A SNP/microsatellite genetic linkage map of the Atlantic cod (Gadus morhua)

A first genetic linkage map of the Atlantic cod ( Gadus morhua ) was produced, based on segregation data from 12 full-sib families of Norwegian origin. The map contained 174 single nucleotide polymorphism markers and 33 microsatellites, distributed on 25 linkage groups and had a length of 1225 cM. A significant difference in recombination rates between sexes was found, the average ratio of female:male recombination rates being 1.78 ± 1.62 (SD).     

Genome-wide variation in the human and fruitfly: a comparison

Average levels of nucleotide diversity are ten-fold lower in humans than in the fruitfly, Drosophila melanogaster. Despite this difference, apparently as a result of a lower population size, patterns of genomic diversity are strikingly similar in being correlated with local rates of recombination, and influenced by similar interactions between positive natural selection and recombination. Both species also show lower levels of variation on average in non-African compared to African populations, reflecting a similar evolutionary history and perhaps both natural selection and founder effects in new environments.     

Bayesian inference of fine-scale recombination rates using population genomic data

Recently, several statistical methods for estimating fine-scale recombination rates using population samples have been developed. However, currently available methods that can be applied to large-scale data are limited to approximated likelihoods. Here, we developed a full-likelihood Markov chain Monte Carlo method for estimating recombination rate under a Bayesian framework. Genealogies underlying a sampling of chromosomes are effectively modelled by using marginal individual single nucleotide polymorphism genealogies related through an ancestral recombination graph. The method is compared with two existing composite-likelihood methods using simulated data.Simulation studies show that our method performs well for different simulation scenarios. The method is applied to two human population genetic variation datasets that have been studied by sperm typing. Our results are consistent with the estimates from sperm crossover analysis.     

High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline

Since the publication of the first comprehensive linkage map for the laboratory mouse, the architecture of recombination as a basic biological process has become amenable to investigation in mammalian model organisms. Here we take advantage of high-density genotyping and the unique pedigree structure of the incipient Collaborative Cross to investigate the roles of sex and genetic background in mammalian recombination. Our results confirm the observation that map length is longer when measured through female meiosis than through male meiosis, but we find that this difference is modified by genotype at loci on both the X chromosome and the autosomes. In addition, we report a striking concentration of crossovers in the distal ends of autosomes in male meiosis that is absent in female meiosis. The presence of this pattern in both single- and double-recombinant chromosomes, combined with the absence of a corresponding asymmetry in the distribution of double-strand breaks, indicates a regulated sequence of events specific to male meiosis that is anchored by chromosome ends. This pattern is consistent with the timing of chromosome pairing and evolutionary constraints on male recombination. Finally, we identify large regions of reduced crossover frequency that together encompass 5% of the genome. Many of these “cold regions” are enriched for segmental duplications, suggesting an inverse local correlation between recombination rate and mutation rate for large copy number variants.     

A microsatellite linkage map for Atlantic salmon (Salmo salar)

A linkage map of the Atlantic salmon is described here consisting of 15 linkage groups containing 50 microsatellite loci with a 14 additional unlinked markers (including three allozymes). The map shows the largest sex-specific recombination rate differences so far found in any vertebrate species (3.92:1 female:male). Homologies with previous linkage mapping studies of Atlantic salmon and rainbow trout are described. An in silico search of the Genbank database carried out using the microsatellites used in the mapping process identified significant matches between the flanking regions of the microsatellite SS11 and the calcium-binding mitochondrial carrier protein, 'Aralar1'.     

Differences in recombination rates on chromosome 23 between German Angus and German Simmental and breed specific linkage mapping

Five paternal half sib families of German Angus (GA) (n = 428) and six of German Simmental (GS) (n = 378) including dams were genotyped with 11 microsatellites (INRA132, RM033, BM1815, BM1258, BOLA-DRB1, BM1818, BM1905, BM1443, CYP21, CSSM5 and DYMS1) derived from chromosome 23. Differences in heterozygosity between the breeds were observed. Significant differences in recombination rates between GA and GS could be demonstrated for the marker intervals INRA132-CSSM5, CYP21-BOLA-DRB1 and BOLA-DRB1-BM1818. The length of the map of GA was 90.5 cM in contrast to 117.8 cM for GS. The breed specific linkage maps show differences in length but confirmation of the order of the markers.     

Recombination rate variation in closely related species

Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.     

