Animal Industry Report Animal Industry Report

AS 650 ASL R1951

2004

A detailed map of pig 4, where the first quantitative trait locus in livestock was mapped

Christopher K. Tuggle Iowa State University

Yuandan Zhang Iowa State University

Max F. Rothschild Iowa State University

Maria Moller Swedish University of Agricultural Sciences

Frida Berg Swedish University of Agricultural Sciences

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Recommended Citation Tuggle, Christopher K.; Zhang, Yuandan; Rothschild, Max F.; Moller, Maria; Berg, Frida; Andersson, Leif; Riquet, Juliette; Milan, Denis; Pomp, Daniel; Archibald, Alan; and Anderson, Susan (2004) "A detailed gene map of pig chromosome 4, where the first quantitative trait locus in livestock was mapped," Animal Industry Report: AS 650, ASL R1951. DOI: https://doi.org/10.31274/ans_air-180814-605 Available at: https://lib.dr.iastate.edu/ans_air/vol650/iss1/110

This Swine is brought to you for free and open access by the Animal Science Research Reports at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Industry Report by an authorized editor of Iowa State University Digital Repository. For more information, please contact [email protected]. A detailed gene map of pig chromosome 4, where the first quantitative trait locus in livestock was mapped

Authors Christopher K. Tuggle, Yuandan Zhang, Max F. Rothschild, Maria Moller, Frida Berg, Leif Andersson, Juliette Riquet, Denis Milan, Daniel Pomp, Alan Archibald, and Susan Anderson

This swine is available in Animal Industry Report: https://lib.dr.iastate.edu/ans_air/vol650/iss1/110 Iowa State University Animal Industry Report 2004 Swine

A detailed gene map of pig chromosome 4, where the first quantitative trait locus in livestock was mapped

A.S. Leaflet R1951 from the possibility of extracting information from homologous regions of other genomes. The molecular Christopher K. Tuggle, Professor of Animal Science identification of underlying QTLs is a challenging Yuandan Zhang, Postdoctoral Research Associate, task and there have not been many success stories Max F. Rothschild, Distinguished Professor of presented yet. A recent compilation of genes identified Animal Science from QTL studies summarized 29 genes so far; 28 those Maria Moller, Frida Berg, Leif Andersson were identified in human/mouse/rat and only one in a Swedish University of Agricultural Sciences livestock animal. Uppsala, Sweden, Juliette Riquet, Denis Milan Porcine chromosome 4 (SSC4) harbor QTLs Laboratoire de Genetique Cellulaire affecting growth, carcass traits and fat deposition. The INRA-Toulouse, France, Daniel Pomp first QTL on SSC4, denoted FAT1, was identified in a Department of Animal Science European wild boar Ð Large White intercross. SSC4 has University of Nebraska-Lincoln previously been shown to share homology with human Alan Archibald, Susan Anderson 1 (HSA1) and 8 (HSA8). SSC4 is divided Roslin Institute into two chromosomal blocks where the entire p arm and Edinburgh, Scotland the q arm proximal to 4q15-16 are homologous to HSA8 and the remaining major part of 4q shares homology with Summary and Implications HSA1. We wanted firstly to establish a dense comparative The first quantitative trait locus (QTL) in pigs, FAT1, map covering the entire SSC4 but also to define the was found on chromosome 4 using a wild-boar intercross. HSA1-HSA8 breakpoint accurately. This has been Further mapping has refined the FAT1 QTL to a region achieved with a combined approach of EST mapping on a conserved on both human and 8. We have radiation hybrid (RH) panel covering the entire now improved the comparative map of the entire SSC4 by chromosome, and by linkage and RH mapping of new mapping 105 loci to pig chromosome 4 (SSC4) and markers developed around the breakpoint and across the defined the specific human chromosome region with FAT1 QTL region. conservation to FAT1, using a combination of physical and linkage mapping. These types of analysis have Materials and Methods resulted in maps with very good agreement. Comparative Primers for physical mapping were designed from pig analysis revealed that the gene order is very well gene sequence (EST) obtained from the Midwest conserved across SSC4 compared to both human Consortium for Pig Reproduction Genomics project chromosome 1 (HSA1) and to HSA8. This refined SSC4 headed by C. Tuggle. These primers amplify specific map and the comparative analysis will be a great aid in gene loci so that the presence of the gene of interest can the search for the candidate genes for the FAT1 locus. be mapped relative to other gene locations using available data (see URL). Genetic linkage mapping was performed Introduction in Sweden using the wild-boar-Yorkshire cross available Comparative genome analysis is a very powerful tool there. All data was analyzed and a comprehensive in the days of the post-genomic era where a wealth of physical and linkage map was created. information has been generated for many eukaryotic genomes. Although significant effort and resources have Results and Discussion been dedicated to farm animals their genome maps are far Genetic Map development from reaching the high resolution available for the human The markers developed were screened for and mouse genome maps. Analysis of the genomes of polymorphisms among our 10 founder animals (2 wild farm animals such as the search for genes underlying boars and 8 Large White) and polymorphism was complex traits; quantitative trait loci (QTLs) or detected. Altogether, 11 genes were added to our economical trait loci (ETLs) can therefore greatly benefit previously published linkage map of SSC4. The linkage map comprising altogether 34 markers spans 135.9 cM (Figure 1). Iowa State University Animal Industry Report 2004 Swine

Physical mapping dense area they could be mapped on the latest RH panel As part of an EST-based comparative mapping developed for pig by colleagues in France. project with the aim to add 700 genes to the RH map (http://pigest.genome.iastate.edu/), we selected HSA1 and Acknowledgements HSA8 genes to improve gene marker density across the This work was supported by USDA-NRICGP 99- entire SSC4. For HSA1, emphasis was placed on 35205-8370. We thank Katie Barry and Darla Hartzler for HSA1q21-24, as we previously showed this was the excellent technical assistance in gene selection. region on HSA1 closest to the FAT1 QTL. Genes were selected for RH mapping based on strength of BLAST score; agreement of human cytogenetic mapping localizations; and equal distribution across human chromosomes. A total of 103 new genes were successfully mapped onto SSC4.

