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.     

High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

A high-density linkage map was constructed for an F2 population derived from an Interspecific cross of cultivated allotetraploid species between Gossypium hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the Interspecific cross of ＂CRI 36 × Hal 7124＂ were genotyped at I 252 polymorphic loci Including a novel marker system, target region amplification polymorphism （TRAP）. The map consists of 1 097 markers, including 697 simple se- quence repeats （SSRs）, 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were Identified In tetraploid cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.     

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/.     

Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop,the Octoploid Cultivated Strawberry (Fragaria × ananassa)

Cultivated strawberry (Fragaria × ananassa) is a genetically complex allo-octoploid crop with 28 pairs of chromosomes (2n = 8x = 56) for which a genome sequence is not yet available. The diploid Fragaria vesca is considered the donor species of one of the octoploid sub-genomes and its available genome sequence can be used as a reference for genomic studies. A wide number of strawberry cultivars are stored in ex situ germplasm collections world-wide but a number of previous studies have addressed the genetic diversity present within a limited number of these collections. Here, we report the development and application of two platforms based on the implementation of Diversity Array Technology (DArT) markers for high-throughput genotyping in strawberry. The first DArT microarray was used to evaluate the genetic diversity of 62 strawberry cultivars that represent a wide range of variation based on phenotype, geographical and temporal origin and pedigrees. A total of 603 DArT markers were used to evaluate the diversity and structure of the population and their cluster analyses revealed that these markers were highly efficient in classifying the accessions in groups based on historical, geographical and pedigree-based cues. The second DArTseq platform took benefit of the complexity reduction method optimized for strawberry and the development of next generation sequencing technologies. The strawberry DArTseq was used to generate a total of 9,386 SNP markers in the previously developed ‘232’ × ‘1392’ mapping population, of which, 4,242 high quality markers were further selected to saturate this map after several filtering steps. The high-throughput platforms here developed for genotyping strawberry will facilitate genome-wide characterizations of large accessions sets and complement other available options.     

Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715–1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.     

Linkage Map of Escherichia coli K-12, Edition 10: The Physical Map

A physical map, EcoMap10, of the now completely sequenced Escherichia coli chromosome is presented. Calculated genomic positions for the eight restriction enzymes BamHI, HindIII, EcoRI, EcoRV, BglI, KpnI, PstI, and PvuII are depicted. Both sequenced and unsequenced Kohara/Isono miniset clones are aligned to this calculated restriction map. DNA sequence searches identify the precise locations of insertion sequence elements and repetitive extragenic palindrome clusters. EcoGene10, a revised set of genes and functionally uncharacterized open reading frames (ORFs), is also depicted on EcoMap10. The complete set of unnamed ORFs in EcoGene10 are assigned provisional names beginning with the letter “y” by using a systematic nomenclature.     

A SNP Based High-Density Linkage Map of Apis cerana Reveals a High Recombination Rate Similar to Apis mellifera

Background

The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee.

Results

F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM.

Conclusion

We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.     

A Preliminary Linkage Map of the Tick, Ixodes scapularis

A linkage map of the Ixodes scapularis genome was constructed based upon segregation amongst 127 loci. These included 84 random amplified polymorphic DNA (RAPD) markers, 32 Sequence-Tagged RAPD (STAR) markers, 5 cDNAs, and 5 microsatellites in 232 F₁ intercross progeny from a single, field-collected P₁ female. A preliminary linkage map of 616 cM was generated across 14 linkage groups with one marker every 10.8 cM. Assuming a genome size of ∼10⁹ bp, the relationship of physical to genetic distance is ∼300 kb/cM in the I. scapularis genome. This revised version was published online in July 2006 with corrections to the Cover Date.     

A Linkage Map of the Canine Genome

A genetic linkage map of the canine genome has been developed by typing 150 microsatellite markers using 17 three-generation pedigrees, composed of 163 F₂individuals. One hundred and thirty-nine markers were linked to at least one other marker with a lod score ≥ 3.0, identifying 30 linkage groups. The largest chromosome had 9 markers spanning 106.1 cM. The average distance between markers was 14.03 cM, and the map covers an estimated 2073 cM. Eleven markers were informative on the mapping panel, but were unlinked to any other marker. These likely represent single markers located on small, distinct canine chromosomes. This map will be the initial resource for mapping canine traits of interest and serve as a foundation for development of a comprehensive canine genetic map.     