猪的雌雄连锁图谱的比较研究

用统计的方法,对以一个商品猪群为参考家系,采用163个微卫星标记和3个I-型分子标记（RYR1、PRKAG3、PIT1）构建的猪常染色体雌、雄连锁图谱的长度进行了比较。结果表明,常染色体的雌性连锁图谱的总长度为2625.9 cM,雄性连锁图谱的总长度为2259.7 cM,二者比率为1.16 ：1;除了1号和14号染色体以外,其余染色体的雌性连锁图谱的长度均比雄性连锁图谱长。1、3、5、6、7、8、10、11、12、13、14、16、17、18号染色体的雌雄连锁图谱的长度差异极显著（P<0.01）;9号染色体的雌雄连锁图谱的长度差异为显著（P<0.05）;2、4、12、15号染色体的雌雄图谱的长度差异不显著。 Abstract：The difference between the length of female- and male-linkage map, which was created with a reference pedigree based on a commercial porcine population and using 163 microsatellite markers as well as 3 type-I markers (RYR1, PRKAG3, PIT1), was statistic analyzed. The results showed that the total length of female linkage map of autosomes is 2625.9 cM and the total length of the male linkage map is 2259.7 cM; the ratio between the total length of the female- and male-linkage maps is 1.16 ：1; except for the chromosomes 1 and 14, the female linkage maps of the other chromosomes are longer than the male linkage maps. The difference between the length of female- and male-linkage maps of chromosomes 1, 3, 5, 6, 7, 8, 10, 11, 12, 13, 14, 16, 17 and 18 is very significant (P<0.01) and the difference of chromosome 9 is significant (P<0.05); but there is no significance on chromosomes 2, 4, 12 and 15.     

High recombination frequency creates genotypic diversity in colonies of the leaf-cutting ant Acromyrmex echinatior

Honeybees are known to have genetically diverse colonies because queens mate with many males and the recombination rate is extremely high. Genetic diversity among social insect workers has been hypothesized to improve general performance of large and complex colonies, but this idea has not been tested in other social insects. Here, we present a linkage map and an estimate of the recombination rate for Acromyrmex echinatior, a leaf-cutting ant that resembles the honeybee in having multiple mating of queens and colonies of approximately the same size. A map of 145 AFLP markers in 22 linkage groups yielded a total recombinational size of 2076 cM and an inferred recombination rate of 161 kb cM(-1) (or 6.2 cM Mb(-1)). This estimate is lower than in the honeybee but, as far as the mapping criteria can be compared, higher than in any other insect mapped so far. Earlier studies on A. echinatior have demonstrated that variation in division of labour and pathogen resistance has a genetic component and that genotypic diversity among workers may thus give colonies of this leaf-cutting ant a functional advantage. The present result is therefore consistent with the hypothesis that complex social life can select for an increased recombination rate through effects on genotypic diversity and colony performance.     

A comprehensive linkage map of the pig based on a wild pig - Large White intercross

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 type I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1–4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.     

A comparative genomic map for Caulanthus amplexicaulis and related species (Brassicaceae)

Adaptation to environment is the cornerstone of ecological genetics. The subject of this study is a wild relative of the sequenced and annotated model plant species, Arabidopsis thaliana. Caulanthus amplexicaulis var. barbarae lives on serpentine soils, known for high concentrations of heavy metals and low concentrations of essential plant macronutrients, and provides a compelling example of an organism’s adaptation to environment. We constructed an F₂ linkage map, using a cross to the nonserpentine sister taxon, C. amplexicaulis var. amplexicaulis. C. amplexicaulis is a member of a highly diverse set of taxa (within the tribe Thelypodieae), described here as the ‘Streptanthoid Complex’ that are adapted to a broad range of environments, yet share a common n = 14 chromosome number and likely arose by a recent radiation. The linkage map consists of 97 polymorphic microsatellite markers, and 40 exon‐primed intron‐crossing markers based on A. thaliana exon sequences and Brassica ESTs. The map covers 14 linkage groups and has a total length of 1513 cM. Both the patterns of marker segregation and the comparative map indicate that C. amplexicaulis is a diploid organism with a compact genome. All exon‐primed intron‐crossing markers, and an unexpectedly large number of microsatellite markers (83%), had significant similarity to the A. thaliana genome, facilitating the development of a comparative genome map. As a proof of principle, we used the comparative map to identify candidate genes underlying differences in sepal colour between the two parent taxa. We demonstrate that the genomic tools developed here will be portable throughout the Streptanthoid Complex.     

Linkage disequilibrium for different scales and applications

Assessing the patterns of linkage disequilibrium (LD) has become an important issue in both evolutionary biology and medical genetics since the rapid accumulation of densely spaced DNA sequence variation data in several organisms. LD deals with the correlation of genetic variation at two or more loci or sites in the genome within a given population. There are a variety of LD measures which range from traditional pairwise LD measures such as D' or r2 to entropy-based multi-locus measures or haplotype-specific approaches. Understanding the evolutionary forces (in particular recombination) that generate the observed variation of LD patterns across genomic regions is addressed by model-based LD analysis. Marker type and its allelic composition also influence the observed LD pattern, microsatellites having a greater power to detect LD in population isolates than SNPs. This review aims to explain basic LD measures and their application properties.