| 1. |
- Groenen, Martien, et al.
(författare)
-
A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
- 2009
-
Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 19:3, s. 510-519
-
Tidskriftsartikel (refereegranskat)abstract
- The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 SNPs on three existing mapping populations in chicken; the Wageningen (WU), East Lansing (EL) and Uppsala (UPP) mapping populations. As many as 8599 SNPs could be included bringing the total number of markers in the current consensus linkage map to 9268. The total length of the sex average map is 3228 cM, considerably smaller than previous estimates using the WU and EL populations, reflecting the higher quality of the new map. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. Sex-specific analysis and comparisons of the maps based on the three individual populations showed prominent heterogeneity in recombination rates between populations but no significant heterogeneity between sexes. The recombination rates in the F1 Red Jungle fowl/White Leghorn males and females were significantly lower compared with those in the WU broiler population, consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. The recombination rate varied considerably among chromosomes as well as along individual chromosomes. An analysis of the sequence composition at recombination hot and cold spots revealed a strong positive correlation between GC-rich sequences and high recombination rates. The GC-rich cohesin binding sites in particular stood out from other GC-rich sequences with a 3.4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding.
|
|
| 2. |
- Wahlberg, Per, et al.
(författare)
-
A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination
- 2007
-
Ingår i: Cytogenetic and Genome Research. - : S. Karger AG. - 1424-8581 .- 1424-859X. ; 117:1-4, s. 22-29
-
Tidskriftsartikel (refereegranskat)abstract
- A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds.
|
|
| 3. |
- Wahlberg, Per, et al.
(författare)
-
Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight
- 2009
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10, s. 248-
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: We have performed Quantitative Trait Loci (QTL) analysis of an F(2) intercross between two chicken lines divergently selected for juvenile body-weight. In a previous study 13 identified loci with effects on body-weight, only explained a small proportion of the large variation in the F(2) population. Epistatic interaction analysis however, indicated that a network of interacting loci with large effect contributed to the difference in body-weight of the parental lines. This previous analysis was, however, based on a sparse microsatellite linkage map and the limited coverage could have affected the main conclusions. Here we present a revised QTL analysis based on a high-density linkage map that provided a more complete coverage of the chicken genome. Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines. RESULTS: We constructed a linkage map comprising 434 genetic markers, covering 31 chromosomes but leaving seven microchromosomes uncovered. The analysis showed that seven regions harbor QTL that influence growth. The pair-wise interaction analysis identified 15 unique QTL pairs and notable is that nine of those involved interactions with a locus on chromosome 7, forming a network of interacting loci. The analysis of ~13,000 SNPs showed that a substantial proportion of the genetic variation present in the founder population has been lost in either of the two selected lines since ~60% of the SNPs polymorphic among lines showed fixation in one of the lines. With the current marker coverage and QTL map resolution we did not observe clear signs of selective sweeps within QTL intervals. CONCLUSION: The results from the QTL analysis using the new improved linkage map are to a large extent in concordance with our previous analysis of this pedigree. The difference in body-weight between the parental chicken lines is caused by many QTL each with a small individual effect. Although the increased chromosomal marker coverage did not lead to the identification of additional QTL, we were able to refine the localization of QTL. The importance of epistatic interaction as a mechanism contributing significantly to the remarkable selection response was further strengthened because additional pairs of interacting loci were detected with the improved map.
|
|
