Fine-Mapping of a Region of Variation in Recombination Rate on BTA23 to the D23S22–D23S23 Interval Using Sperm Typing and Meiotic Breakpoint Analysis

Park, Chankyu; Frank, M. T.; Lewin, Harris A.

doi:10.1006/geno.1999.5869

Cited by 11 publications

(12 citation statements)

References 34 publications

(44 reference statements)

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“…During meiosis, selection against a chromosomal inversion can be reduced through the formation of a loop structure during the first metaphase (McClintock 1931(McClintock , 1933 or the suppression of recombination in the region (e.g., Martin et al 1994;Brown et al 1998). Such suppression due to the presence of a small inversion has previously been demonstrated to be the cause of a fine-scale difference in recombination rate between bulls (Park et al 1995(Park et al , 1999. It follows that selection against an inversion may occur primarily at a postzygotic level.…”

Section: Introductionmentioning

confidence: 88%

Examination of a region showing linkage map discrepancies across sheep breeds

McRae

Beraldi

2006

Mamm Genome

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The availability of accurate linkage maps is an important step for the localization of genetic variants of interest. However, most studies in livestock assume the published map is applicable in their population despite the large differences between the breeds of a species. A region of sheep Chromosome 1 was previously identified as providing evidence for a marker order inconsistent with the published linkage map. In this study the identified region was investigated in more detail. Four microsatellite markers covering the central 5 cM of the inconsistent region and two flanking markers were genotyped in three sheep breeds, a commercial population (Charollais), an experimental population (Scottish Blackface), and a feral population (Soay). With the inclusion of the published linkage map, this provided evidence for three different marker orders across four sheep populations. Evidence for selection in this region was investigated using both a single-point allelic competition model and a multipoint allele-sharing statistic. Only the Charollais population provided evidence for selection, with significant transmission bias observed at marker BM7145. The implications of variation in linkage maps on the design and analysis of fine-mapping studies are discussed.

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Section: Introductionmentioning

confidence: 88%

Examination of a region showing linkage map discrepancies across sheep breeds

McRae

Beraldi

2006

Mamm Genome

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“…Sperm typing studies have revealed significant variations between individual human males [8] and between individual bulls [9,10] in the fine-scale rate of crossing over. Such studies, however, can only be performed on male recombination, so the only access to fine-scale patterns of female recombination could only be obtained through a classical analysis of families [11].…”

Section: Introductionmentioning

confidence: 99%

“…This variation may be multifactorial, including differences in sex, genetic background, haplotype, age, recombination-promoting sequences, chromosome size, sequence homology, and sites for initiation of chromosome pairing [10]. For instance, the presence of recombination hotspots within mouse major histocompatibiltiy complex (MHC) have been detected in some specific MHC haplotypes [16,17], therefore the frequency of recombination in this region can vary among individuals or strains carrying different haplotypes.…”

Section: Introductionmentioning

confidence: 99%

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

Iannuccelli

Duan

et al. 2010

BMC Genomics

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BackgroundVariations in recombination fraction (θ) among chromosomal regions, individuals and families have been observed and have an important impact on quantitative trait loci (QTL) mapping studies. Such variations on porcine chromosome X (SSC-X) and on other mammalian chromosome X are rarely explored. The emerging assembly of pig sequence provides exact physical location of many markers, facilitating the study of a fine-scale recombination landscape of the pig genome by comparing a clone-based physical map to a genetic map. Using large offspring of F1 females from two large-scale resource populations (Large White ♂ × Chinese Meishan ♀, and White Duroc ♂ × Chinese Erhualian ♀), we were able to evaluate the heterogeneity in θ for a specific interval among individual F1 females.ResultsAlignments between the cytogenetic map, radiation hybrid (RH) map, genetic maps and clone map of SSC-X with the physical map of human chromosome X (HSA-X) are presented. The most likely order of 60 markers on SSC-X is inferred. The average recombination rate across SSC-X is of ~1.27 cM/Mb. However, almost no recombination occurred in a large region of ~31 Mb extending from the centromere to Xq21, whereas in the surrounding regions and in the Xq telomeric region a recombination rate of 2.8-3.3 cM/Mb was observed, more than twice the chromosome-wide average rate. Significant differences in θ among F1 females within each population were observed for several chromosomal intervals. The largest variation was observed in both populations in the interval UMNP71-SW1943, or more precisely in the subinterval UMNP891-UMNP93. The individual variation in θ over this subinterval was found associated with F1 females' maternal haplotypes (Chinese pig haplotypes) and independent of paternal haplotype (European pig haplotypes). The θ between UMNP891 and UMNP93 for haplotype 1122 and 4311 differed by more than fourteen-fold (10.3% vs. 0.7%).ConclusionsThis study reveals marked regional, individual and haplotype-specific differences in recombination rate on SSC-X. Lack of recombination in such a large region makes it impossible to narrow QTL interval using traditional fine-mapping approaches. The relationship between recombination variation and haplotype polymorphism is shown for the first time in pigs.

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“…For the second method, single sperm cells were first pre-amplified by either multiple PCR or whole genome amplification (WGA) to produce sufficient DNA for further multiple genotyping reactions to identify and localize meiotic recombinants. Although multiple PCR has been more widely used for single sperm analysis (20–22), WGA seems to be more promising and preferred for fine mapping of meiotic recombination sites because it can amplify many more marker loci than multiple PCR. Primer extension pre-amplification (PEP) was developed to amplify single sperm DNA on the whole genome level in 1992 (23) and first applied for localization of recombination sites in 1994 (15).…”

Section: Introductionmentioning

confidence: 99%

Genome amplification of single sperm using multiple displacement amplification

Jiang¹

2005

Nucleic Acids Research

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Sperm typing is an effective way to study recombination rate on a fine scale in regions of interest. There are two strategies for the amplification of single meiotic recombinants: repulsion-phase allele-specific PCR and whole genome amplification (WGA). The former can selectively amplify single recombinant molecules from a batch of sperm but is not scalable for high-throughput operation. Currently, primer extension pre-amplification is the only method used in WGA of single sperm, whereas it has limited capacity to produce high-coverage products enough for the analysis of local recombination rate in multiple large regions. Here, we applied for the first time a recently developed WGA method, multiple displacement amplification (MDA), to amplify single sperm DNA, and demonstrated its great potential for producing high-yield and high-coverage products. In a 50 μl reaction, 76 or 93% of loci can be amplified at least 2500- or 250-fold, respectively, from single sperm DNA, and second-round MDA can further offer >200-fold amplification. The MDA products are usable for a variety of genetic applications, including sequencing and microsatellite marker and single nucleotide polymorphism (SNP) analysis. The use of MDA in single sperm amplification may open a new era for studies on local recombination rates.

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Fine-Mapping of a Region of Variation in Recombination Rate on BTA23 to the D23S22–D23S23 Interval Using Sperm Typing and Meiotic Breakpoint Analysis

Cited by 11 publications

References 34 publications

Examination of a region showing linkage map discrepancies across sheep breeds

Examination of a region showing linkage map discrepancies across sheep breeds

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

Genome amplification of single sperm using multiple displacement amplification

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