Comparative mapping Comparative mapping of SSC4 confirms clearly that SSC4 corresponds to two large blocks on human chromosomes 1 and 8 (Figure 2). Information of the corresponding human gene homology is presented for 101 genes/markers from the RH and linkage maps, 34 that maps to HSA8 and 67 to HSA1. The markers cover the entire length of SSC4 but an emphasis has been made to put markers within the region harbouring the FAT1 QTL, 23 markers has been added to this region (Figure 2). The comparative genome analysis also clearly reveals that there are no major rearrangements between the two synteny blocks. The gene order seems to be overall very well conserved as opposed to several other porcine chromosomes that display several large intrachromosomal rearrangements. However there is some evidence to suggest a small inversion of the gene order compared to HSA8 around the centromere on SSC4. FAT1

Improved Mapping of the FAT1 QTL QTL There appears to be several QTLs affecting, growth, Region fat, and carcass traits on porcine chromosome 4. Our intention of creating a dense comparative gene map between SSC4 and HSA1/8 has clearly been fulfilled by adding another 101 genes/markers to the map and an additional 5 markers where comparative information has not yet been obtained. The FAT1 QTL region which boundaries are defined by the Sw1364 Ð S0214 markers has had an increase of 23 genes/markers. We used two different methods to develop SSC4 chromosome maps; radiation hybrid mapping and linkage mapping. The maps are in very good agreement, however on some parts of the linkage map, the gene order could not be resolved due to no recombination events between markers. To resolve the order of the markers on the most Figure 1. Genetic Linkage map of Pig Chromosome 4, emphasizing the FAT1 region.

This map contains 33 markers, of which 11 are newly reported in this paper. Iowa State University Animal Industry Report 2004 Swine

HSA8 GPT1 SIAHBP1 14 SSC4 0 SLA DDEF1 MY NSE2 C8FWC GPT1 SQLE SIAHBP1 ZHX1 12 SNTB 0 TOG390531 SLA 5 OXR1 DDEF1 ZFPM2 NSE2 ATP6V1C1 MYC PABPC1 LOC157567 C8FW RNF1 SQLE 5 10 LAPTM4B9 ZHX1 KIAA1750 0 PGCP SNTB UQCRB 1 PLEKHF2 ZFPM2 CBFA2T1 OXR1 DKFZp762O07 ATP6V1C1 6 PABPC 80 IMAGE:361836 LOC1575671 5 RNF1 LOC83690 PLEKHF29 10 UQCRB PGC LAPTM4B KIAA1750P CBFA2T1 TO IMAGE:361836 60 MGC39325X 5 LOC8369 MGC2217 PLAG TOG390530 MOS TO 5MGC39325 A1TP6V1H X MGC2217 MCM4 PLAG MO 15 UBE2V 1 ATP6V1HS 2 MCM4 UBE2V 40 ATP1B12 SELE ADRB3 ATP1B1 POU2F KIAA15131 SERPINC RXRG PIG SELEC SDHC NDUFS FCER1G SSC15 ATP1B1 2 PPOX USF1 20 POU2F1 DUSP1 APOA2 KIAA1513 NCSTN RXR 2 SSC9 HSA1 DUSP12 ATP1A2 GSDHC KCNJ PEA1 COP NDUFS2FCER1GAPOA2 9 5PEA1 AH32 PPOX 5 CASQ16 USF1 APCS COPANCST PEA15NH326 MRPL2 ATP1A2CASQ BCA 25 4 16 KCNJ91 FDPS MGC13102 EFNAN 0 APCS KIAA04461 MRPL2 KIAA0080 KIAA0446BCAN MGC131024 KIAA0907 RUSC1 KIAA0907 HAX1 KIAA0080 NICE-3 SLC39A1 FDPSRUSC1 ILF2 EFNA SNAPAP NICE-31 HAX 30 14 SLC39A1 SPRR1 0 SNAPAP1ILF2 SELENBP1B SPRR1 KIAA1441 SELENBP1B TMSG1 KIAA1441 APH-1A SEMA6C SEMA6CSPEC SPEC TMSG1 LASS2 1LASS DKFZP434K1772MCL1 MCL1 DKFZP434K1772 1 2 12 LOC126964 HIST2H2A APH-1A 0 CGI-143LOC126964A 35 HIST2H2A CGI-143 NGF A NGF BTSHB BTSHB FLJ22457 FLJ22457 SLC16A4 SLC16A4 AD-020 AD-020 AMY1A AMY1A LOC5099 10 9 RPL5 0 LOC5099 9 RPL 5 UOX SSC6 PRKACB

Figure 2. A comparative map of SSC4 and HSA1/HSA8 chromosomes. The porcine distances are given in Rays (measure of physical distance) and the human in Millions of base pairs from sequence. Green signifies high level of confidence in the porcine position; while blue is most likely position for that gene. The red box indicates a region of possible gene order difference between pig and human.