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

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 11:159

First Online: 09 March 2010Received: 15 May 2009Accepted: 09 March 2010


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.

AbbreviationsINRANational Institute of Agricultural Research in France

JXAUJiangxi Agricultural University JXAU

LWlarge white pigs

MSMeishan pigs

WDwhite Duroc pigs

SSC-Xporcine chromosome X

HSA-Xhuman chromosome X

MHCmajor histocompatibility complex

QTLquantitative trait locus

RHradiation hybrid

BACbacterial artificial chromosome

cRcenti Ray

cMcenti Morgan


θrecombination fraction

IMpRHthe INRA-University of Minnesota porcine radiation hybrid panel

IMNpRH2the INRA Minnesota Nevada porcine Radiation Hybrid panel 2.

LH-1LH-2, LH3 and LH-C respectively represent the interval SW1903-SW245, SW1608-S0218, SW1943-SW1608 and UMNP71-SW1943, which showed linkage heterogeneity among F1 females from single or both pig resource populations.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-11-159 contains supplementary material, which is available to authorized users.

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Author: Junwu Ma - Nathalie Iannuccelli - Yanyu Duan - Weibing Huang - Beili Guo - Juliette Riquet - Lusheng Huang - Denis Milan


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