A Second-Generation Genetic Linkage Map of the Domestic Dog, Canis familiaris

Abstract Purebred strains, pronounced phenotypic variation, and a high incidence of heritable disease make the domestic dog uniquely suited to complement genetic analyses in humans and mice. A comprehensive genetic linkage map would afford many opportunities in dogs, ranging from the positional cloning of disease genes to the dissection of quantitative differences in size, shape, and behavior. Here we report a canine linkage map with the number of mapped loci expanded to 276 and 10-cM coverage extended to 75–90% of the genome. Most of the 38 canine autosomes are likely represented in the collection of 39 autosomal linkage groups. Eight markers were sufficiently informative to detect linkage at distances of 10–13 cM, yet remained unlinked to any other marker. Taken together, the results suggested a genome size of about 27 M. As in other species, the genetic length varied between sexes, with the female autosomal distance being ∼1.4-fold greater than that of male meioses. Fifteen markers anchored well-described genes on the map, thereby serving as landmarks for comparative mapping in dogs. We discuss the utility of the current map and outline steps necessary for future map improvement.

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Integration of the Aedes aegypti Mosquito Genetic Linkage and Physical Maps

Genetics ◽

10.1093/genetics/157.3.1299 ◽

2001 ◽

Vol 157 (3) ◽

pp. 1299-1305

Author(s):

S E Brown ◽

D W Severson ◽

L A Smith ◽

D L Knudson

Keyword(s):

Aedes Aegypti ◽

Linkage Map ◽

Genetic Linkage ◽

Positional Cloning ◽

Genetic Linkage Map ◽

Physical Map ◽

Chromosome 1 ◽

Chromosome 2 ◽

Metaphase Chromosomes ◽

Physical Maps

Abstract Two approaches were used to correlate the Aedes aegypti genetic linkage map to the physical map. STS markers were developed for previously mapped RFLP-based genetic markers so that large genomic clones from cosmid libraries could be found and placed to the metaphase chromosome physical maps using standard FISH methods. Eight cosmids were identified that contained eight RFLP marker sequences, and these cosmids were located on the metaphase chromosomes. Twenty-one cDNAs were mapped directly to metaphase chromosomes using a FISH amplification procedure. The chromosome numbering schemes of the genetic linkage and physical maps corresponded directly and the orientations of the genetic linkage maps for chromosomes 2 and 3 were inverted relative to the physical maps. While the chromosome 2 linkage map represented essentially 100% of chromosome 2, ∼65% of the chromosome 1 linkage map mapped to only 36% of the short p-arm and 83% of the chromosome 3 physical map contained the complete genetic linkage map. Since the genetic linkage map is a RFLP cDNA-based map, these data also provide a minimal estimate for the size of the euchromatic regions. The implications of these findings on positional cloning in A. aegypti are discussed.

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A genetic linkage map of mouse chromosome 10: localization of eighteen molecular markers using a single interspecific backcross.

Genetics ◽

10.1093/genetics/125.4.855 ◽

1990 ◽

Vol 125 (4) ◽

pp. 855-866

Author(s):

M J Justice ◽

L D Siracusa ◽

D J Gilbert ◽

N Heisterkamp ◽

J Groffen ◽

...

Keyword(s):

Linkage Map ◽

Mouse Chromosome ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Molecular Genetic ◽

Interspecific Backcross ◽

Mus Spretus ◽

Chromosome 10 ◽

Genetic Length ◽

First Time

Abstract Interspecific mouse backcross analysis was used to generate a molecular genetic linkage map of mouse chromosome 10. The map locations of the Act-2, Ahi-1, Bcr, Braf, Cdc-2a, Col6a-1, Col6a-2, Cos-1, Esr, Fyn, Gli, Ifg, Igf-1, Myb, Pah, pgcha, Ros-1 and S100b loci were determined. These loci extend over 80% of the genetic length of the chromosome, providing molecular access to many regions of chromosome 10 for the first time. The locations of the genes mapped in this study extend the known regions of synteny between mouse chromosome 10 and human chromosomes 6, 10, 12 and 21, and reveal a novel homology segment between mouse chromosome 10 and human chromosome 22. Several loci may lie close to, or correspond to, known mutations. Preferential transmission of Mus spretus-derived alleles was observed for loci mapping to the central region of mouse chromosome 10.

