploid population derived from the cross Express 617×R53 and to study correlations to other seed traits. Field experiments were performed in Germany for 2years at two locations with two replicates. Seeds harvested from open pollinated plants were used for all analyses, including a laboratory test for seed dormancy. A previously developed molecular marker map of the doubled haploid population was used to map QTL of the relevant traits. For primary, secondary and total seed dormancy, the results showed significant effects of the genotypes and their interactions, with years and locations. Two, four and five QTL were detected for primary, secondary and total seed dormancy which explained 19, 35 and 42% of the phenotypic variance, respectively. Results show that secondary seed dormancy is a heritable trait and that selection for low secondary seed dormancy is possible.

Genetic dissection of yield-related traits in a recombinant inbred line population created using a key breeding parent in China’s wheat breeding

Understanding the genetics underlying yield formation of wheat is important for increasing wheat yield potential in breeding programs. Nanda2419 was a widely used cultivar for wheat production and breeding in China. In this study, we evaluated yield components and a few yield-related traits of a recombinant inbred line (RIL) population created by crossing Nanda2419 with the indigenous cultivar Wangshuibai in three to four trials at different geographical locations. Negative and positive correlations were found among some of these evaluated traits. Five traits had over 50% trial-wide broad sense heritability. Using a framework marker map of the genome constructed with this population, quantitative trait loci (QTL) were identified for all traits, and epistatic loci were identified for seven of them. Our results confirmed some of the previously reported QTLs in wheat and identified several new ones, including QSn.nau-6D for effective tillers, QGn.nau-4B.2 for kernel number, QGw.nau-4D for kernel weight, QPh.nau-4B.2 and QPh.nau-4A for plant height, and QFlw.nau-5A.1 for flag leaf width. In the investigated population, Nanda2419 contributed all QTLs associated with higher kernel weight, higher leaf chlorophyll content, and a major QTL associated with wider flag leaf. Seven chromosome regions were related to more than one trait. Four QTL clusters contributed positively to breeding goal-based trait improvement through the Nanda2419 alleles and were detected in trials set in different ecological regions. The findings of this study are relevant to the molecular improvement of wheat yield and to the goal of screening cultivars for better breeding parents.

820 Urinary Peptide Analysis Differentiates Pancreatic Cancer From Chronic Pancreatitis

Objectives: Differentiation of pancreatic cancer (PCA) from chronic pancreatitis (CP) is challenging. We searched for peptide markers in urine to develop a diagnostic peptide marker model. Methods: Capillary electrophoresis–mass spectrometry was used to search for peptides in urine of patients with PCA (n = 39) or CP (n = 41). Statistical different peptides were included in a peptide multimarker model. Peptide markers were sequence identified and validated by immunoassay and immunohistochemistry (IHC). Results: Applied to a validation cohort of 54 patients with PCA and 52 patients with CP, the peptide model correctly classified 47 patients with PCA and 44 patients with CP (area under the curve, 0.93; 87% sensitivity; 85% specificity). All 5 patients with PCA with concomitant CP were classified positive. Urine proteome analysis outperformed carbohydrate antigen 19-9 (area under the curve, 0.84) by a 15% increase in sensitivity at the same specificity. From 99 healthy subjects, only four were misclassified. Fetuin-A was the most prominent peptide marker source for PCA as verified by immunoassay and IHC. In silico protease mapping of the peptide markers' terminal sequences pointed to increased meprin-A activity in PCA, which in IHC was associated with neoangiogenesis. Conclusions: Urinary proteome analysis differentiates PCA from CP and may serve as PCA screening tool.

WDR81 Is Necessary for Purkinje and Photoreceptor Cell Survival

The gene encoding the WD repeat-containing protein 81 (WDR81) has recently been described as the disease locus in a consanguineous family that suffers from cerebellar ataxia, mental retardation, and quadrupedal locomotion syndrome (CAMRQ2). Adult mice from the N-ethyl-N-nitrosourea-induced mutant mouse line nur5 display tremor and an abnormal gait, as well as Purkinje cell degeneration and photoreceptor cell loss. We have used polymorphic marker mapping to demonstrate that affected nur5 mice carry a missense mutation, L1349P, in the Wdr81 gene. Moreover, homozygous nur5 mice that carry a wild-type Wdr81 transgene are rescued from the abnormal phenotype, indicating that Wdr81 is the causative gene in nur5. WDR81 is expressed in Purkinje cells and photoreceptor cells, among other CNS neurons, and like the human mutation, the nur5 modification lies in the predicted major facilitator superfamily domain of the WDR81 protein. Electron microscopy analysis revealed that a subset of mitochondria in Purkinje cell dendrites of the mutant animals displayed an aberrant, large spheroid-like structure. Moreover, immunoelectron microscopy and analysis of mitochondrial-enriched cerebellum fractions indicate that WDR81 is localized in mitochondria of Purkinje cell neurons. Because the nur5 mouse mutant demonstrates phenotypic similarities to the human disease, it provides a valuable genetic model for elucidating the pathogenic mechanism of the WDR81 mutation in CAMRQ2.