A Microsatellite Linkage Map of the Porcine Genome

We report the most extensive genetic linkage map for a livestock species produced to date. We have linked 376 microsatellite (MS) loci with seven restriction fragment length polymorphic loci in a backcross reference population. The 383 markers were placed into 24 linkage groups which span 1997 cM. Seven additional MS did not fall into a linkage group. Linkage groups are assigned to 13 autosomes and the X chromosome (haploid n = 19). This map provides the basis for genetic analysis of quantitative inheritance of phenotypic and physiologic traits in swine.     

Linkage Map of the Honey Bee, Apis Mellifera, Based on Rapd Markers

A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkage groups. We estimate the total genome size to be ~3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species.     

A Genetic Linkage Map for Cattle

We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL).     

A Review of Photoperiodic Flowering Research in Strawberry (Fragaria spp.)

Throughout the last century many researchers have examined the physiology and molecular events surrounding an important milestone in plant development—the transition to flowering. Breakthroughs over the last decade have brought great molecular resolution to the process, allowing researchers to peer into the former black box that once obfuscated the mechanisms governing this evolutionarily and agriculturally important transition. Foundational studies in the physiology of flowering regulation have been performed in many species, but the greatest mechanistic clarity has come from studies in Arabidopsis thaliana. At the same time parallel efforts by researchers, nurserymen and farmers queried the wide variation in strawberry (Fragaria spp) flowering habits. The complex ranging flowering behaviors driven by the cumbersome genetics of the cultivated octoploid strawberry have slowed the understanding in this crop, yet a remarkable literature exists that documents examination of flowering in the genus. Strawberry is a high-value crop and a comprehensive understanding of flowering behaviors is required to optimize production and streamline breeding efforts. Studies in strawberry may offer new insights into quantitative mechanisms that shape the floral transition, and new mechanisms may be identified. Moreover, strawberry is a member of the Rosaceae, a family containing valuable fruit, nut and ornamental crops. Findings in strawberry will likely translate well to other crops in the family. This review compiles a century of observations and experimental results, and looks forward to the unique opportunities that may arise from contemporary studies of flowering time in this genus.     

The Control of Runner Development in the Strawberry Fragaria ananassa Duch

Factors controlling runnering of strawberry plants were studiedunder controlled and semi-controlled environments. Increasinglylong exposures to conditions favourable for runnering causeda subsequent increase in number of runners, their total length,number of daughters, and of dry matter produced by mother plants.Leaf and crown numbers of the mother plant showed no such parallelincrease. Temperature supplement to foliage, combined with alight interruption in the dark period, produced the greatestvegetative effect-except again on leaf number-when comparedto either factor individually, normal day extension for threehours by itself or combined with temperature supplement. Itwas suggested that the promotive effects of temperature andphotoperiod on runnering were due to increased activation ofvegetative buds on the rosette crown. Upon comparing constantand diurnally fluctuating temperatures under a constant longphoto-period in the phytotron it was found that, while all othermeasured vegetative criteria were closely similar, the totalrunner length produced by plants under fluctuating temperatureswas almost double that of those under constant temperatures.A temperature gradient from root to shoot stimulated vegetativegrowth in comparison to a gradient in the opposite directionand to lack of such gradient, irrespective of whether the temperaturecommon to both root and shoot was high or low. This was interpretedas resulting from either different temperature requirementsfor aerial and subterranean organs or from the occurrence oftranslocation gradients of substances which promote vegetativedevelopment of the shoots, e.g. kinins and gibberellin-likesubstances. The time interval between rooting of daughter plants and onsetof runnering was increased the later the rooting occurred, possiblydue to the advancing seasonal decline in conditions favourablefor vegetative development. The positional influence of theorder of the daughter along the runner chain, which was markedin flowering, was not found.     

A Genetic Linkage Map of the Male Goat Genome

This paper presents a first genetic linkage map of the goat genome. Primers derived from the flanking sequences of 612 bovine, ovine and goat microsatellite markers were gathered and tested for amplification with goat DNA under standardized PCR conditions. This screen made it possible to choose a set of 55 polymorphic markers that can be used in the three species and to define a panel of 223 microsatellites suitable for the goat. Twelve half-sib paternal goat families were then used to build a linkage map of the goat genome. The linkage analysis made it possible to construct a meiotic map covering 2300 cM, i.e., >80% of the total estimated length of the goat genome. Moreover, eight cosmids containing microsatellites were mapped by fluorescence in situ hybridization in goat and sheep. Together with 11 microsatellite-containing cosmids previously mapped in cattle (and supposing conservation of the banding pattern between this species and the goat) and data from the sheep map, these results made the orientation of 15 linkage groups possible. Furthermore, 12 coding sequences were mapped either genetically or physically, providing useful data for comparative mapping.     