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A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms

Development ◽

10.1242/dev.123.1.451 ◽

1996 ◽

Vol 123 (1) ◽

pp. 451-460 ◽

Cited By ~ 8

Author(s):

E.W. Knapik ◽

A. Goodman ◽

O.S. Atkinson ◽

C.T. Roberts ◽

M. Shiozawa ◽

...

Keyword(s):

Linkage Map ◽

Genetic Markers ◽

Genetic Linkage ◽

Positional Cloning ◽

Genetic Linkage Map ◽

Physical Map ◽

Sequence Length ◽

Mapping Tool ◽

Length Polymorphisms ◽

Simple Sequence

The ultimate informativeness of the zebrafish mutations described in this issue will rest in part on the ability to clone these genes. However, the genetic infrastructure required for the positional cloning in zebrafish is still in its infancy. Here we report a reference cross panel of DNA, consisting of 520 F2 progeny (1040 meioses) that has been anchored to a zebrafish genetic linkage map by 102 simple sequence length polymorphisms. This reference cross DNA provides: (1) a panel of DNA from the cross that was used to construct the genetic linkage map, upon which polymorphic gene(s) and genetic markers can be mapped; (2) a fine order mapping tool, with a maximum resolution of 0.1 cM; and (3) a foundation for the development of a physical map (an ordered array of clones each containing a known portion of the genome). This reference cross DNA will serve as a resource enabling investigators to relate genes or genetic markers directly to a single genetic linkage map and avoid the problem of integrating different maps with different genetic markers, as must be currently done when using randomly amplified polymorphic DNA markers, or as has occurred with human genetic linkage maps.

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Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa

Genome ◽

10.1139/g07-113 ◽

2008 ◽

Vol 51 (3) ◽

pp. 169-176 ◽

Cited By ~ 38

Author(s):

Keita Suwabe ◽

Colin Morgan ◽

Ian Bancroft

Keyword(s):

Molecular Markers ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Linkage Groups ◽

Indel Markers ◽

A Genome ◽

High Level ◽

High Degree ◽

Genetic Integration

An integrated linkage map between B. napus and B. rapa was constructed based on a total of 44 common markers comprising 41 SSR (33 BRMS, 6 Saskatoon, and 2 BBSRC) and 3 SNP/indel markers. Between 3 and 7 common markers were mapped onto each of the linkage groups A1 to A10. The position and order of most common markers revealed a high level of colinearity between species, although two small regions on A4, A5, and A10 revealed apparent local inversions between them. These results indicate that the A genome of Brassica has retained a high degree of colinearity between species, despite each species having evolved independently after the integration of the A and C genomes in the amphidiploid state. Our results provide a genetic integration of the Brassica A genome between B. napus and B. rapa. As the analysis employed sequence-based molecular markers, the information will accelerate the exploitation of the B. rapa genome sequence for the improvement of oilseed rape.

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Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

BMC Genomics ◽

10.1186/1471-2164-11-594 ◽

2010 ◽

Vol 11 (1) ◽

Cited By ~ 49

Author(s):

Jinsong Xu ◽

Xiaoju Qian ◽

Xiaofeng Wang ◽

Ruiyuan Li ◽

Xiaomao Cheng ◽

...

Keyword(s):

Brassica Napus ◽

Linkage Map ◽

Ssr Markers ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

A Genome

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Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa

Genome ◽

10.1139/g2012-066 ◽

2012 ◽

Vol 55 (12) ◽

pp. 813-823 ◽

Cited By ~ 18

Author(s):

Berisso Kebede ◽

Kuljit Cheema ◽

David L. Greenshields ◽

Changxi Li ◽

Gopalan Selvaraj ◽

...

