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Comparative Mapping of Human Chromosome 10 to Pig Chromosomes 10 and 14*

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Comparative Mapping of Human Chromosome 10 to Pig Chromosomes 10 and 14* SHORT COMMUNICATION doi:10.1111/j.1365-2052.2004.01165.x Comparative mapping of human chromosome 10 to pig chromosomes 10 and 14* D. Nonneman and G. A. Rohrer USDA, ARS, US Meat Animal Research Center, Clay Center, NE, USA Summary Identification of predictive markers in QTL regions that impact production traits in com- mercial populations of swine is dependent on construction of dense comparative maps with human and mouse genomes. Chromosomal painting in swine suggests that large genomic blocks are conserved between pig and human, while mapping of individual genes reveals that gene order can be quite divergent. High-resolution comparative maps in regions affecting traits of interest are necessary for selection of positional candidate genes to evaluate nucleotide variation causing phenotypic differences. The objective of this study was to construct an ordered comparative map of human chromosome 10 and pig chro- mosomes 10 and 14. As a large portion of both pig chromosomes are represented by HSA10, genes at regularly spaced intervals along this chromosome were targeted for placement in the porcine genome. A total of 29 genes from human chromosome 10 were mapped to porcine chromosomes 10 (SSC10) and 14 (SSC14) averaging about 5 Mb dis- tance of human DNA per marker. Eighteen genes were assigned by linkage in the MARC mapping population, five genes were physically assigned with the IMpRH mapping panel and seven genes were assigned on both maps. Seventeen genes from human 10p mapped to SSC10, and 12 genes from human 10q mapped to SSC14. Comparative maps of mam- malian species indicate that chromosomal segments are conserved across several species and represent syntenic blocks with distinct breakpoints. Development of comparative maps containing several species should reveal conserved syntenic blocks that will allow us to better define QTL regions in livestock. Keywords comparative map, gene, human chromosome 10, microsatellite, SNP, SSC10, SSC14. Sufficient variation in production traits exists in commercial quite divergent. High-resolution comparative maps in populations of livestock to exploit allelic variation of regions affecting traits of interest are necessary for devel- superior animals to increase production efficiency and opment of additional neighbouring markers and selection of improve the quality of livestock products. Identification of positional candidate genes to evaluate for nucleotide vari- predictive markers that impact production traits in swine ation causing phenotypic differences. Although high-den- can be achieved by constructing dense comparative maps sity physical and linkage maps exist in the pig, gene order with human and mouse genomes. Bidirectional chromoso- for most regions is poorly defined. The sequencing of vast mal painting experiments suggest that large genomic blocks numbers of porcine ESTs and SNP genotyping has greatly are conserved between pig and human (Johansson et al. enabled mapping and assignment of a large number of 1995; Goureau et al. 1996), while mapping of individual genes to comparative maps (Fahrenkrug et al. 2002a). genes or regions suggest that for many regions gene order is The objective of this study was to construct a systematic ordered comparative map of human chromosome 10 with pig chromosomes 10 and 14. Several economically Address for correspondence important reproductive and carcass traits have been dis- D. Nonneman, USDA, ARS, US Meat Animal Research Center, Spur covered on both pig chromosomes (Rohrer & Keele 1998a,b; 18D, PO Box 166, Clay Center, NE 68933-0166, USA. Rohrer et al. 1999; Rohrer 2000; Wada et al. 2000; Hirooka et al. 2001; Malek et al. 2001a,b). As a large por- E-mail: [email protected] *The nucleotide sequence data reported in this paper have been sub- tion of both pig chromosomes are represented by HSA10, mitted to GenBank and have been assigned the accession numbers genes at regularly spaced intervals along this chromosome AY368174–AY368203. with available porcine sequence were targeted for place- Accepted for publication 2 June 2004 ment in the porcine genome. 