scholarly journals An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 282-295 ◽  
Author(s):  
Elizabeth S Jones ◽  
Natalia L Mahoney ◽  
Michael D Hayward ◽  
Ian P Armstead ◽  
J Gilbert Jones ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Linkage Map ◽  
Genetic Map ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Genetic Linkage Map ◽  
Population Based ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

Genetic map of triticale compiling DArT, SSR, and AFLP markers

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 391-401 ◽  
Author(s):  
M. Tyrka ◽  
P.T. Bednarek ◽  
A. Kilian ◽  
M. Wędzony ◽  
T. Hura ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Genetic Linkage Map ◽  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Structural Rearrangements ◽  
Linkage Groups ◽  
Array Technology ◽  
Dh Lines ◽  
Simple Sequence

A set of 90 doubled haploid (DH) lines derived from F1plants that originated from a cross between × Triticosecale Wittm. ‘Saka3006’ and ×Triticosecale Wittm. ‘Modus’, via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

An SSR-based genetic linkage map for perennial ryegrass (Lolium perenne L.)

2002 ◽  
Vol 105 (4) ◽  
pp. 577-584 ◽  
Author(s):  
E. Jones ◽  
M. Dupal ◽  
J. Dumsday ◽  
L. Hughes ◽  
J. Forster
Keyword(s):  
Linkage Map ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Lolium Perenne L

A framework linkage map of perennial ryegrass based on SSR markers

Genome ◽  
2006 ◽  
Vol 49 (4) ◽  
pp. 354-364 ◽  
Author(s):  
G P Gill ◽  
P L Wilcox ◽  
D J Whittaker ◽  
R A Winz ◽  
P Bickerstaff ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Marker Loci ◽  
Simple Sequence

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher® libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.Key words: Framework map, perennial ryegrass, SSR, simple sequence repeat, GeneThresher, Lolium perenne.

scholarly journals A genetic linkage map for cattle.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 619-639 ◽  
Author(s):  
M D Bishop ◽  
S M Kappes ◽  
J W Keele ◽  
R T Stone ◽  
S L Sunden ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Markers ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Bovine Genome ◽  
Type I ◽  
Linkage Groups ◽  
Y Chromosomes ◽  
Economic Trait

Abstract 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).

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

scholarly journals A genetic linkage map for the domesticated silkworm, Bombyx mori, based on restriction fragment length polymorphisms

1995 ◽  
Vol 66 (2) ◽  
pp. 109-126 ◽  
Author(s):  
Jinrui Shi ◽  
David G. Heckel ◽  
Marian R. Goldsmith
Keyword(s):  
Linkage Map ◽  
Bombyx Mori ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Restriction Fragment Length Polymorphisms ◽  
Genetic Maps ◽  
Crossing Over ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

SummaryWe present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori, based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.

scholarly journals Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1277-1288
Author(s):  
Stephen L Johnson ◽  
Michael A Gates ◽  
Michele Johnson ◽  
William S Talbot ◽  
Sally Horne ◽  
...  
Keyword(s):  
Linkage Group ◽  
Linkage Analysis ◽  
Genetic Analysis ◽  
Linkage Map ◽  
Rapid Method ◽  
Genetic Map ◽  
Dna Polymorphisms ◽  
Linkage Groups

Abstract The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.

scholarly journals A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Guosong Zhang ◽  
Jie Li ◽  
Jiajia Zhang ◽  
Xia Liang ◽  
Tao Wang ◽  
...  
Keyword(s):  
Sex Determination ◽  
Linkage Map ◽  
Candidate Genes ◽  
Genetic Map ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
High Density ◽  
Hypoxia Tolerance ◽  
Genome Wide ◽  
Pelteobagrus Vachelli

Abstract Background A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. Results By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map’ length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. Conclusions We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

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