Chronology of Lateglacial ice flow reorganization and deglaciation in the Gotthard Pass area, Central Swiss Alps, based on cosmogenic 10Be and in situ14C

We reconstruct the timing of ice flow reconfiguration and deglaciation of the Central Alpine Gotthard Pass, Switzerland, using cosmogenic 10Be and in situ14C surface exposure dating. Combined with mapping of glacial erosional markers, exposure ages of bedrock surfaces reveal progressive glacier downwasting from the maximum LGM ice volume and a gradual reorganization of the paleoflow pattern with a southward migration of the ice divide. Exposure ages of ∼16–14 ka (snow corrected) give evidence for continuous early Lateglacial ice cover and indicate that the first deglaciation was contemporaneous with the decay of the large Gschnitz glacier system. In agreement with published ages from other Alpine passes, these data support the concept of large transection glaciers that persisted in the high Alps after the breakdown of the LGM ice masses in the foreland and possibly decayed as late as the onset of the Bølling warming. A younger group of ages around ∼12–13 ka records the timing of deglaciation following local glacier readvance during the Egesen stadial. Glacial erosional features and the distribution of exposure ages consistently imply that Egesen glaciers were of comparatively small volume and were following a topographically controlled paleoflow pattern. Dating of a boulder close to the pass elevation gives a minimum age of 11.1 ± 0.4 ka for final deglaciation by the end of the Younger Dryas. In situ14C data are overall in good agreement with the 10Be ages and confirm continuous exposure throughout the Holocene. However, in situ14C demonstrates that partial surface shielding, e.g. by snow, has to be incorporated in the exposure age calculations and the model of deglaciation.

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

RAD‐Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene

Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a ‘supergene’ of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a lack of genetic markers. With a view to re-establish Cepaea as a prominent model of molecular ecology, we made six laboratory crosses of Cepaea nemoralis, five of which segregated for shell ground colour (C) and the presence or absence of bands (B). First, scoring of colour and banding in 323 individuals found no recombination between the C and B loci of the supergene. Second, using restriction site–associated DNA sequencing (RAD-Seq) of two parents and 22 offspring, we identified 44 anonymous markers putatively linked to the colour (C) and banding (B) loci. The genotype of eleven of the most promising RAD-Seq markers was independently validated in the same 22 offspring, then up to a further 146 offspring were genotyped. The closest RAD-Seq markers scored are within ∼0.6 centimorgan (cM) of the C-B supergene linkage group, with the combined loci together forming a 35.8 cM linkage map of markers that flank both sides of the Cepaea C-B supergene.

A New Genetic Linkage Map of the Zygomycete Fungus Phycomyces blakesleeanus

Phycomyces blakesleeanus is a member of the subphylum Mucoromycotina. A genetic map was constructed from 121 progeny of a cross between two wild type isolates of P. blakesleeanus with 134 markers. The markers were mostly PCR-RFLPs. Markers were located on 46 scaffolds of the genome sequence, covering more than 97% of the genome. Analysis of the alleles in the progeny revealed nine or 12 linkage groups, depending on the log of the odds (LOD) score, across 1583.4 cM at LOD 5. The linkage groups were overlaid on previous mapping data from crosses between mutants, aided by new identification of the mutations in primary metabolism mutant strains. The molecular marker map, the phenotype map and the genome sequence are overall congruent, with some exceptions. The new genetic map provides a genome-wide estimate for recombination, with the average of 33.2 kb per cM. This frequency is one piece of evidence for meiosis during zygospore development in Mucoromycotina species. At the same time as meiosis, transmission of non-recombinant chromosomes is also evident in the mating process in Phycomyces. The new map provides scaffold ordering for the genome sequence and a platform upon which to identify the genes in mutants that are affected in traits of interest, such as carotene biosynthesis, phototropism or gravitropism, using positional cloning.