338 Ó 2004 International Society for Animal Genetics, Animal Genetics, 35, 338–343 Comparative mapping of porcine chromosomes 10 and 14 339 Primer pairs for amplification of genomic DNA were assigned with the IMpRH mapping panel and seven genes designed from porcine EST sequences in TIGR Gene Indices were assigned on both maps. Seventeen genes from human (TIGR website; http://www.tigr.org/tdb/ssgi/) or from 10p mapped to SSC10, and 12 genes from human 10q sequences deposited in GenBank (Table 1) using Primer 3 mapped to SSC14. (Rozen & Skaletsky 2000; code available at: http://www- Seventeen loci from human chromosome 10p all mapped genome.wi.mit.edu/genome_software/other/primer3.html). to SSC10q (Table 1). This corresponds to about 30 Mb of Genes were targeted by their position on human chromo- human DNA that is represented by about 60 cM on the some 10 (UCSC version hg16 based on NCBI Build 34; porcine linkage map or an average distance of <4 cM Golden Path website; http://genome.ucsc.edu/) and avail- (>2 Mb of human DNA) per marker. Thirteen genes were ability of porcine EST sequence. Intronic and 3¢-UTR regions linkage mapped using SNP, 10 loci were mapped by ra- of porcine genes were targeted for amplification and diation hybrid mapping (Table 2); seven loci (AKR1C2, sequencing for SNP discovery in a PTC-200 DNA engine CREM, EPC1, GDI2, IDI1, MRC1 and VIM) were placed on (MJ Research Inc, Watertown, MA, USA) using Hot StarÒ both maps. Three genes (GATA3, NUDT5 and SUV39H2) Taq polymerase (Qiagen, Valencia, CA, USA) and 100 ng of were mapped using the RH panel, because the SNP found in genomic DNA in 25 ll reactions (Fahrenkrug et al. 2002b). the sequence were not informative enough to map them on Amplicons that contained a SNP that was heterozygous the linkage map (Table 2). CREM was mapped using two in the common sire or in at least two of the dams were microsatellites (SB79 and SB81) that were found in a BAC mapped using a primer extension assay on the Sequenom that contained CREM and on the RH panel because the MassArrayTM system (San Diego, CA, USA). Linkage ana- sequence did not contain SNP and the introns are too large lyses were performed for SNP across seven families to amplify across. The gene order is primarily arranged (86 progeny) of the MARC swine reference population from telomere to centromere of human 10p to the telomere (Rohrer et al. 1996; CRIMAP v2.4; Green et al. 1990). and centromere of porcine 10q, as previously described Multipoint locations for all mapped markers are based on (Hiraiwa et al. 2001; Nonneman & Rohrer 2003). On the latest published swine genetic map (Rohrer et al. 1996; SSC10, gene order is conserved from 105 to 127 cM, cor- http://www.marc.usda.gov/). responding to 5–13 Mb on human chromosome 10. Rear- Genes were physically mapped using the 118-clone rangement of genes near the centromere of SSC10q was INRA–University of Minnesota porcine 7000Rad Radiation found involving CREM, EPC1 and GAD2; PIP5K2A and Hybrid (IMpRH) panel (Yerle et al. 1998). Primers used BMI1. CREM is the most centromeric human 10p marker were described above, or designed from intron sequences that mapped near the center of SSC10q. Despite a com- obtained with the original EST primers. Amplifications were parative mapping approach targeting human genes, a large performed in 15 ll PCR using 12.5 ng panel DNA, 1.5 mM gap in marker coverage exists in the pig between 109 and Ò MgCl2, 200 lM dNTPs, 1 lM each primer, 0.25 U Hot Star 125 cM (CUGBP2 and ITIH2; Fig. 1). This is a region Taq and 1X of supplied buffer. The PCR mixture was held at which corresponds to approximately 8–11 Mb on human 94 °C for 15 min, and cycled 40 times at 94 °C for 20 s, the 10p, an area devoid of any known genes or ESTs. This indicated annealing temperature for 30 s (Table 2) and could be a recombination hotspot in the pig, which would extension at 72 °C for 1–1.5 min, followed by a final expand the linkage map in that region. No recombination extension at 72 °C for 5 min. Data were analysed for two- was seen for two groups of markers, VIM, MRC1 and EPC1, point and multipoint linkage (Hawken et al. 1999) with the and for PIP5K2A and BMI1. However, the order for VIM, IMpRH mapping tool and submitted to the IMpRH database MRC1 and EPC1 was determined on the IMpRH panel (http://imprh.toulouse.inra.fr/). Carthagene (http:// (Table 2). www.inra.fr/bia/T/CarthaGene/) was used to estimate Twelve genes from human 10q were mapped to SSC14q; multipoint marker distance and order using all public DEPP was the only locus mapped using only the RH panel markers in the IMpRH database (http://imprh.tou and 11 genes were linkage mapped using SNP (Table 1). louse.inra.fr/) and those developed in this study to PPYR1 and NCOA were mapped using multiple SNP in the approximate position of RH mapped markers on the MARC same amplicon, and an indel was used to map CTBP2. DEPP linkage map. is the most centromeric human 10q marker that was A total of 29 genes from human chromosome 10 were assigned to the RH map. These markers cover about 60 cM mapped to porcine chromosomes 10 (SSC10) and 14 on the SSC14 and about 90 Mb of human DNA for an (SSC14) averaging about 5 Mb distance of human DNA per average marker distance of 5 cM in the pig or about 7.5 Mb marker. All amplicons were sequenced and had significant in human. Gene order was colinear for most of human 10q identity to the porcine and human target exon sequences.
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