Microsatellite markers for Fragaria from ‘Strawberry Festival’ expressed sequence tags

We present 37 microsatellite primer pairs developed from a cDNA library of Fragaria ^xananassa Duch. cv. Strawberry Festival. Polymorphism was high and the number of presumptive alleles of 13 expressed sequence tag–simple sequence repeats (EST–SSRs) in 70 strawberry cultivars ranged from five to 32 per primer pairs, averaging 16.1. Cross‐species amplification was also high and ranged from 89% in Fragaria vesca L. to 100% in the progenitor species of octoploid strawberry, Fragaria chiloensis (L.) Duch. and Fragaria virginiana Duch.     

Fruit Set and Growth in Strawberry, Fragaria x ananassa Duch.

The application of GA₃in aqueous solution to leaves or flowersof hermaphrodite cultivars of strawberry, Redgauntlet and Rabunda,prevented growth of the receptacle despite hand pollination.This inhibitory effect occurred only when GA₃ was applied priorto anthesis. Although viable pollen was produced and germinatedto grow down the styles of treated plants, no seeds were formed.Receptacle growth failed underneath the unfertilized carpels,but the basal region devoid of carpels enlarged and ripened.The effect of GA₃ was the same in vivo and for flowers grownin vitro. ABA and BAP also inhibited growth of pollinated flowersin vitro, but neither substance stimulated growth of the baseof the receptacle. 2-NOA stimulated receptacle growth of pollinatedflowers but did not overcome the inhibitory effect of GA₃. Removal of fertile carpels 9 days after pollination preventedfurther receptacle growth. GA₃ treatment of the bare receptaclere-started growth but was less effective than 2-NOA. No growth substance treatment induced parthenocarpic developmentin these cultivars when unopened buds were emasculated and culturedwithout pollination, although GA₃ induced some swelling of thereceptacle base. Fragaria x ananassa Duch., strawberry fruit set, fruit growth, growth regulators     

A High-density Linkage Map of Lotus japonicus Based on AFLP and SSR Markers

A collection of 94 F₆ individuals derived from crosses between Lotus japonicus, Gifu B-129 (G) and Miyakojima MG-20 (M) were used for mapping. By using the HEGS running system, 427 EcoRI/MseI primer pairs were selected to generate a total of 2053 markers, consisting of 739 G-associated dominant markers, 674 M-associated dominant markers, 640 co-dominant markers, 95 SSR markers and 2 dCAPS markers. Excluding heavily distorted markers, 1588 were mapped to six chromosomes of the L. japonicus genome based on the 97 reference markers. This linkage map consisted of 1023 unique markers (excluding duplicated markers) and covered a total of 508.5 cM of the genome with an average chromosome length of 84.7 cM and interval distance of 0.50 cM. Fifteen quantitative traits loci for eight morphological traits were also mapped. This linkage map will provide a useful framework for physical map construction in L. japonicus in the near future.Key words: Lotus japonicus, AFLP, SSR, linkage map, HEGS (high efficiency genome scanning)     

A Linkage Map of Endogenous Murine Leukemia Proviruses

Thirty endogenous proviruses belonging to the modified polytropic (Mpmv) class of murine leukemia virus (MLV) were identified by proviral-cellular DNA junction fragment segregation in several sets of recombinant inbred mice. Twenty-six Mpmv loci were mapped to chromosomal regions by matching proviral strain distribution patterns to those of previously assigned genes. Like other endogenous nonecotropic MLVs, Mpmv loci were present on several chromosomes in all strains examined. We pooled recombinant inbred strain linkage data from 110 MLV loci and selected marker genes in order to construct a chromosomal linkage map. Every mouse chromosome was found to harbor at least one proviral insertion, and several regions contained multiple integrations. However, the overall distribution of the 110 mapped proviruses did not deviate significantly from a random distribution. Because of their polymorphism in inbred strains of mice, and the ability to score as many as 57 proviruses per strain using only three hybridization probes, the nonecotropic MLVs mapped in common strains of mice offer a significant advantage over older methods (e.g., biochemical or individual restriction fragment polymorphisms) as genetic markers. These endogenous insertion elements should also be useful for assessing strain purity, and for studying the relatedness of common and not-so-common inbred strains.