A Comprehensive Linkage Map of the Dog Genome

Wong, Aaron K.; Ruhe, Alison L.; Dumont, Beth L.; Robertson, Kathryn; Guerrero, Giovanna; Shull, Sheila M.; Ziegle, Janet; Millon, L. V.; Broman, Karl W.; Payseur, Bret A.; Neff, Mark W.

doi:10.1534/genetics.109.106831

Cited by 91 publications

(101 citation statements)

References 77 publications

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“…A pedigree-based linkage map indicates that the genetic map of the dog genome is similar in length to that of other mammals (Wong et al 2010). From this analysis, it is evident that recombination rates vary at a megabase scale in the dog and generally increase near telomeres, consistent with studies in many other species (Yu et al 2001;Kong et al 2002;Shifman et al 2006).…”

Section: Kingdom;supporting

confidence: 74%

Death ofPRDM9coincides with stabilization of the recombination landscape in the dog genome

Axelsson

Webster²,

Ratnakumar³

et al. 2011

Genome Res.

126

179

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Analysis of diverse eukaryotes has revealed that recombination events cluster in discrete genomic locations known as hotspots. In humans, a zinc-finger protein, PRDM9, is believed to initiate recombination in >40% of hotspots by binding to a specific DNA sequence motif. However, the PRDM9 coding sequence is disrupted in the dog genome assembly, raising questions regarding the nature and control of recombination in dogs. By analyzing the sequences of PRDM9 orthologs in a number of dog breeds and several carnivores, we show here that this gene was inactivated early in canid evolution. We next use patterns of linkage disequilibrium using more than 170,000 SNP markers typed in almost 500 dogs to estimate the recombination rates in the dog genome using a coalescent-based approach. Broad-scale recombination rates show good correspondence with an existing linkage-based map. Significant variation in recombination rate is observed on the fine scale, and we are able to detect over 4000 recombination hotspots with high confidence. In contrast to human hotspots, 40% of canine hotspots are characterized by a distinct peak in GC content. A comparative genomic analysis indicates that these peaks are present also as weaker peaks in the panda, suggesting that the hotspots have been continually reinforced by accelerated and strongly GC biased nucleotide substitutions, consistent with the long-term action of biased gene conversion on the dog lineage. These results are consistent with the loss of PRDM9 in canids, resulting in a greater evolutionary stability of recombination hotspots. The genetic determinants of recombination hotspots in the dog genome may thus reflect a fundamental process of relevance to diverse animal species.

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Section: Kingdom;supporting

confidence: 74%

Death ofPRDM9coincides with stabilization of the recombination landscape in the dog genome

Axelsson

Webster²,

Ratnakumar³

et al. 2011

Genome Res.

126

179

View full text Add to dashboard Cite

show abstract

“…This pattern has been noted in fish (Sakamoto et al 2000;, humans (Broman et al 1998;Clark et al 2010), dogs (Wong et al 2010), and mice Paigen et al 2008), although there are some exceptions [e.g., opossums (Samollow et al , 2007]. Utilizing data from a recent fine-scale analysis of sex-specific recombination rate in humans (Kong et al 2010), we display an example of this pattern in Figure 1B.…”

Section: Females Recombine At Relatively Higher Rates Near Centromeressupporting

confidence: 64%

Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates

2012

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Theories to explain the prevalence of sex and recombination have long been a central theme of evolutionary biology. Yet despite decades of attention dedicated to the evolution of sex and recombination, the widespread pattern of sex differences in the recombination rate is not well understood and has received relatively little theoretical attention. Here, we argue that female meiotic drivers-alleles that increase in frequency by exploiting the asymmetric cell division of oogenesis-present a potent selective pressure favoring the modification of the female recombination rate. Because recombination plays a central role in shaping patterns of variation within and among dyads, modifiers of the female recombination rate can function as potent suppressors or enhancers of female meiotic drive. We show that when female recombination modifiers are unlinked to female drivers, recombination modifiers that suppress harmful female drive can spread. By contrast, a recombination modifier tightly linked to a driver can increase in frequency by enhancing female drive. Our results predict that rapidly evolving female recombination rates, particularly around centromeres, should be a common outcome of meiotic drive. We discuss how selection to modify the efficacy of meiotic drive may contribute to commonly observed patterns of sex differences in recombination.

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“…The recombination rate of a gene located on a chromosome (autosomal) is different between females and males because of the number of crossing-over events that occur during meiosis I. Differences in recombination rates between sexes have been identified in many species; for example, humans (Dib et al 1996), dogs (Wong et al 2010), crocodiles (Miles et al 2009), and fish. In fish, recombination rates have generally been reported to be higher in females compared to males ranging from 3.25:1 in rainbow trout (Sakamoto et al 2000), 7.4:1 in the Japanese flounder (Coimbra et al 2003), 1.37:1 in Atlantic salmon (Lien et al 2011), 2.2:1 in the silver carp (Guo et al 2013), 2:1 in the Atlantic halibut (Reid et al 2007), 1.5:1 in the kelp grouper ), 1.03:1 in the orange-spotted grouper (You et al 2013), and 1.19:1 in the white grouper (Dor et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

et al. 2016

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To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F 1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using nonparametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1 % of the genomewide significance and accounted for 14.6-18.9 and 14.7-18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.

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A Comprehensive Linkage Map of the Dog Genome

Cited by 91 publications

References 77 publications

Death ofPRDM9coincides with stabilization of the recombination landscape in the dog genome

Death ofPRDM9coincides with stabilization of the recombination landscape in the dog genome

Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

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