Keyword(s):

Linkage Map ◽

Ssr Markers ◽

Brassica Rapa ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Recombinant Inbred Lines ◽

Phenotypic Variance ◽

Environment Interaction ◽

Seed Color ◽

A Genome

A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ∼70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B1S1 population (F1 backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B1S2). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa.

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Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape)

Genome ◽

10.1139/g95-149 ◽

1995 ◽

Vol 38 (6) ◽

pp. 1122-1131 ◽

Cited By ~ 236

Author(s):

I. A. P. Parkin ◽

A. G. Sharpe ◽

D. J. Keith ◽

D. J. Lydiate

Keyword(s):

Brassica Napus ◽

Linkage Map ◽

Oilseed Rape ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Resynthesized Brassica Napus ◽

Disomic Inheritance ◽

A Genome ◽

C Genome ◽

Homoeologous Chromosomes

A genetic linkage map consisting of 399 RFLP-defined loci was generated from a cross between resynthesized Brassica napus (an interspecific B. rapa × B. oleracea hybrid) and "natural" oilseed rape. The majority of loci exhibited disomic inheritance of parental alleles demonstrating that B. rapa chromosomes were each pairing exclusively with recognisable A-genome homologues in B. napus and that B. oleracea chromosomes were pairing similarly with C-genome homologues. This behaviour identified the 10 A genome and 9 C genome linkage groups of B. napus and demonstrated that the nuclear genomes of B. napus, B. rapa, and B. oleracea have remained essentially unaltered since the formation of the amphidiploid species, B. napus. A range of unusual marker patterns, which could be explained by aneuploidy and nonreciprocal translocations, were observed in the mapping population. These chromosome abnormalities were probably caused by associations between homoeologous chromosomes at meiosis in the resynthesized parent and the F1 plant leading to nondisjunction and homoeologous recombination.Key words: genetic linkage map, homoeologous recombination, Brassica rapa, Brassica oleracea, genome organization.

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An intervarietal genetic linkage map of Indian bread wheat (Triticum aestivum L.) and QTL maps for some metric traits

Genetics Research ◽

10.1017/s0016672307008828 ◽

2007 ◽

Vol 89 (3) ◽

pp. 165-179 ◽

Cited By ~ 4

Author(s):

E. NALINI ◽

S. G. BHAGWAT ◽

N. JAWALI

Keyword(s):

Triticum Aestivum ◽

Linkage Map ◽

Bread Wheat ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Flag Leaf ◽

D Genome ◽

Wheat Varieties ◽

A Genome ◽

Metric Traits

SummaryBread wheat (Triticum aestivum L.) exhibits very narrow genetic diversity and hence there is high relatedness among cultivated varieties. However, a population generated from an intervarietal cross, with the parents differing in a large number of traits, could lead to the generation of QTL maps which will be useful in practice. In this report a genetic linkage map of wheat is constructed using a cross between two Indian bread wheat varieties: Sonalika and Kalyansona. The linkage map consisted of 236 markers and spanned a distance of 3639 cM, with 1211·2 cM for the A genome, 1669·2 cM for the B genome, 192·4 cM for the D genome and 566·2 cM for unassigned groups. Linkage analysis defined 37 linkage groups of which 24 were assigned to 17 chromosomes. The genetic map was used to identify QTLs by composite internal mapping (CIM) for three metric traits, viz. culm length (CL), flag leaf length (FLL) and flag leaf breadth (FLB). Of 25 QTLs identified in this study, 15 have not been reported previously. Multitrait CIM (MCIM) analysis was carried out for traits that were significantly correlated such as FLB–FLL and CL–FLB–FLL. Detection of a large number of QTLs for the three traits analysed suggests that in parent cultivars that are not too diverse, the differences at genetic level detected as polymorphisms may be mostly associated with QTLs for the observed differences.

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