Human-mouse comparative mapping of the genomic region containing CDK6: localization of an evolutionary breakpoint

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

Download Full-text

Comparative Mapping Between Coho Salmon (Oncorhynchus kisutch) and Three Other Salmonids Suggests a Role for Chromosomal Rearrangements in the Retention of Duplicated Regions Following a Whole Genome Duplication Event

G3 Genes|Genome|Genetics ◽

10.1534/g3.114.012294 ◽

2014 ◽

Vol 4 (9) ◽

pp. 1717-1730 ◽

Cited By ~ 37

Author(s):

M. Kodama ◽

M. S. O. Brieuc ◽

R. H. Devlin ◽

J. J. Hard ◽

K. A. Naish

Keyword(s):

Comparative Mapping ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Coho Salmon ◽

Chromosomal Rearrangements ◽

Oncorhynchus Kisutch ◽

Duplication Event ◽

Whole Genome ◽

Genome Duplication Event ◽

Whole Genome Duplication Event

Download Full-text

Molecular and Functional Mapping of the Piebald Deletion Complex on Mouse Chromosome 14

Genetics ◽

10.1093/genetics/157.2.803 ◽

2001 ◽

Vol 157 (2) ◽

pp. 803-815

Author(s):

Jeffrey J Roix ◽

Aaron Hagge-Greenberg ◽

Dennis M Bissonnette ◽

Sandra Rodick ◽

Liane B Russell ◽

...

Keyword(s):

Mouse Chromosome ◽

System Development ◽

Genomic Region ◽

Nervous System Development ◽

Chromosome 14 ◽

Developmental Defects ◽

Oak Ridge ◽

Recessive Mutations ◽

Large Deletions ◽

Critical Regions

Abstract The piebald deletion complex is a set of overlapping chromosomal deficiencies surrounding the endothelin receptor B locus collected during the Oak Ridge specific-locus-test mutagenesis screen. These chromosomal deletions represent an important resource for genetic studies to dissect the functional content of a genomic region, and several developmental defects have been associated with mice homozygous for distinct piebald deletion alleles. We have used molecular markers to order the breakpoints for 20 deletion alleles that span a 15.7–18-cM region of distal mouse chromosome 14. Large deletions covering as much as 11 cM have been identified that will be useful for regionally directed mutagenesis screens to reveal recessive mutations that disrupt development. Deletions identified as having breakpoints positioned within previously described critical regions have been used in complementation studies to further define the functional intervals associated with the developmental defects. This has focused our efforts to isolate genes required for newborn respiration and survival, skeletal patterning and morphogenesis, and central nervous system development.

Download Full-text

Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11010027 ◽

2020 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Archana Khadgi ◽

Courtney A. Weber

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genomic Region ◽

Rubus Idaeus ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Red Raspberry ◽

Genome Wide ◽

A Genome ◽

Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

Download Full-text

An FGA Frameshift Variant Associated with Afibrinogenemia in Dachshunds

Genes ◽

10.3390/genes12071065 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1065

Author(s):

Reinhard Mischke ◽

Julia Metzger ◽

Ottmar Distl

Keyword(s):

Protein Sequence ◽

Sanger Sequencing ◽

Selective Breeding ◽

Genome Wide Association Study ◽

Frameshift Mutation ◽

Homozygosity Mapping ◽

Genomic Region ◽

Severe Bleeding ◽

Genome Wide ◽

A Genome

Congenital fibrinogen disorders are very rare in dogs. Cases of afibrinogenemia have been reported in Bernese Mountain, Bichon Frise, Cocker Spaniel, Collie, Lhasa Apso, Viszla, and St. Bernard dogs. In the present study, we examined four miniature wire-haired Dachshunds with afibrinogenemia and ascertained their pedigree. Homozygosity mapping and a genome-wide association study identified a candidate genomic region at 50,188,932–64,187,680 bp on CFA15 harboring FGB (fibrinogen beta chain), FGA (fibrinogen alpha chain), and FGG (fibrinogen gamma-B chain). Sanger sequencing of all three fibrinogen genes in two cases and validation of the FGA-associated mutation (FGA:g.6296delT, NC_006597.3:g.52240694delA, rs1152388481) in pedigree members showed a perfect co-segregation with afibrinogenemia-affected phenotypes, obligate carriers, and healthy animals. In addition, the rs1152388481 variant was validated in 393 Dachshunds and samples from 33 other dog breeds. The rs1152388481 variant is predicted to modify the protein sequence of both FGA transcripts (FGA201:p.Ile486Met and FGA-202:p.Ile555Met) leading to proteins truncated by 306 amino acids. The present data provide evidence for a novel FGA truncating frameshift mutation that is very likely to explain the cases of severe bleeding due to afibrinogenemia in a Dachshund family. This mutation has already been spread in Dachshunds through carriers before cases were ascertained. Genetic testing allows selective breeding to prevent afibrinogenemia-affected puppies in the future.

Download Full-text

white+ Transgene Insertions Presenting a Dorsal/Ventral Pattern Define a Single Cluster of Homeobox Genes That Is Silenced by the Polycomb-group Proteins in Drosophila melanogaster

Genetics ◽

10.1093/genetics/149.1.257 ◽

1998 ◽

Vol 149 (1) ◽

pp. 257-275 ◽

Cited By ~ 4

Author(s):

Sophie Netter ◽

Marie-Odile Fauvarque ◽

Ruth Diez del Corral ◽

Jean-Maurice Dura ◽

Dario Coen

Keyword(s):

Chromatin Structure ◽

Target Genes ◽

Position Effect ◽

Phenotypic Expression ◽

Positional Information ◽

Genomic Region ◽

Polycomb Group ◽

Position Effect Variegation ◽

Trithorax Group ◽

Clear Cut

AbstractWe used the white gene as an enhancer trap and reporter of chromatin structure. We collected white+ transgene insertions presenting a peculiar pigmentation pattern in the eye: white expression is restricted to the dorsal half of the eye, with a clear-cut dorsal/ventral (D/V) border. This D/V pattern is stable and heritable, indicating that phenotypic expression of the white reporter reflects positional information in the developing eye. Localization of these transgenes led us to identify a unique genomic region encompassing 140 kb in 69D1–3 subject to this D/V effect. This region contains at least three closely related homeobox-containing genes that are constituents of the iroquois complex (IRO-C). IRO-C genes are coordinately regulated and implicated in similar developmental processes. Expression of these genes in the eye is regulated by the products of the Polycomb -group (Pc-G) and trithorax-group (trx-G) genes but is not modified by classical modifiers of position-effect variegation. Our results, together with the report of a Pc -G binding site in 69D, suggest that we have identified a novel cluster of target genes for the Pc-G and trx-G products. We thus propose that ventral silencing of the whole IRO-C in the eye occurs at the level of chromatin structure in a manner similar to that of the homeotic gene complexes, perhaps by local compaction of the region into a heterochromatin-like structure involving the Pc-G products.

Download Full-text